From 10b99750bb318e566721c6690805a2627cc97197 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 8 Apr 2026 14:00:29 +0000 Subject: [PATCH 01/15] Initial plan From e72cd59ad375e3b6de5ee6baae627c8bd6de82d6 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 8 Apr 2026 14:34:42 +0000 Subject: [PATCH 02/15] Add plot_serocurve() and population_params attribute to run_mod() Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/18e7ea90-f52f-49ce-a5fb-4e77aec451d2 Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com> --- DESCRIPTION | 2 +- NAMESPACE | 1 + NEWS.md | 10 + R/Run_Mod.R | 104 +++++- R/plot_serocurve.R | 308 ++++++++++++++++++ data/nepal_sees_jags_output.rda | Bin 226179 -> 392550 bytes inst/examples/examples-plot_serocurve.R | 41 +++ man/nepal_sees_jags_output.Rd | 2 +- man/plot_predicted_curve.Rd | 2 +- man/plot_serocurve.Rd | 124 +++++++ man/run_mod.Rd | 6 +- man/use_att_names.Rd | 2 +- .../serocurve-newperson-single-strat.svg | 77 +++++ ...serocurve-population-facet-antigen-iso.svg | 139 ++++++++ .../serocurve-population-facet-strat.svg | 128 ++++++++ .../serocurve-population-multi-strat.svg | 78 +++++ .../serocurve-population-no-ci.svg | 69 ++++ .../serocurve-population-single-strat.svg | 71 ++++ tests/testthat/test-plot_serocurve.R | 80 +++++ tests/testthat/test-run_mod.R | 10 +- 20 files changed, 1239 insertions(+), 15 deletions(-) create mode 100644 R/plot_serocurve.R create mode 100644 inst/examples/examples-plot_serocurve.R create mode 100644 man/plot_serocurve.Rd create mode 100644 tests/testthat/_snaps/plot_serocurve/serocurve-newperson-single-strat.svg create mode 100644 tests/testthat/_snaps/plot_serocurve/serocurve-population-facet-antigen-iso.svg create mode 100644 tests/testthat/_snaps/plot_serocurve/serocurve-population-facet-strat.svg create mode 100644 tests/testthat/_snaps/plot_serocurve/serocurve-population-multi-strat.svg create mode 100644 tests/testthat/_snaps/plot_serocurve/serocurve-population-no-ci.svg create mode 100644 tests/testthat/_snaps/plot_serocurve/serocurve-population-single-strat.svg create mode 100644 tests/testthat/test-plot_serocurve.R diff --git a/DESCRIPTION b/DESCRIPTION index ea5d92de0..a46b14176 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9047 +Version: 0.0.0.9048 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), diff --git a/NAMESPACE b/NAMESPACE index 2db4d027e..85f628ac5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -13,6 +13,7 @@ export(plot_jags_dens) export(plot_jags_effect) export(plot_jags_trace) export(plot_predicted_curve) +export(plot_serocurve) export(post_summ) export(postprocess_jags_output) export(prep_data) diff --git a/NEWS.md b/NEWS.md index 89199522a..7b01ac6b9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,15 @@ # serodynamics (development version) +* Added `plot_serocurve()` for graphical visualization of population-level + serodynamic curves using posterior samples of the `mu.par` hyperparameter + (or optionally the "newperson" subject). Supports 95% credible interval + ribbons, stratified curves with colour or faceting, and multiple + antigen-isotypes (#74). + +* `run_mod()` now monitors the `mu.par` hyperparameter and stores its + posterior samples (transformed to the original parameter scale) in a + `population_params` attribute of the returned `sr_model` object (#74). + * Added dev container configuration for persistent, cached development environment that includes R, JAGS, and all dependencies preinstalled, making Copilot Workspace sessions much faster. diff --git a/R/Run_Mod.R b/R/Run_Mod.R index 25e75d601..718601e0c 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -59,6 +59,10 @@ #' for all observations. #' - An optional `"jags.post"` attribute, included when argument #' `with_post` = TRUE. +#' - `population_params`: A [dplyr::tbl_df] with posterior samples of the +#' population-level parameters (`mu.par`), transformed to the original +#' parameter scale. Columns: `Chain`, `Iteration`, `antigen_iso`, `y0`, +#' `y1`, `t1`, `alpha`, `shape`, `Stratification`. #' @inheritDotParams prep_priors #' @export #' @example inst/examples/run_mod-examples.R @@ -94,6 +98,19 @@ run_mod <- function(data, ## Creating output list for jags.post jags_post_final <- list() + ## Creating a shell to accumulate population-level (mu.par) parameter samples + pop_params_out <- data.frame( + "Chain" = NA_integer_, + "Iteration" = NA_integer_, + "antigen_iso" = NA_character_, + "y0" = NA_real_, + "y1" = NA_real_, + "t1" = NA_real_, + "alpha" = NA_real_, + "shape" = NA_real_, + "Stratification" = NA_character_ + ) + # For loop for running stratifications for (i in strat_list) { # Creating if else statement for running the loop @@ -117,7 +134,7 @@ run_mod <- function(data, niter <- niter # nr of iterations for posterior sample nthin <- round(niter / nmc) # thinning needed to produce nmc from niter - tomonitor <- c("y0", "y1", "t1", "alpha", "shape") + tomonitor <- c("y0", "y1", "t1", "alpha", "shape", "mu.par") jags_post <- runjags::run.jags( model = file_mod, @@ -140,10 +157,81 @@ run_mod <- function(data, # Unpacking and cleaning MCMC output. jags_unpack <- ggmcmc::ggs(jags_post[["mcmc"]]) - # Adding attributes - mod_atts <- attributes(jags_unpack) - # Only keeping necessary attributes - mod_atts <- mod_atts[4:8] + # Capture model-level metadata attributes from ggmcmc before any filtering. + # We want nChains, nParameters, nIterations, nBurnin, nThin (indices 4–8). + mod_atts_raw <- attributes(jags_unpack)[4:8] + + # Extract and process population-level (mu.par) parameter samples. + # mu.par[iso, param_idx]: iso is first index, param index is second. + mu_par_rows <- jags_unpack |> + dplyr::filter(grepl("^mu\\.par\\[", .data$Parameter)) + + if (nrow(mu_par_rows) > 0) { + antigen_iso_labels <- attributes(longdata)$antigens + param_names <- c( + "1" = "y0_log", + "2" = "y1_increment_log", + "3" = "t1_log", + "4" = "alpha_log", + "5" = "shape_minus1_log" + ) + mu_par_processed <- mu_par_rows |> + dplyr::mutate( + antigen_iso_idx = as.integer( + sub("^mu\\.par\\[(\\d+),.*", "\\1", .data$Parameter) + ), + param_idx = as.character( + sub("^mu\\.par\\[\\d+,(\\d+)\\]", "\\1", .data$Parameter) + ) + ) |> + dplyr::mutate( + antigen_iso = factor( + .data$antigen_iso_idx, + labels = antigen_iso_labels + ), + param_name = unname(param_names[.data$param_idx]) + ) |> + dplyr::select( + all_of(c("Chain", "Iteration", "antigen_iso", "param_name", "value")) + ) |> + tidyr::pivot_wider( + names_from = "param_name", + values_from = "value" + ) |> + dplyr::mutate( + y0 = exp(.data$y0_log), + y1 = .data$y0 + exp(.data$y1_increment_log), + t1 = exp(.data$t1_log), + alpha = exp(.data$alpha_log), + shape = exp(.data$shape_minus1_log) + 1, + Stratification = i, + antigen_iso = as.character(.data$antigen_iso) + ) |> + dplyr::select( + -all_of( + c( + "y0_log", + "y1_increment_log", + "t1_log", + "alpha_log", + "shape_minus1_log" + ) + ) + ) + pop_params_out <- rbind(pop_params_out, mu_par_processed) + } + + # Remove mu.par rows before further processing (existing code expects only + # subject/iso-indexed parameters such as y0, y1, t1, alpha, shape). + jags_unpack <- jags_unpack |> + dplyr::filter(!grepl("^mu\\.par\\[", .data$Parameter)) + + # Adjust nParameters so it reflects only the subject/iso-level scalars, + # not the mu.par hyperparameter scalars. + n_mu_par_params <- length(unique(mu_par_rows$Parameter)) + mod_atts <- mod_atts_raw + mod_atts$nParameters <- + mod_atts_raw$nParameters - as.integer(n_mu_par_params) # extracting antigen-iso combinations to correctly number # then by the order they are estimated by the program. @@ -194,6 +282,12 @@ run_mod <- function(data, jags_out <- jags_out |> structure("priors" = attributes(priorspec)$used_priors) + # Attaching population-level (mu.par) parameter samples as an attribute + pop_params_out <- pop_params_out[complete.cases(pop_params_out), ] + pop_params_out <- dplyr::as_tibble(pop_params_out) + jags_out <- jags_out |> + structure(population_params = pop_params_out) + # Calculating fitted and residuals # Renaming columns using attributes from as_case_data fit_res <- calc_fit_mod(modeled_dat = jags_out, diff --git a/R/plot_serocurve.R b/R/plot_serocurve.R new file mode 100644 index 000000000..6c7a2c736 --- /dev/null +++ b/R/plot_serocurve.R @@ -0,0 +1,308 @@ +#' @title Plot Estimated Serodynamic Curves at the Population Level +#' @description +#' Plots the estimated antibody response curve derived from posterior samples +#' of population-level (`mu.par`) or "new person" parameters from a fitted +#' [run_mod()] model. A median curve with an optional 95% credible interval +#' ribbon is produced for each requested antigen-isotype and stratification +#' combination. +#' +#' @param model An `sr_model` object returned by [run_mod()]. +#' @param antigen_iso A [character] vector of antigen-isotype combinations to +#' plot. Defaults to all antigen-isotypes present in `model`. +#' @param strat A [character] vector of stratification levels to include. +#' Defaults to all stratification levels present in `model`. +#' @param param_source [character]; which posterior samples to use for the +#' curve. Options: +#' - `"population"` (default): uses population-level `mu.par` samples stored +#' in `attr(model, "population_params")`. +#' - `"newperson"`: uses posterior samples for the `"newperson"` subject +#' (a subject with no observed data whose posterior is drawn entirely from +#' the population-level prior). +#' @param show_ci [logical]; if [TRUE] (default), draws a 95% credible +#' interval ribbon around the median curve. +#' @param show_all_curves [logical]; if [TRUE], overlays all individual +#' posterior-sample curves (can be slow for large numbers of samples). +#' Defaults to [FALSE]. +#' @param alpha_samples [numeric]; transparency level (0–1) for individual +#' sample curves when `show_all_curves = TRUE`. Defaults to `0.3`. +#' @param log_y [logical]; if [TRUE], applies a [log10] transformation to the +#' y-axis. Defaults to [FALSE]. +#' @param log_x [logical]; if [TRUE], applies a pseudo-log10 transformation to +#' the x-axis. Defaults to [FALSE]. +#' @param xlim (Optional) A numeric vector of length 2 giving custom x-axis +#' limits. +#' @param facet_by_antigen_iso [logical]; if [TRUE], facets the plot by +#' antigen-isotype. Defaults to [TRUE] when multiple antigen-isotypes are +#' requested. +#' @param facet_by_strat [logical]; if [TRUE], facets the plot by +#' stratification level. When [FALSE] (default), different stratification +#' levels are shown as different colours on the same panel. +#' @param ncol [integer]; number of columns when faceting. If [NULL] +#' (default), a sensible value is chosen automatically. +#' +#' @return A [ggplot2::ggplot] object. +#' @export +#' +#' @example inst/examples/examples-plot_serocurve.R +plot_serocurve <- function( + model, + antigen_iso = unique(model$Iso_type), + strat = unique(model$Stratification), + param_source = "population", + show_ci = TRUE, + show_all_curves = FALSE, + alpha_samples = 0.3, + log_y = FALSE, + log_x = FALSE, + xlim = NULL, + facet_by_antigen_iso = length(antigen_iso) > 1, + facet_by_strat = FALSE, + ncol = NULL) { + + param_source <- match.arg(param_source, c("population", "newperson")) + + # ---- Retrieve posterior samples of curve parameters -------------------- + if (param_source == "population") { + pop_params <- attr(model, "population_params") + if (is.null(pop_params)) { + cli::cli_abort( + c( + "The {.arg model} object does not have a {.field population_params}", + " attribute.", + "i" = paste0( + "Re-fit the model with a version of {.fun run_mod} that monitors", + " {.code mu.par}." + ) + ) + ) + } + param_samples <- pop_params |> + dplyr::filter( + .data$antigen_iso %in% .env$antigen_iso, + .data$Stratification %in% .env$strat + ) |> + dplyr::mutate( + antigen_iso = factor(.data$antigen_iso), + Stratification = factor(.data$Stratification) + ) + } else { + # "newperson": extract from the long-format sr_model tibble + param_samples <- model |> + dplyr::filter( + .data$Subject == "newperson", + .data$Iso_type %in% .env$antigen_iso, + .data$Stratification %in% .env$strat + ) |> + dplyr::select( + all_of( + c("Chain", "Iteration", "Parameter", "Iso_type", "Stratification", + "value") + ) + ) |> + tidyr::pivot_wider( + names_from = "Parameter", + values_from = "value" + ) |> + dplyr::rename(antigen_iso = "Iso_type") |> + dplyr::mutate( + antigen_iso = factor(.data$antigen_iso), + Stratification = factor(.data$Stratification) + ) + # "shape" column is already on the untransformed scale in the sr_model + } + + # Add a unique sample identifier for line grouping + param_samples <- param_samples |> + dplyr::mutate( + sample_id = paste0(.data$Chain, "_", .data$Iteration, "_", + .data$antigen_iso, "_", .data$Stratification) + ) + + # ---- Compute predicted curves over a grid of time points --------------- + tx <- seq(0, 1200, by = 5) + + serocourse_all <- param_samples |> + dplyr::reframe( + t = .env$tx, + res = ab(.data$t, .data$y0, .data$y1, .data$t1, .data$alpha, + .data$shape), + .by = all_of( + c("Chain", "Iteration", "antigen_iso", "Stratification", "sample_id") + ) + ) + + # ---- Summarise to median + 95 % CI ------------------------------------- + curve_summary <- serocourse_all |> + dplyr::summarise( + .by = all_of(c("antigen_iso", "Stratification", "t")), + res_med = stats::quantile(.data$res, probs = 0.50, na.rm = TRUE), + res_low = stats::quantile(.data$res, probs = 0.025, na.rm = TRUE), + res_high = stats::quantile(.data$res, probs = 0.975, na.rm = TRUE) + ) + + # ---- Determine whether to colour by stratification --------------------- + n_strat <- length(unique(param_samples$Stratification)) + multi_strat <- n_strat > 1 && !facet_by_strat + + # ---- Build the ggplot -------------------------------------------------- + p <- ggplot2::ggplot() + + ggplot2::theme_minimal() + + ggplot2::labs(x = "Time since onset", y = "Assay result") + + ggplot2::theme(legend.position = "bottom") + + if (show_all_curves) { + if (multi_strat) { + p <- p + + ggplot2::geom_line( + data = serocourse_all, + ggplot2::aes( + x = .data$t, + y = .data$res, + group = .data$sample_id, + colour = .data$Stratification + ), + alpha = alpha_samples + ) + } else { + p <- p + + ggplot2::geom_line( + data = serocourse_all, + ggplot2::aes( + x = .data$t, + y = .data$res, + group = .data$sample_id, + colour = "samples" + ), + alpha = alpha_samples + ) + } + } + + if (show_ci) { + if (multi_strat) { + p <- p + + ggplot2::geom_ribbon( + data = curve_summary, + ggplot2::aes( + x = .data$t, + ymin = .data$res_low, + ymax = .data$res_high, + fill = .data$Stratification + ), + alpha = 0.2, + inherit.aes = FALSE + ) + } else { + p <- p + + ggplot2::geom_ribbon( + data = curve_summary, + ggplot2::aes( + x = .data$t, + ymin = .data$res_low, + ymax = .data$res_high, + fill = "ci" + ), + alpha = 0.2, + inherit.aes = FALSE + ) + } + } + + # Median line + if (multi_strat) { + p <- p + + ggplot2::geom_line( + data = curve_summary, + ggplot2::aes( + x = .data$t, + y = .data$res_med, + colour = .data$Stratification + ), + linewidth = 1, + inherit.aes = FALSE + ) + } else { + p <- p + + ggplot2::geom_line( + data = curve_summary, + ggplot2::aes( + x = .data$t, + y = .data$res_med, + colour = "median" + ), + linewidth = 1, + inherit.aes = FALSE + ) + } + + # ---- Legend for single-stratification plots ---------------------------- + if (!multi_strat) { + color_vals <- c("median" = "red") + color_labels <- c("median" = "Median") + + if (show_all_curves) { + color_vals["samples"] <- "gray" + color_labels["samples"] <- "Posterior samples" + } + + fill_vals <- c("ci" = "red") + fill_labels <- c("ci" = "95% credible interval") + + p <- p + + ggplot2::scale_color_manual( + name = "", + values = color_vals, + labels = color_labels, + guide = ggplot2::guide_legend(override.aes = list(shape = NA)) + ) + + ggplot2::scale_fill_manual( + name = "", + values = fill_vals, + labels = fill_labels, + guide = ggplot2::guide_legend(override.aes = list(color = NA)) + ) + } + + # ---- Faceting ---------------------------------------------------------- + facet_vars <- character(0) + if (facet_by_antigen_iso) facet_vars <- c(facet_vars, "antigen_iso") + if (facet_by_strat) facet_vars <- c(facet_vars, "Stratification") + + if (length(facet_vars) > 0) { + facet_formula <- stats::as.formula( + paste("~", paste(facet_vars, collapse = " + ")) + ) + if (is.null(ncol)) { + n_panels <- length(unique(interaction( + curve_summary[[facet_vars[1]]], + if (length(facet_vars) > 1) curve_summary[[facet_vars[2]]] else NULL + ))) + ncol <- if (n_panels == 1) { + 1 + } else if (n_panels <= 4) { + 2 + } else { + NULL + } + } + p <- p + ggplot2::facet_wrap(facet_formula, ncol = ncol) + } + + # ---- Log scales -------------------------------------------------------- + if (log_y) { + p <- p + ggplot2::scale_y_log10() + } + if (log_x) { + p <- p + + ggplot2::scale_x_continuous( + trans = scales::pseudo_log_trans(sigma = 1, base = 10) + ) + } + + # ---- Custom x-axis limits ---------------------------------------------- + if (!is.null(xlim)) { + p <- p + ggplot2::coord_cartesian(xlim = xlim) + } + + return(p) +} diff --git a/data/nepal_sees_jags_output.rda b/data/nepal_sees_jags_output.rda index 25de55ea1f76bd76ad726ef5a7e54833cc9710b1..a1ed6c2d742dec50934da2da614cb368cb7cfc09 100644 GIT binary patch literal 392550 zcmeFZcR1YNzc2ck84MG>_dX0l5JWe62{C#XErRGFdNS%DdPsCLqKi)Sl7>ivAbKxB z^j^dD{q4QazV|-+p7T8SIp;q2kF(bLtoB~B-mmpu?^R~a`izpflaz>}8IOV4j^(N< ze#-sp|Dl9oA_QySptynZ-!XjrDYu@qHM4*}SFpM=5b-0KrPL)IA{=muf 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antigen_iso = "HlyE_IgA", + facet_by_strat = TRUE +) +print(p3) + +# Multiple antigen-isotypes, faceted, without CI +p4 <- plot_serocurve( + model = model, + antigen_iso = c("HlyE_IgA", "HlyE_IgG"), + facet_by_antigen_iso = TRUE, + show_ci = FALSE +) +print(p4) + +# Using "newperson" posterior samples instead of mu.par +p5 <- plot_serocurve( + model = model, + antigen_iso = "HlyE_IgA", + param_source = "newperson" +) +print(p5) diff --git a/man/nepal_sees_jags_output.Rd b/man/nepal_sees_jags_output.Rd index 2bd139153..4ea195d17 100644 --- a/man/nepal_sees_jags_output.Rd +++ b/man/nepal_sees_jags_output.Rd @@ -5,7 +5,7 @@ \alias{nepal_sees_jags_output} \title{SEES Typhoid run_mod jags output} \format{ -An S3 object of class \code{sr_model}: A \link[dplyr:tbl_df]{dplyr::tbl_df} that contains the +An S3 object of class \code{sr_model}: A \link[dplyr:defunct]{dplyr::tbl_df} that contains the posterior predictive distribution of the person-specific parameters for a "new person" with no observed data (\code{Subject = "newperson"}) and posterior distributions of the person-specific parameters for two arbitrarily-chosen diff --git a/man/plot_predicted_curve.Rd b/man/plot_predicted_curve.Rd index 7e2fabde6..b5638b881 100644 --- a/man/plot_predicted_curve.Rd +++ b/man/plot_predicted_curve.Rd @@ -31,7 +31,7 @@ samples from the posterior distribution of the model parameters.} \item{antigen_iso}{The antigen isotype to plot; for example, "HlyE_IgA" or "HlyE_IgG".} -\item{dataset}{(Optional) A \link[dplyr:tbl_df]{dplyr::tbl_df} with observed antibody response +\item{dataset}{(Optional) A \link[dplyr:defunct]{dplyr::tbl_df} with observed antibody response data. Must contain: \itemize{ diff --git a/man/plot_serocurve.Rd b/man/plot_serocurve.Rd new file mode 100644 index 000000000..383e09a12 --- /dev/null +++ b/man/plot_serocurve.Rd @@ -0,0 +1,124 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plot_serocurve.R +\name{plot_serocurve} +\alias{plot_serocurve} +\title{Plot Estimated Serodynamic Curves at the Population Level} +\usage{ +plot_serocurve( + model, + antigen_iso = unique(model$Iso_type), + strat = unique(model$Stratification), + param_source = "population", + show_ci = TRUE, + show_all_curves = FALSE, + alpha_samples = 0.3, + log_y = FALSE, + log_x = FALSE, + xlim = NULL, + facet_by_antigen_iso = length(antigen_iso) > 1, + facet_by_strat = FALSE, + ncol = NULL +) +} +\arguments{ +\item{model}{An \code{sr_model} object returned by \code{\link[=run_mod]{run_mod()}}.} + +\item{antigen_iso}{A \link{character} vector of antigen-isotype combinations to +plot. Defaults to all antigen-isotypes present in \code{model}.} + +\item{strat}{A \link{character} vector of stratification levels to include. +Defaults to all stratification levels present in \code{model}.} + +\item{param_source}{\link{character}; which posterior samples to use for the +curve. Options: +\itemize{ +\item \code{"population"} (default): uses population-level \code{mu.par} samples stored +in \code{attr(model, "population_params")}. +\item \code{"newperson"}: uses posterior samples for the \code{"newperson"} subject +(a subject with no observed data whose posterior is drawn entirely from +the population-level prior). +}} + +\item{show_ci}{\link{logical}; if \link{TRUE} (default), draws a 95\% credible +interval ribbon around the median curve.} + +\item{show_all_curves}{\link{logical}; if \link{TRUE}, overlays all individual +posterior-sample curves (can be slow for large numbers of samples). +Defaults to \link{FALSE}.} + +\item{alpha_samples}{\link{numeric}; transparency level (0–1) for individual +sample curves when \code{show_all_curves = TRUE}. Defaults to \code{0.3}.} + +\item{log_y}{\link{logical}; if \link{TRUE}, applies a \link{log10} transformation to the +y-axis. Defaults to \link{FALSE}.} + +\item{log_x}{\link{logical}; if \link{TRUE}, applies a pseudo-log10 transformation to +the x-axis. Defaults to \link{FALSE}.} + +\item{xlim}{(Optional) A numeric vector of length 2 giving custom x-axis +limits.} + +\item{facet_by_antigen_iso}{\link{logical}; if \link{TRUE}, facets the plot by +antigen-isotype. Defaults to \link{TRUE} when multiple antigen-isotypes are +requested.} + +\item{facet_by_strat}{\link{logical}; if \link{TRUE}, facets the plot by +stratification level. When \link{FALSE} (default), different stratification +levels are shown as different colours on the same panel.} + +\item{ncol}{\link{integer}; number of columns when faceting. If \link{NULL} +(default), a sensible value is chosen automatically.} +} +\value{ +A \link[ggplot2:ggplot]{ggplot2::ggplot} object. +} +\description{ +Plots the estimated antibody response curve derived from posterior samples +of population-level (\code{mu.par}) or "new person" parameters from a fitted +\code{\link[=run_mod]{run_mod()}} model. A median curve with an optional 95\% credible interval +ribbon is produced for each requested antigen-isotype and stratification +combination. +} +\examples{ +model <- serodynamics::nepal_sees_jags_output + +# Population-level curve for a single antigen-isotype +p1 <- plot_serocurve( + model = model, + antigen_iso = "HlyE_IgA", + strat = "typhi" +) +print(p1) + +# Population-level curves for both stratifications, coloured by stratum +p2 <- plot_serocurve( + model = model, + antigen_iso = "HlyE_IgA" +) +print(p2) + +# Facet by stratification instead of colouring +p3 <- plot_serocurve( + model = model, + antigen_iso = "HlyE_IgA", + facet_by_strat = TRUE +) +print(p3) + +# Multiple antigen-isotypes, faceted, without CI +p4 <- plot_serocurve( + model = model, + antigen_iso = c("HlyE_IgA", "HlyE_IgG"), + facet_by_antigen_iso = TRUE, + show_ci = FALSE +) +print(p4) + +# Using "newperson" posterior samples instead of mu.par +p5 <- plot_serocurve( + model = model, + antigen_iso = "HlyE_IgA", + param_source = "newperson" +) +print(p5) +} diff --git a/man/run_mod.Rd b/man/run_mod.Rd index 08f914275..d46d4a814 100644 --- a/man/run_mod.Rd +++ b/man/run_mod.Rd @@ -93,7 +93,7 @@ If specified, must be 2 values long: }} } \value{ -An \code{sr_model} class object: a subclass of \link[dplyr:tbl_df]{dplyr::tbl_df} that +An \code{sr_model} class object: a subclass of \link[dplyr:defunct]{dplyr::tbl_df} that contains MCMC samples from the joint posterior distribution of the model parameters, conditional on the provided input \code{data}, including the following: @@ -132,6 +132,10 @@ including the following: for all observations. \item An optional \code{"jags.post"} attribute, included when argument \code{with_post} = TRUE. +\item \code{population_params}: A \link[dplyr:defunct]{dplyr::tbl_df} with posterior samples of the +population-level parameters (\code{mu.par}), transformed to the original +parameter scale. Columns: \code{Chain}, \code{Iteration}, \code{antigen_iso}, \code{y0}, +\code{y1}, \code{t1}, \code{alpha}, \code{shape}, \code{Stratification}. } } } diff --git a/man/use_att_names.Rd b/man/use_att_names.Rd index f43fcef0c..9a2151e0e 100644 --- a/man/use_att_names.Rd +++ b/man/use_att_names.Rd @@ -16,7 +16,7 @@ The input \link{data.frame} with columns named after attributes. \description{ \code{use_att_names} takes prepared longitudinal data for antibody kinetic modeling and names columns using attribute values to allow merging -with a modeled \code{\link[=run_mod]{run_mod()}} output \link[dplyr:tbl_df]{dplyr::tbl_df}. The column names include +with a modeled \code{\link[=run_mod]{run_mod()}} output \link[dplyr:defunct]{dplyr::tbl_df}. 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font-family: sans;' textLength='192.25px' lengthAdjust='spacingAndGlyphs'>serocurve-population-single-strat</text> +</g> +</svg> diff --git a/tests/testthat/test-plot_serocurve.R b/tests/testthat/test-plot_serocurve.R new file mode 100644 index 000000000..ad57c0e87 --- /dev/null +++ b/tests/testthat/test-plot_serocurve.R @@ -0,0 +1,80 @@ +test_that( + desc = "plot_serocurve() works with population param_source (default)", + code = { + skip_if(getRversion() < "4.4.1") + + sr_model <- serodynamics::nepal_sees_jags_output + + # Single antigen-iso, single stratum + p1 <- plot_serocurve( + model = sr_model, + antigen_iso = "HlyE_IgA", + strat = "typhi" + ) + vdiffr::expect_doppelganger("serocurve-population-single-strat", p1) + + # Multiple strata coloured (default) + p2 <- plot_serocurve( + model = sr_model, + antigen_iso = "HlyE_IgA" + ) + vdiffr::expect_doppelganger("serocurve-population-multi-strat", p2) + + # Faceted by stratification + p3 <- plot_serocurve( + model = sr_model, + antigen_iso = "HlyE_IgA", + facet_by_strat = TRUE + ) + vdiffr::expect_doppelganger("serocurve-population-facet-strat", p3) + + # Multiple antigen-isotypes, faceted + p4 <- plot_serocurve( + model = sr_model, + antigen_iso = c("HlyE_IgA", "HlyE_IgG"), + facet_by_antigen_iso = TRUE + ) + vdiffr::expect_doppelganger("serocurve-population-facet-antigen-iso", p4) + + # Without CI + p5 <- plot_serocurve( + model = sr_model, + antigen_iso = "HlyE_IgA", + strat = "typhi", + show_ci = FALSE + ) + vdiffr::expect_doppelganger("serocurve-population-no-ci", p5) + } +) + +test_that( + desc = "plot_serocurve() works with newperson param_source", + code = { + skip_if(getRversion() < "4.4.1") + + sr_model <- serodynamics::nepal_sees_jags_output + + p6 <- plot_serocurve( + model = sr_model, + antigen_iso = "HlyE_IgA", + strat = "typhi", + param_source = "newperson" + ) + vdiffr::expect_doppelganger("serocurve-newperson-single-strat", p6) + } +) + +test_that( + desc = "plot_serocurve() errors when population_params attribute is missing", + code = { + # Strip the population_params attribute to simulate an old sr_model object + sr_model_old <- serodynamics::nepal_sees_jags_output + attr(sr_model_old, "population_params") <- NULL + + expect_error( + plot_serocurve(sr_model_old, antigen_iso = "HlyE_IgA", + param_source = "population"), + regexp = "population_params" + ) + } +) diff --git a/tests/testthat/test-run_mod.R b/tests/testthat/test-run_mod.R index b4eef502d..2d5c6ce34 100644 --- a/tests/testthat/test-run_mod.R +++ b/tests/testthat/test-run_mod.R @@ -28,7 +28,7 @@ test_that( results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals")) |> + rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> expect_snapshot_value(style = "deparse") results |> @@ -68,7 +68,7 @@ test_that( results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals")) |> + rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> expect_snapshot_value(style = "deparse") results |> @@ -107,7 +107,7 @@ test_that( results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals")) |> + rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> expect_snapshot_value(style = "deparse") results |> @@ -147,7 +147,7 @@ test_that( results |> attributes() |> - rlist::list.remove(c("row.names", "jags.post", "fitted_residuals")) |> + rlist::list.remove(c("row.names", "jags.post", "fitted_residuals", "population_params")) |> expect_snapshot_value(style = "serialize") results |> @@ -185,7 +185,7 @@ test_that( results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals")) |> + rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> expect_snapshot_value(style = "serialize") results |> From 7c8e12b4956c26b6a7bb580804e3ebee697bce8c Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 9 Apr 2026 04:48:56 +0000 Subject: [PATCH 03/15] Use mon_popparams branch implementation; update plot_serocurve() for correct population_params format Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/6f0bb3ad-fcef-4813-b663-5194422cd517 Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com> --- R/Run_Mod.R | 267 ++++++++---------- R/as_case_data.R | 26 +- R/ex_popparams.R | 13 + R/nepal_sees_jags_output.R | 9 +- R/param_recode.R | 17 ++ R/plot_predicted_curve.R | 4 +- R/plot_serocurve.R | 57 +++- R/post_summ.R | 4 +- R/prep_popparams.R | 15 + R/unpack_jags.R | 100 +++++++ R/use_att_names.R | 2 +- data/nepal_sees_jags_output.rda | Bin 392550 -> 731274 bytes inst/WORDLIST | 1 + inst/examples/examples-plot_serocurve.R | 9 +- man/ex_popparams.Rd | 22 ++ man/nepal_sees_jags_output.Rd | 9 +- man/param_recode.Rd | 21 ++ man/plot_predicted_curve.Rd | 4 +- man/plot_serocurve.Rd | 14 +- man/post_summ.Rd | 4 +- man/prep_popparams.Rd | 23 ++ man/run_mod.Rd | 25 +- man/unpack_jags.Rd | 31 ++ man/use_att_names.Rd | 2 +- .../darwin/run_mod/popparam-summary-stats.csv | 31 ++ tests/testthat/_snaps/run_mod.md | 60 +--- .../_snaps/run_mod/popparam-summary-stats.csv | 31 ++ tests/testthat/test-internal-popparams.R | 173 ++++++++++++ tests/testthat/test-run_mod.R | 58 ++-- 29 files changed, 761 insertions(+), 271 deletions(-) create mode 100644 R/ex_popparams.R create mode 100644 R/param_recode.R create mode 100644 R/prep_popparams.R create mode 100644 R/unpack_jags.R create mode 100644 man/ex_popparams.Rd create mode 100644 man/param_recode.Rd create mode 100644 man/prep_popparams.Rd create mode 100644 man/unpack_jags.Rd create mode 100644 tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv create mode 100644 tests/testthat/_snaps/run_mod/popparam-summary-stats.csv create mode 100644 tests/testthat/test-internal-popparams.R diff --git a/R/Run_Mod.R b/R/Run_Mod.R index 718601e0c..48d202bf1 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -26,7 +26,11 @@ #' should be included as an element of the [list] object returned by `run_mod()` #' (see `Value` section below for details). #' Note: These objects can be large. -#' @returns An `sr_model` class object: a subclass of [dplyr::tbl_df] that +#' @param with_pop_params A [logical] value specifying whether population +#' level parameters should be included as an attribute entitled +#' `population_params`. Excluded as default. +#' Note: These objects can be large. +#' @returns An `sr_model` class object: a subclass of [tibble::tbl_df] that #' contains MCMC samples from the joint posterior distribution of the model #' parameters, conditional on the provided input `data`, #' including the following: @@ -49,6 +53,17 @@ #' - `nIterations`: Number of iteration specified. #' - `nBurnin`: Number of burn ins. #' - `nThin`: Thinning number (niter/nmc). +#' - `population_params`: Optionally included modeled population parameters +#' indexed by +#' `Iteration`, +#' `Chain`, `Parameter`, `Iso_type`, and `Stratification`. Excluded as +#' default. Includes the following modeled population parameters: +#' - `mu.par` = The population means of the host-specific model parameters +#' (on logarithmic scales). +#' - `prec.par` = The population precision matrix of the hyperparameters +#' (with diagonal elements equal to inverse variances). +#' - `prec.logy` = A vector of population precisions (inverse variances), +#' one per antigen/isotype combination. #' - `priors`: A [list] that summarizes the input priors, including: #' - `mu_hyp_param` #' - `prec_hyp_param` @@ -59,10 +74,6 @@ #' for all observations. #' - An optional `"jags.post"` attribute, included when argument #' `with_post` = TRUE. -#' - `population_params`: A [dplyr::tbl_df] with posterior samples of the -#' population-level parameters (`mu.par`), transformed to the original -#' parameter scale. Columns: `Chain`, `Iteration`, `antigen_iso`, `y0`, -#' `y1`, `t1`, `alpha`, `shape`, `Stratification`. #' @inheritDotParams prep_priors #' @export #' @example inst/examples/run_mod-examples.R @@ -75,6 +86,7 @@ run_mod <- function(data, niter = 100, strat = NA, with_post = FALSE, + with_pop_params = FALSE, ...) { ## Conditionally creating a stratification list to loop through if (is.na(strat)) { @@ -84,33 +96,19 @@ run_mod <- function(data, } ## Creating a shell to output results - jags_out <- data.frame( - "Iteration" = NA, - "Chain" = NA, - "Parameter" = NA, - "value" = NA, - "Parameter_sub" = NA, - "Subject" = NA, - "Iso_type" = NA, - "Stratification" = NA + jags_out <- tibble::tibble( + "Iteration" = integer(), + "Chain" = integer(), + "value" = numeric(), + "Subject" = character(), + "Parameter" = character(), + "Iso_type" = character(), + "Stratification" = character() ) ## Creating output list for jags.post jags_post_final <- list() - ## Creating a shell to accumulate population-level (mu.par) parameter samples - pop_params_out <- data.frame( - "Chain" = NA_integer_, - "Iteration" = NA_integer_, - "antigen_iso" = NA_character_, - "y0" = NA_real_, - "y1" = NA_real_, - "t1" = NA_real_, - "alpha" = NA_real_, - "shape" = NA_real_, - "Stratification" = NA_character_ - ) - # For loop for running stratifications for (i in strat_list) { # Creating if else statement for running the loop @@ -134,7 +132,12 @@ run_mod <- function(data, niter <- niter # nr of iterations for posterior sample nthin <- round(niter / nmc) # thinning needed to produce nmc from niter - tomonitor <- c("y0", "y1", "t1", "alpha", "shape", "mu.par") + tomonitor <- c("y0", "y1", "t1", "alpha", "shape") + # Conditional statement for including population parameters + if (with_pop_params) { + tomonitor <- c(tomonitor, "mu.par", "prec.par", + "prec.logy") + } jags_post <- runjags::run.jags( model = file_mod, @@ -155,138 +158,106 @@ run_mod <- function(data, jags_post_final[[i]] <- jags_post # Unpacking and cleaning MCMC output. - jags_unpack <- ggmcmc::ggs(jags_post[["mcmc"]]) - - # Capture model-level metadata attributes from ggmcmc before any filtering. - # We want nChains, nParameters, nIterations, nBurnin, nThin (indices 4–8). - mod_atts_raw <- attributes(jags_unpack)[4:8] - - # Extract and process population-level (mu.par) parameter samples. - # mu.par[iso, param_idx]: iso is first index, param index is second. - mu_par_rows <- jags_unpack |> - dplyr::filter(grepl("^mu\\.par\\[", .data$Parameter)) - - if (nrow(mu_par_rows) > 0) { - antigen_iso_labels <- attributes(longdata)$antigens - param_names <- c( - "1" = "y0_log", - "2" = "y1_increment_log", - "3" = "t1_log", - "4" = "alpha_log", - "5" = "shape_minus1_log" - ) - mu_par_processed <- mu_par_rows |> - dplyr::mutate( - antigen_iso_idx = as.integer( - sub("^mu\\.par\\[(\\d+),.*", "\\1", .data$Parameter) - ), - param_idx = as.character( - sub("^mu\\.par\\[\\d+,(\\d+)\\]", "\\1", .data$Parameter) - ) - ) |> - dplyr::mutate( - antigen_iso = factor( - .data$antigen_iso_idx, - labels = antigen_iso_labels - ), - param_name = unname(param_names[.data$param_idx]) - ) |> - dplyr::select( - all_of(c("Chain", "Iteration", "antigen_iso", "param_name", "value")) - ) |> - tidyr::pivot_wider( - names_from = "param_name", - values_from = "value" - ) |> - dplyr::mutate( - y0 = exp(.data$y0_log), - y1 = .data$y0 + exp(.data$y1_increment_log), - t1 = exp(.data$t1_log), - alpha = exp(.data$alpha_log), - shape = exp(.data$shape_minus1_log) + 1, - Stratification = i, - antigen_iso = as.character(.data$antigen_iso) - ) |> - dplyr::select( - -all_of( - c( - "y0_log", - "y1_increment_log", - "t1_log", - "alpha_log", - "shape_minus1_log" - ) - ) - ) - pop_params_out <- rbind(pop_params_out, mu_par_processed) - } - - # Remove mu.par rows before further processing (existing code expects only - # subject/iso-indexed parameters such as y0, y1, t1, alpha, shape). - jags_unpack <- jags_unpack |> - dplyr::filter(!grepl("^mu\\.par\\[", .data$Parameter)) - - # Adjust nParameters so it reflects only the subject/iso-level scalars, - # not the mu.par hyperparameter scalars. - n_mu_par_params <- length(unique(mu_par_rows$Parameter)) - mod_atts <- mod_atts_raw - mod_atts$nParameters <- - mod_atts_raw$nParameters - as.integer(n_mu_par_params) + jags_packed <- ggmcmc::ggs(jags_post[["mcmc"]]) + # Adding attributes + mod_atts <- attributes(jags_packed) + # Select necessary attributes by name for robustness across platforms + mod_atts <- mod_atts[c("nChains", "nParameters", "nIterations", + "nBurnin", "nThin", "description")] + # extracting antigen-iso combinations to correctly number - # then by the order they are estimated by the program. + # them by the order they are estimated by the program. iso_dat <- data.frame(attributes(longdata)$antigens) - iso_dat <- iso_dat |> dplyr::mutate(Subnum = as.numeric(row.names(iso_dat))) - # Working with jags unpacked ggs outputs to clarify parameter and subject - jags_unpack <- jags_unpack |> - dplyr::mutate( - Subnum = sub(".*,", "", .data$Parameter), - Parameter_sub = sub("\\[.*", "", .data$Parameter), - Subject = sub("\\,.*", "", .data$Parameter) - ) |> - dplyr::mutate( - Subnum = as.numeric(sub("\\].*", "", .data$Subnum)), - Subject = sub(".*\\[", "", .data$Subject) - ) - # Merging isodat in to ensure we are classifying antigen_iso - jags_unpack <- dplyr::left_join(jags_unpack, iso_dat, by = "Subnum") + iso_dat <- iso_dat |> dplyr::mutate(Subnum = row.names(iso_dat)) + + # Unpacking the mcmc object + jags_unpacked <- unpack_jags(jags_packed) + + # Merging isodat in to ensure we are classifying antigen_iso. + jags_unpacked <- dplyr::left_join(jags_unpacked, iso_dat, + by = "Subnum") + + # Adding in ID name ids <- data.frame(attr(longdata, "ids")) |> - mutate(Subject = as.character(dplyr::row_number())) - jags_unpack <- dplyr::left_join(jags_unpack, ids, by = "Subject") - jags_final <- jags_unpack |> - dplyr::select(!c("Subnum", "Subject")) |> + dplyr::mutate(Subject = as.character(dplyr::row_number())) + jags_final <- dplyr::left_join(jags_unpacked, ids, + by = "Subject") |> dplyr::rename(c("Iso_type" = "attributes.longdata..antigens", - "Subject" = "attr.longdata...ids..")) + "Subject_mcmc" = "attr.longdata...ids..")) |> + # Subject handling: + # * For individual-level parameters, the left join above finds a row in + # attr(longdata, "ids"), so Subject_mcmc contains the subject ID. + # * For population-level parameters (e.g., mu.par, prec.par, prec.logy), + # there is no matching ID, so Subject_mcmc is NA. In that case we + # intentionally keep the original Subject value from unpack_jags, + # which holds the parameter name and serves as the identifier. + dplyr::mutate(Subject_mcmc = ifelse(is.na(.data$Subject_mcmc), + .data$Subject, + .data$Subject_mcmc)) |> + # At this point, jags_unpacked contains: + # * Parameter: original JAGS parameter names (e.g., "y0[1,2]") + # * Param: cleaned parameter names used elsewhere in the package. + # We drop the original JAGS-style Parameter column and keep the + # cleaned names, then rename Param back to Parameter so that all + # downstream code consistently uses a single "Parameter" column + # containing cleaned parameter names. + # Drop the temporary Subject (now only used as a fallback for population + # parameters) and rename Subject_mcmc back to Subject for downstream use. + dplyr::select(!c("Subnum", "Subject", "Parameter")) |> + dplyr::rename(c("Subject" = "Subject_mcmc", + "Parameter" = "Param")) + # Creating a label for the stratification, if there is one. # If not, will add in "None". jags_final$Stratification <- i - ## Creating output - jags_out <- data.frame(rbind(jags_out, jags_final)) + # Creating output as a data frame with the + # jags output results for each stratification rbinded. + jags_out <- dplyr::bind_rows(jags_out, jags_final) } - # Ensuring output does not have any NAs - jags_out <- jags_out[complete.cases(jags_out), ] - # Outputting the finalized jags output as a data frame with the - # jags output results for each stratification rbinded. - - # Making output a tibble and restructing. - jags_out <- dplyr::as_tibble(jags_out) |> - select(!c("Parameter")) |> - rename("Parameter" = "Parameter_sub") + + if (with_pop_params) { + # Preparing population parameters + population_params <- prep_popparams(jags_out) + population_params <- population_params[, c( + "Iteration", "Chain", "Parameter", "Iso_type", + "Stratification", "Population_Parameter", "value" + )] + + # Taking out population parameters + jags_out <- ex_popparams(jags_out) + } + + # Making output a tibble and restructuring. jags_out <- jags_out[, c("Iteration", "Chain", "Parameter", "Iso_type", "Stratification", "Subject", "value")] - current_atts <- attributes(jags_out) - current_atts <- c(current_atts, mod_atts) - attributes(jags_out) <- current_atts - - # Adding priors - jags_out <- jags_out |> - structure("priors" = attributes(priorspec)$used_priors) + current_atts <- attributes(jags_out) + # Explicitly build the attribute list in the correct order to ensure that + # `class` appears immediately after `names` and `row.names`. + # The dplyr operations above can carry ggmcmc attributes (nChains, etc.) + # from jags_packed into jags_out, placing `class` at the end. We use + # mod_atts (named selection from jags_packed) as the authoritative source + # for the ggmcmc-style metadata attributes. + new_atts <- list( + names = current_atts$names, + row.names = current_atts$row.names, + class = union("sr_model", current_atts$class), + nChains = mod_atts$nChains, + nParameters = mod_atts$nParameters, + nIterations = mod_atts$nIterations, + nBurnin = mod_atts$nBurnin, + nThin = mod_atts$nThin, + description = mod_atts$description + ) + attributes(jags_out) <- new_atts - # Attaching population-level (mu.par) parameter samples as an attribute - pop_params_out <- pop_params_out[complete.cases(pop_params_out), ] - pop_params_out <- dplyr::as_tibble(pop_params_out) + # Adding population parameters optionally and priors in as attributes + if (with_pop_params) { + jags_out <- jags_out |> + structure(population_params = population_params) + } jags_out <- jags_out |> - structure(population_params = pop_params_out) + structure(priors = attributes(priorspec)$used_priors) # Calculating fitted and residuals # Renaming columns using attributes from as_case_data @@ -300,7 +271,5 @@ run_mod <- function(data, jags_out <- jags_out |> structure(jags.post = jags_post_final) } - jags_out <- jags_out |> - structure(class = union("sr_model", class(jags_out))) jags_out } diff --git a/R/as_case_data.R b/R/as_case_data.R index eb55b1409..80dfbffb1 100644 --- a/R/as_case_data.R +++ b/R/as_case_data.R @@ -51,10 +51,24 @@ as_case_data <- function( visit_num = dplyr::row_number() ) |> serocalculator::set_id_var(id_var) |> - structure( - class = union("case_data", class(data)), - biomarker_var = biomarker_var, - timeindays = time_in_days, - value_var = value_var - ) + (\(x) { + current_atts <- attributes(x) + # Explicitly order attributes so that class comes immediately after + # names and row.names, which is the expected position for tibble + # subclasses. tibble::as_tibble() on a subclass can reorder + # standard attributes, so we rebuild them in the correct order. + # Use current_atts$id_var to preserve any standardization done by + # serocalculator::set_id_var (e.g., renaming the ID column to "id"). + new_atts <- list( + names = current_atts$names, + row.names = current_atts$row.names, + class = union("case_data", class(data)), + id_var = current_atts$id_var, + biomarker_var = biomarker_var, + timeindays = time_in_days, + value_var = value_var + ) + attributes(x) <- new_atts + x + })() } diff --git a/R/ex_popparams.R b/R/ex_popparams.R new file mode 100644 index 000000000..7a565776e --- /dev/null +++ b/R/ex_popparams.R @@ -0,0 +1,13 @@ +#' @title Excluding population parameters +#' @author Sam Schildhauer +#' @description +#' `ex_popparams` excludes estimated population parameters from final output +#' [data.frame]. +#' @param x A [data.frame] with a `Subject` variable. +#' @returns A filtered [data.frame] excluding population parameters. +#' @keywords internal +ex_popparams <- function(x) { + x <- x |> + dplyr::filter(!(.data$Subject %in% c("mu.par", "prec.par", "prec.logy"))) + return(x) +} diff --git a/R/nepal_sees_jags_output.R b/R/nepal_sees_jags_output.R index fb75a06c7..4f7a6926f 100644 --- a/R/nepal_sees_jags_output.R +++ b/R/nepal_sees_jags_output.R @@ -8,7 +8,8 @@ #' which is the diagnosis type (typhoid or #' paratyphoid). Keeping only IDs `"newperson"`, `"sees_npl_1"`, `"sees_npl_2"`. #' -#' @format An S3 object of class `sr_model`: A [dplyr::tbl_df] that contains the +#' @format An S3 object of class `sr_model`: A [tibble::tbl_df] that contains +#' the #' posterior predictive distribution of the person-specific parameters for a #' "new person" with no observed data (`Subject = "newperson"`) and posterior #' distributions of the person-specific parameters for two arbitrarily-chosen @@ -26,7 +27,11 @@ #' `sees_npl_2`} #' \item{value}{Estimated value of the parameter} #' \item{attributes}{A [list] of `attributes` that summarize the jags inputs, -#' priors, and optional jags_post mcmc object} +#' priors, optional jags_post mcmc object, and population-level parameters. +#' Includes a `population_params` attribute with posterior samples of the +#' population-level parameters (`mu.par`, `prec.par`, `prec.logy`), indexed +#' by `Iteration`, `Chain`, `Parameter`, `Iso_type`, `Stratification`, and +#' `Population_Parameter`.} #' } #' @source reference study: <https://doi.org/10.1016/S2666-5247(22)00114-8> "nepal_sees_jags_output" diff --git a/R/param_recode.R b/R/param_recode.R new file mode 100644 index 000000000..de05454b5 --- /dev/null +++ b/R/param_recode.R @@ -0,0 +1,17 @@ +#' @title Parameter recode +#' @author Sam Schildhauer +#' @description +#' `param_recode` recodes character numbers as their corresponding parameter. +#' @param x A [vector] of character numbers that represent parameters. +#' @returns A [vector] with recoded values. +#' @keywords internal +param_recode <- function(x) { + dplyr::recode( + x, + "1" = "y0", + "2" = "y1", + "3" = "t1", + "4" = "alpha", + "5" = "shape" + ) +} diff --git a/R/plot_predicted_curve.R b/R/plot_predicted_curve.R index 3a0d46545..ae7825954 100644 --- a/R/plot_predicted_curve.R +++ b/R/plot_predicted_curve.R @@ -7,12 +7,12 @@ #' and shows all individual #' sampled curves. #' -#' @param model An `sr_model` object (returned by [run_mod()]) containing +#' @param model An `sr_model` object (returned by [run_mod]) containing #' samples from the posterior distribution of the model parameters. #' @param ids The participant IDs to plot; for example, `"sees_npl_128"`. #' @param antigen_iso The antigen isotype to plot; for example, "HlyE_IgA" or #' "HlyE_IgG". -#' @param dataset (Optional) A [dplyr::tbl_df] with observed antibody response +#' @param dataset (Optional) A [tibble::tbl_df] with observed antibody response #' data. #' Must contain: #' - `timeindays` diff --git a/R/plot_serocurve.R b/R/plot_serocurve.R index 6c7a2c736..d65a3b3fa 100644 --- a/R/plot_serocurve.R +++ b/R/plot_serocurve.R @@ -14,7 +14,8 @@ #' @param param_source [character]; which posterior samples to use for the #' curve. Options: #' - `"population"` (default): uses population-level `mu.par` samples stored -#' in `attr(model, "population_params")`. +#' in `attr(model, "population_params")`. Requires the model to have been +#' fitted with `run_mod(..., with_pop_params = TRUE)`. #' - `"newperson"`: uses posterior samples for the `"newperson"` subject #' (a subject with no observed data whose posterior is drawn entirely from #' the population-level prior). @@ -23,7 +24,7 @@ #' @param show_all_curves [logical]; if [TRUE], overlays all individual #' posterior-sample curves (can be slow for large numbers of samples). #' Defaults to [FALSE]. -#' @param alpha_samples [numeric]; transparency level (0–1) for individual +#' @param alpha_samples [numeric]; transparency level (0-1) for individual #' sample curves when `show_all_curves = TRUE`. Defaults to `0.3`. #' @param log_y [logical]; if [TRUE], applies a [log10] transformation to the #' y-axis. Defaults to [FALSE]. @@ -70,21 +71,48 @@ plot_serocurve <- function( "The {.arg model} object does not have a {.field population_params}", " attribute.", "i" = paste0( - "Re-fit the model with a version of {.fun run_mod} that monitors", - " {.code mu.par}." + "Re-fit the model with", + " {.code run_mod(..., with_pop_params = TRUE)}." ) ) ) } + # The population_params tibble has columns: + # Iteration, Chain, Parameter, Iso_type, Stratification, + # Population_Parameter, value + # Filter to mu.par rows only, then pivot wider and transform from log scale. param_samples <- pop_params |> dplyr::filter( - .data$antigen_iso %in% .env$antigen_iso, + .data$Population_Parameter == "mu.par", + .data$Iso_type %in% .env$antigen_iso, .data$Stratification %in% .env$strat ) |> + dplyr::select( + all_of( + c("Chain", "Iteration", "Parameter", "Iso_type", "Stratification", + "value") + ) + ) |> + tidyr::pivot_wider( + names_from = "Parameter", + values_from = "value", + names_prefix = "log_" + ) |> dplyr::mutate( - antigen_iso = factor(.data$antigen_iso), + y0 = exp(.data$log_y0), + y1 = .data$y0 + exp(.data$log_y1), + t1 = exp(.data$log_t1), + alpha = exp(.data$log_alpha), + shape = exp(.data$log_shape) + 1 + ) |> + dplyr::select( + -dplyr::starts_with("log_") + ) |> + dplyr::mutate( + Iso_type = factor(.data$Iso_type), Stratification = factor(.data$Stratification) ) + antigen_iso_col <- "Iso_type" } else { # "newperson": extract from the long-format sr_model tibble param_samples <- model |> @@ -103,19 +131,20 @@ plot_serocurve <- function( names_from = "Parameter", values_from = "value" ) |> - dplyr::rename(antigen_iso = "Iso_type") |> dplyr::mutate( - antigen_iso = factor(.data$antigen_iso), + Iso_type = factor(.data$Iso_type), Stratification = factor(.data$Stratification) ) - # "shape" column is already on the untransformed scale in the sr_model + antigen_iso_col <- "Iso_type" } # Add a unique sample identifier for line grouping param_samples <- param_samples |> dplyr::mutate( - sample_id = paste0(.data$Chain, "_", .data$Iteration, "_", - .data$antigen_iso, "_", .data$Stratification) + sample_id = paste0( + .data$Chain, "_", .data$Iteration, "_", + .data[[antigen_iso_col]], "_", .data$Stratification + ) ) # ---- Compute predicted curves over a grid of time points --------------- @@ -127,14 +156,14 @@ plot_serocurve <- function( res = ab(.data$t, .data$y0, .data$y1, .data$t1, .data$alpha, .data$shape), .by = all_of( - c("Chain", "Iteration", "antigen_iso", "Stratification", "sample_id") + c("Chain", "Iteration", antigen_iso_col, "Stratification", "sample_id") ) ) # ---- Summarise to median + 95 % CI ------------------------------------- curve_summary <- serocourse_all |> dplyr::summarise( - .by = all_of(c("antigen_iso", "Stratification", "t")), + .by = all_of(c(antigen_iso_col, "Stratification", "t")), res_med = stats::quantile(.data$res, probs = 0.50, na.rm = TRUE), res_low = stats::quantile(.data$res, probs = 0.025, na.rm = TRUE), res_high = stats::quantile(.data$res, probs = 0.975, na.rm = TRUE) @@ -265,7 +294,7 @@ plot_serocurve <- function( # ---- Faceting ---------------------------------------------------------- facet_vars <- character(0) - if (facet_by_antigen_iso) facet_vars <- c(facet_vars, "antigen_iso") + if (facet_by_antigen_iso) facet_vars <- c(facet_vars, antigen_iso_col) if (facet_by_strat) facet_vars <- c(facet_vars, "Stratification") if (length(facet_vars) > 0) { diff --git a/R/post_summ.R b/R/post_summ.R index 011adc358..c7f7b43fa 100644 --- a/R/post_summ.R +++ b/R/post_summ.R @@ -2,7 +2,7 @@ #' @title Summary Table of Jags Posterior Estimates #' @author Sam Schildhauer #' @description -#' `post_summ()` takes a [list] output from [serodynamics::run_mod()] +#' `post_summ()` takes a [list] output from [run_mod] #' to summary table for parameter, antigen/antibody, and stratification #' combination. #' Defaults will produce every combination of antigen/antibody, parameters, @@ -14,7 +14,7 @@ #' - t1 = time to peak #' - r = shape parameter #' - alpha = decay rate -#' @param data A [list] outputted from [run_mod()]. +#' @param data A [list] outputted from [run_mod]. #' @param iso Specify [character] string to produce tables of only a #' specific antigen/antibody combination, entered with quotes. Default outputs #' all antigen/antibody combinations. diff --git a/R/prep_popparams.R b/R/prep_popparams.R new file mode 100644 index 000000000..8ecb6751b --- /dev/null +++ b/R/prep_popparams.R @@ -0,0 +1,15 @@ +#' @title Preparing population parameters +#' @author Sam Schildhauer +#' @description +#' `prep_popparams` filters a [data.frame] to only include population +#' parameters and renames the `Subject` variable as `Population_Parameter`. +#' @param x A [data.frame] with a `Subject` variable. +#' @returns A filtered [data.frame] with the `Subject` variable renamed to +#' `Population_Parameter`. +#' @keywords internal +prep_popparams <- function(x) { + x <- x |> + dplyr::filter(.data$Subject %in% c("mu.par", "prec.par", "prec.logy")) |> + dplyr::rename(Population_Parameter = "Subject") + return(x) +} diff --git a/R/unpack_jags.R b/R/unpack_jags.R new file mode 100644 index 000000000..84bef9c7c --- /dev/null +++ b/R/unpack_jags.R @@ -0,0 +1,100 @@ +#' @title Unpacking MCMC Object +#' @author Sam Schildhauer +#' @description +#' `unpack_jags()` takes a long-format MCMC sample (typically created by +#' applying [ggmcmc::ggs()] to the `mcmc` component of [run_mod] output) +#' and unpacks it into separate rows for individual-level curve parameters +#' and population-level hyperparameters/precision terms. +#' @param data A [tibble::tbl_df] in [ggmcmc::ggs()] / MCMC-long format, +#' usually `ggmcmc::ggs(jags_post[["mcmc"]])` where `jags_post` comes from +#' [run_mod]. Must contain at least `Iteration`, `Chain`, `Parameter`, +#' and `value` columns. +#' @returns A [tibble::tbl_df] that +#' contains MCMC samples from the joint posterior distribution of the model +#' with unpacked individual-level parameters (e.g., `y0`, `y1`, `t1`, +#' `alpha`, `shape`) and population-level parameters (e.g., `mu.par`, +#' `prec.par`, `prec.logy`), along with isotypes and subjects. +#' @keywords internal +unpack_jags <- function(data) { + + # Convert Parameter column to character if it's a factor (from ggmcmc::ggs) + if (is.factor(data$Parameter)) { + data$Parameter <- as.character(data$Parameter) + } + + unpack_with_pattern <- function(data, filter_pattern, regex_pattern, + subject_repl, subnum_repl, param_fun) { + data |> + dplyr::filter(startsWith(.data$Parameter, paste0(filter_pattern, "["))) |> + dplyr::mutate( + Subject = gsub(regex_pattern, subject_repl, .data$Parameter), + Subnum = gsub(regex_pattern, subnum_repl, .data$Parameter), + Param = param_fun(.data$Parameter, regex_pattern) + ) + } + + # Regular expressions for unpacking + regex_twoidx <- "([[:alnum:].]+)\\[([0-9]+),([0-9]+)\\]" # e.g. x[1,2] + regex_threeidx <- "([[:alnum:].]+)\\[([0-9]+),([0-9]+),([0-9]+)\\]" + # e.g. x[1,2,3] + regex_oneidx <- "([[:alnum:].]+)\\[([0-9]+)\\]" # e.g. x[1] + + # Unpacking mu.par + # Separating population parameters from the rest of the data + jags_mupar <- unpack_with_pattern( + data = data, + filter_pattern = "mu.par", + regex_pattern = regex_twoidx, + subject_repl = "\\1", + subnum_repl = "\\2", + param_fun = function(param, pattern) { + param_recode(gsub(pattern, "\\3", param)) + } + ) + + # Unpacking prec.par + jags_precpar <- unpack_with_pattern( + data = data, + filter_pattern = "prec.par", + regex_pattern = regex_threeidx, + subject_repl = "\\1", + subnum_repl = "\\2", + param_fun = function(param, pattern) { + paste0( + param_recode(gsub(pattern, "\\3", param)), ", ", + param_recode(gsub(pattern, "\\4", param)) + ) + } + ) + + # Unpacking prec.logy + jags_preclogy <- unpack_with_pattern( + data = data, + filter_pattern = "prec.logy", + regex_pattern = regex_oneidx, + subject_repl = "\\1", + subnum_repl = "\\2", + param_fun = function(param, pattern) { + "prec.logy" + } + ) + + # Working with jags unpacked ggs outputs to clarify parameter and subject + jags_unpack_params <- data |> + dplyr::mutate( + Subject = gsub(regex_twoidx, "\\2", .data$Parameter), + Subnum = gsub(regex_twoidx, "\\3", .data$Parameter), + Param = gsub(regex_twoidx, "\\1", .data$Parameter) + ) |> + dplyr::filter(.data$Param %in% c("y0", "y1", "t1", "alpha", "shape")) + + # Putting data frame together + jags_unpack_bind <- dplyr::bind_rows( + jags_unpack_params, + jags_mupar, + jags_precpar, + jags_preclogy + ) + + return(jags_unpack_bind) +} diff --git a/R/use_att_names.R b/R/use_att_names.R index b72128587..6f6515421 100644 --- a/R/use_att_names.R +++ b/R/use_att_names.R @@ -2,7 +2,7 @@ #' @description #' `use_att_names` takes prepared longitudinal data for antibody kinetic #' modeling and names columns using attribute values to allow merging -#' with a modeled [run_mod()] output [dplyr::tbl_df]. 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zZm~LIfhumWNxz>C&9izw7Yd>BQgIMc<b(^qJv{0vkW%3w)cTAHk_W)x^0um4BLMlb zn!tan6%x-Zo_}xlYvIuBw4yk`Udhn&B50ElS{kT0v-(U1eX7xJJ?skF*-AQJ17V#Y z(XQ>K;VN@O>5QNe^5W(Xtc$n4R04n}fM&??(9H6l{+0RTH>7tx#hBfNf1UwD@R}+E z2lt!kj1<sB9@E2KeW=W6t&pN}@H4>j(IWMx^G$-W0k!Fw->uYPc*S~NqAHjZD@WWw zTHVsh7Ff}2!Tff2%xsmsgtSOA@Od6i<ZhWyyJ_=NwFO|j!JmY{5B@IXig2MJu8rf` D^5!Fb diff --git a/inst/WORDLIST b/inst/WORDLIST index 8ea3768d3..a0716aa22 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -43,6 +43,7 @@ onwards params pkgdown prec +precisions preinstalling rhat seroconversion diff --git a/inst/examples/examples-plot_serocurve.R b/inst/examples/examples-plot_serocurve.R index 2223f8266..d532107ba 100644 --- a/inst/examples/examples-plot_serocurve.R +++ b/inst/examples/examples-plot_serocurve.R @@ -1,6 +1,7 @@ +# nepal_sees_jags_output already includes population_params model <- serodynamics::nepal_sees_jags_output -# Population-level curve for a single antigen-isotype +# Population-level curve for a single antigen-isotype and stratum p1 <- plot_serocurve( model = model, antigen_iso = "HlyE_IgA", @@ -25,10 +26,10 @@ print(p3) # Multiple antigen-isotypes, faceted, without CI p4 <- plot_serocurve( - model = model, - antigen_iso = c("HlyE_IgA", "HlyE_IgG"), + model = model, + antigen_iso = c("HlyE_IgA", "HlyE_IgG"), facet_by_antigen_iso = TRUE, - show_ci = FALSE + show_ci = FALSE ) print(p4) diff --git a/man/ex_popparams.Rd b/man/ex_popparams.Rd new file mode 100644 index 000000000..b389d8358 --- /dev/null +++ b/man/ex_popparams.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ex_popparams.R +\name{ex_popparams} +\alias{ex_popparams} +\title{Excluding population parameters} +\usage{ +ex_popparams(x) +} +\arguments{ +\item{x}{A \link{data.frame} with a \code{Subject} variable.} +} +\value{ +A filtered \link{data.frame} excluding population parameters. +} +\description{ +\code{ex_popparams} excludes estimated population parameters from final output +\link{data.frame}. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/nepal_sees_jags_output.Rd b/man/nepal_sees_jags_output.Rd index 4ea195d17..809166d7a 100644 --- a/man/nepal_sees_jags_output.Rd +++ b/man/nepal_sees_jags_output.Rd @@ -5,7 +5,8 @@ \alias{nepal_sees_jags_output} \title{SEES Typhoid run_mod jags output} \format{ -An S3 object of class \code{sr_model}: A \link[dplyr:defunct]{dplyr::tbl_df} that contains the +An S3 object of class \code{sr_model}: A \link[tibble:tbl_df-class]{tibble::tbl_df} that contains +the posterior predictive distribution of the person-specific parameters for a "new person" with no observed data (\code{Subject = "newperson"}) and posterior distributions of the person-specific parameters for two arbitrarily-chosen @@ -23,7 +24,11 @@ Contains 40,000 \code{rows}, 7 \code{columns}, and model \code{attributes}. \code{sees_npl_2}} \item{value}{Estimated value of the parameter} \item{attributes}{A \link{list} of \code{attributes} that summarize the jags inputs, -priors, and optional jags_post mcmc object} +priors, optional jags_post mcmc object, and population-level parameters. +Includes a \code{population_params} attribute with posterior samples of the +population-level parameters (\code{mu.par}, \code{prec.par}, \code{prec.logy}), indexed +by \code{Iteration}, \code{Chain}, \code{Parameter}, \code{Iso_type}, \code{Stratification}, and +\code{Population_Parameter}.} } } \source{ diff --git a/man/param_recode.Rd b/man/param_recode.Rd new file mode 100644 index 000000000..60e648b01 --- /dev/null +++ b/man/param_recode.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/param_recode.R +\name{param_recode} +\alias{param_recode} +\title{Parameter recode} +\usage{ +param_recode(x) +} +\arguments{ +\item{x}{A \link{vector} of character numbers that represent parameters.} +} +\value{ +A \link{vector} with recoded values. +} +\description{ +\code{param_recode} recodes character numbers as their corresponding parameter. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/plot_predicted_curve.Rd b/man/plot_predicted_curve.Rd index b5638b881..0bb77d835 100644 --- a/man/plot_predicted_curve.Rd +++ b/man/plot_predicted_curve.Rd @@ -23,7 +23,7 @@ plot_predicted_curve( ) } \arguments{ -\item{model}{An \code{sr_model} object (returned by \code{\link[=run_mod]{run_mod()}}) containing +\item{model}{An \code{sr_model} object (returned by \link{run_mod}) containing samples from the posterior distribution of the model parameters.} \item{ids}{The participant IDs to plot; for example, \code{"sees_npl_128"}.} @@ -31,7 +31,7 @@ samples from the posterior distribution of the model parameters.} \item{antigen_iso}{The antigen isotype to plot; for example, "HlyE_IgA" or "HlyE_IgG".} -\item{dataset}{(Optional) A \link[dplyr:defunct]{dplyr::tbl_df} with observed antibody response +\item{dataset}{(Optional) A \link[tibble:tbl_df-class]{tibble::tbl_df} with observed antibody response data. Must contain: \itemize{ diff --git a/man/plot_serocurve.Rd b/man/plot_serocurve.Rd index 383e09a12..7acaad11d 100644 --- a/man/plot_serocurve.Rd +++ b/man/plot_serocurve.Rd @@ -33,7 +33,8 @@ Defaults to all stratification levels present in \code{model}.} curve. Options: \itemize{ \item \code{"population"} (default): uses population-level \code{mu.par} samples stored -in \code{attr(model, "population_params")}. +in \code{attr(model, "population_params")}. Requires the model to have been +fitted with \code{run_mod(..., with_pop_params = TRUE)}. \item \code{"newperson"}: uses posterior samples for the \code{"newperson"} subject (a subject with no observed data whose posterior is drawn entirely from the population-level prior). @@ -46,7 +47,7 @@ interval ribbon around the median curve.} posterior-sample curves (can be slow for large numbers of samples). Defaults to \link{FALSE}.} -\item{alpha_samples}{\link{numeric}; transparency level (0–1) for individual +\item{alpha_samples}{\link{numeric}; transparency level (0-1) for individual sample curves when \code{show_all_curves = TRUE}. Defaults to \code{0.3}.} \item{log_y}{\link{logical}; if \link{TRUE}, applies a \link{log10} transformation to the @@ -80,9 +81,10 @@ ribbon is produced for each requested antigen-isotype and stratification combination. } \examples{ +# nepal_sees_jags_output already includes population_params model <- serodynamics::nepal_sees_jags_output -# Population-level curve for a single antigen-isotype +# Population-level curve for a single antigen-isotype and stratum p1 <- plot_serocurve( model = model, antigen_iso = "HlyE_IgA", @@ -107,10 +109,10 @@ print(p3) # Multiple antigen-isotypes, faceted, without CI p4 <- plot_serocurve( - model = model, - antigen_iso = c("HlyE_IgA", "HlyE_IgG"), + model = model, + antigen_iso = c("HlyE_IgA", "HlyE_IgG"), facet_by_antigen_iso = TRUE, - show_ci = FALSE + show_ci = FALSE ) print(p4) diff --git a/man/post_summ.Rd b/man/post_summ.Rd index 54980e08d..239faa1bc 100644 --- a/man/post_summ.Rd +++ b/man/post_summ.Rd @@ -12,7 +12,7 @@ post_summ( ) } \arguments{ -\item{data}{A \link{list} outputted from \code{\link[=run_mod]{run_mod()}}.} +\item{data}{A \link{list} outputted from \link{run_mod}.} \item{iso}{Specify \link{character} string to produce tables of only a specific antigen/antibody combination, entered with quotes. Default outputs @@ -36,7 +36,7 @@ A \link{data.frame} summarizing estimate mean, standard deviation (SD), median, and quantiles (2.5\%, 25.0\%, 50.0\%, 75.0\%, 97.5\%). } \description{ -\code{post_summ()} takes a \link{list} output from \code{\link[=run_mod]{run_mod()}} +\code{post_summ()} takes a \link{list} output from \link{run_mod} to summary table for parameter, antigen/antibody, and stratification combination. Defaults will produce every combination of antigen/antibody, parameters, diff --git a/man/prep_popparams.Rd b/man/prep_popparams.Rd new file mode 100644 index 000000000..b4f4d3d26 --- /dev/null +++ b/man/prep_popparams.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/prep_popparams.R +\name{prep_popparams} +\alias{prep_popparams} +\title{Preparing population parameters} +\usage{ +prep_popparams(x) +} +\arguments{ +\item{x}{A \link{data.frame} with a \code{Subject} variable.} +} +\value{ +A filtered \link{data.frame} with the \code{Subject} variable renamed to +\code{Population_Parameter}. +} +\description{ +\code{prep_popparams} filters a \link{data.frame} to only include population +parameters and renames the \code{Subject} variable as \code{Population_Parameter}. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/run_mod.Rd b/man/run_mod.Rd index d46d4a814..78db77816 100644 --- a/man/run_mod.Rd +++ b/man/run_mod.Rd @@ -14,6 +14,7 @@ run_mod( niter = 100, strat = NA, with_post = FALSE, + with_pop_params = FALSE, ... ) } @@ -42,6 +43,11 @@ should be included as an element of the \link{list} object returned by \code{run (see \code{Value} section below for details). Note: These objects can be large.} +\item{with_pop_params}{A \link{logical} value specifying whether population +level parameters should be included as an attribute entitled +\code{population_params}. Excluded as default. +Note: These objects can be large.} + \item{...}{ Arguments passed on to \code{\link[=prep_priors]{prep_priors}} \describe{ @@ -93,7 +99,7 @@ If specified, must be 2 values long: }} } \value{ -An \code{sr_model} class object: a subclass of \link[dplyr:defunct]{dplyr::tbl_df} that +An \code{sr_model} class object: a subclass of \link[tibble:tbl_df-class]{tibble::tbl_df} that contains MCMC samples from the joint posterior distribution of the model parameters, conditional on the provided input \code{data}, including the following: @@ -120,6 +126,19 @@ including the following: \item \code{nIterations}: Number of iteration specified. \item \code{nBurnin}: Number of burn ins. \item \code{nThin}: Thinning number (niter/nmc). +\item \code{population_params}: Optionally included modeled population parameters +indexed by +\code{Iteration}, +\code{Chain}, \code{Parameter}, \code{Iso_type}, and \code{Stratification}. Excluded as +default. Includes the following modeled population parameters: +\itemize{ +\item \code{mu.par} = The population means of the host-specific model parameters +(on logarithmic scales). +\item \code{prec.par} = The population precision matrix of the hyperparameters +(with diagonal elements equal to inverse variances). +\item \code{prec.logy} = A vector of population precisions (inverse variances), +one per antigen/isotype combination. +} \item \code{priors}: A \link{list} that summarizes the input priors, including: \itemize{ \item \code{mu_hyp_param} @@ -132,10 +151,6 @@ including the following: for all observations. \item An optional \code{"jags.post"} attribute, included when argument \code{with_post} = TRUE. -\item \code{population_params}: A \link[dplyr:defunct]{dplyr::tbl_df} with posterior samples of the -population-level parameters (\code{mu.par}), transformed to the original -parameter scale. Columns: \code{Chain}, \code{Iteration}, \code{antigen_iso}, \code{y0}, -\code{y1}, \code{t1}, \code{alpha}, \code{shape}, \code{Stratification}. } } } diff --git a/man/unpack_jags.Rd b/man/unpack_jags.Rd new file mode 100644 index 000000000..f4a41c482 --- /dev/null +++ b/man/unpack_jags.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/unpack_jags.R +\name{unpack_jags} +\alias{unpack_jags} +\title{Unpacking MCMC Object} +\usage{ +unpack_jags(data) +} +\arguments{ +\item{data}{A \link[tibble:tbl_df-class]{tibble::tbl_df} in \code{\link[ggmcmc:ggs]{ggmcmc::ggs()}} / MCMC-long format, +usually \code{ggmcmc::ggs(jags_post[["mcmc"]])} where \code{jags_post} comes from +\link{run_mod}. Must contain at least \code{Iteration}, \code{Chain}, \code{Parameter}, +and \code{value} columns.} +} +\value{ +A \link[tibble:tbl_df-class]{tibble::tbl_df} that +contains MCMC samples from the joint posterior distribution of the model +with unpacked individual-level parameters (e.g., \code{y0}, \code{y1}, \code{t1}, +\code{alpha}, \code{shape}) and population-level parameters (e.g., \code{mu.par}, +\code{prec.par}, \code{prec.logy}), along with isotypes and subjects. +} +\description{ +\code{unpack_jags()} takes a long-format MCMC sample (typically created by +applying \code{\link[ggmcmc:ggs]{ggmcmc::ggs()}} to the \code{mcmc} component of \link{run_mod} output) +and unpacks it into separate rows for individual-level curve parameters +and population-level hyperparameters/precision terms. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/use_att_names.Rd b/man/use_att_names.Rd index 9a2151e0e..5367bf7fe 100644 --- a/man/use_att_names.Rd +++ b/man/use_att_names.Rd @@ -16,7 +16,7 @@ The input \link{data.frame} with columns named after attributes. \description{ \code{use_att_names} takes prepared longitudinal data for antibody kinetic modeling and names columns using attribute values to allow merging -with a modeled \code{\link[=run_mod]{run_mod()}} output \link[dplyr:defunct]{dplyr::tbl_df}. The column names include +with a modeled \link{run_mod} output \link[tibble:tbl_df-class]{tibble::tbl_df}. The column names include \code{Subject}, \code{Iso_type}, \code{t}, and \code{result}. } \keyword{internal} diff --git a/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv b/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv new file mode 100644 index 000000000..8a7b29a59 --- /dev/null +++ b/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv @@ -0,0 +1,31 @@ +Parameter,mean,sd +alpha,-4.8276,0.200665 +"alpha, alpha",2.56363,0.368743 +"alpha, shape",-0.610002,0.872237 +"alpha, t1",0.253244,0.910382 +"alpha, y0",-0.269962,0.623738 +"alpha, y1",-0.052442,0.187775 +shape,-0.627015,0.0691708 +"shape, alpha",-0.610002,0.872237 +"shape, shape",9.52829,2.70326 +"shape, t1",4.04278,3.12409 +"shape, y0",-2.43068,3.82725 +"shape, y1",-1.03352,0.430277 +t1,0.463903,0.0405599 +"t1, alpha",0.253244,0.910382 +"t1, shape",4.04278,3.12409 +"t1, t1",18.8339,5.49919 +"t1, y0",0.778855,4.44261 +"t1, y1",0.0564977,0.659988 +y0,0.78573,0.110742 +"y0, alpha",-0.269962,0.623738 +"y0, shape",-2.43068,3.82725 +"y0, t1",0.778855,4.44261 +"y0, y0",11.1517,4.71125 +"y0, y1",0.230998,0.401854 +y1,5.87676,0.185882 +"y1, alpha",-0.052442,0.187775 +"y1, shape",-1.03352,0.430277 +"y1, t1",0.0564977,0.659988 +"y1, y0",0.230998,0.401854 +"y1, y1",0.706827,0.126534 diff --git a/tests/testthat/_snaps/run_mod.md b/tests/testthat/_snaps/run_mod.md index 14cf70420..7a53344b9 100644 --- a/tests/testthat/_snaps/run_mod.md +++ b/tests/testthat/_snaps/run_mod.md @@ -1,64 +1,20 @@ -# results are consistent with simulated data - - list(names = c("Iteration", "Chain", "Parameter", "Iso_type", - "Stratification", "Subject", "value"), class = c("sr_model", - "tbl_df", "tbl", "data.frame"), nChains = 2L, nParameters = 505L, - nIterations = 10L, nBurnin = 200, nThin = 1, priors = list( - mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, - 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), - wishdf_param = 20, prec_logy_hyp_param = c(4, 1))) - # results are consistent with SEES data list(names = c("Iteration", "Chain", "Parameter", "Iso_type", "Stratification", "Subject", "value"), class = c("sr_model", "tbl_df", "tbl", "data.frame"), nChains = 2L, nParameters = 440L, - nIterations = 100L, nBurnin = 20, nThin = 1, priors = list( - mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, - 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), - wishdf_param = 20, prec_logy_hyp_param = c(4, 1))) + nIterations = 100L, nBurnin = 20, nThin = 1, description = "jags_post[[\"mcmc\"]]", + priors = list(mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, + 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), wishdf_param = 20, + prec_logy_hyp_param = c(4, 1))) # results are consistent with unstratified SEES data list(names = c("Iteration", "Chain", "Parameter", "Iso_type", "Stratification", "Subject", "value"), class = c("sr_model", "tbl_df", "tbl", "data.frame"), nChains = 2L, nParameters = 1890L, - nIterations = 100L, nBurnin = 20, nThin = 1, priors = list( - mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, - 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), - wishdf_param = 20, prec_logy_hyp_param = c(4, 1))) - -# results are consistent with unstratified SEES data with jags.post included - - WAoAAAACAAQEAgACAwAAAAITAAAACAAAABAAAAAHAAQACQAAAAlJdGVyYXRpb24ABAAJAAAA - BUNoYWluAAQACQAAAAlQYXJhbWV0ZXIABAAJAAAACElzb190eXBlAAQACQAAAA5TdHJhdGlm - aWNhdGlvbgAEAAkAAAAHU3ViamVjdAAEAAkAAAAFdmFsdWUAAAAQAAAABAAEAAkAAAAIc3Jf - bW9kZWwABAAJAAAABnRibF9kZgAEAAkAAAADdGJsAAQACQAAAApkYXRhLmZyYW1lAAAADQAA - AAEAAAACAAAADQAAAAEAAAdiAAAADQAAAAEAAABkAAAADgAAAAFANAAAAAAAAAAAAA4AAAAB - P/AAAAAAAAAAAAITAAAABQAAAA4AAAAFP/AAAAAAAABAHAAAAAAAAD/wAAAAAAAAwBAAAAAA - AAC/8AAAAAAAAAAAAA4AAAAFP/AAAAAAAAA+5Pi1iONo8T/wAAAAAAAAP1BiTdLxqfw/8AAA - AAAAAAAAAA4AAAAFP/AAAAAAAABASQAAAAAAAD/wAAAAAAAAQCQAAAAAAAA/8AAAAAAAAAAA - AA4AAAABQDQAAAAAAAAAAAAOAAAAAkAQAAAAAAAAP/AAAAAAAAAAAAQCAAAAAQAEAAkAAAAF - bmFtZXMAAAAQAAAABQAEAAkAAAAMbXVfaHlwX3BhcmFtAAQACQAAAA5wcmVjX2h5cF9wYXJh - bQAEAAkAAAALb21lZ2FfcGFyYW0ABAAJAAAADHdpc2hkZl9wYXJhbQAEAAkAAAATcHJlY19s - b2d5X2h5cF9wYXJhbQAAAP4AAAQCAAAB/wAAABAAAAAIAAQACQAAAAVuYW1lcwAEAAkAAAAF - Y2xhc3MABAAJAAAAB25DaGFpbnMABAAJAAAAC25QYXJhbWV0ZXJzAAQACQAAAAtuSXRlcmF0 - aW9ucwAEAAkAAAAHbkJ1cm5pbgAEAAkAAAAFblRoaW4ABAAJAAAABnByaW9ycwAAAP4= - -# results are consistent with unstratified SEES data with modified priors - - WAoAAAACAAQEAgACAwAAAAITAAAACAAAABAAAAAHAAQACQAAAAlJdGVyYXRpb24ABAAJAAAA - BUNoYWluAAQACQAAAAlQYXJhbWV0ZXIABAAJAAAACElzb190eXBlAAQACQAAAA5TdHJhdGlm - aWNhdGlvbgAEAAkAAAAHU3ViamVjdAAEAAkAAAAFdmFsdWUAAAAQAAAABAAEAAkAAAAIc3Jf - bW9kZWwABAAJAAAABnRibF9kZgAEAAkAAAADdGJsAAQACQAAAApkYXRhLmZyYW1lAAAADQAA - AAEAAAACAAAADQAAAAEAAAdiAAAADQAAAAEAAABkAAAADgAAAAFANAAAAAAAAAAAAA4AAAAB - P/AAAAAAAAAAAAITAAAABQAAAA4AAAAFP/AAAAAAAABAEAAAAAAAAD/wAAAAAAAAwAgAAAAA - AAC/8AAAAAAAAAAAAA4AAAAFP4R64UeuFHs/Gjbi6xxDLT+EeuFHrhR7P1BiTdLxqfw/hHrh - R64UewAAAA4AAAAFP/AAAAAAAABANAAAAAAAAD/wAAAAAAAAQCQAAAAAAAA/8AAAAAAAAAAA - AA4AAAABQCQAAAAAAAAAAAAOAAAAAkAIAAAAAAAAP/AAAAAAAAAAAAQCAAAAAQAEAAkAAAAF - bmFtZXMAAAAQAAAABQAEAAkAAAAMbXVfaHlwX3BhcmFtAAQACQAAAA5wcmVjX2h5cF9wYXJh - bQAEAAkAAAALb21lZ2FfcGFyYW0ABAAJAAAADHdpc2hkZl9wYXJhbQAEAAkAAAATcHJlY19s - b2d5X2h5cF9wYXJhbQAAAP4AAAQCAAAB/wAAABAAAAAIAAQACQAAAAVuYW1lcwAEAAkAAAAF - Y2xhc3MABAAJAAAAB25DaGFpbnMABAAJAAAAC25QYXJhbWV0ZXJzAAQACQAAAAtuSXRlcmF0 - aW9ucwAEAAkAAAAHbkJ1cm5pbgAEAAkAAAAFblRoaW4ABAAJAAAABnByaW9ycwAAAP4= + nIterations = 100L, nBurnin = 20, nThin = 1, description = "jags_post[[\"mcmc\"]]", + priors = list(mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, + 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), wishdf_param = 20, + prec_logy_hyp_param = c(4, 1))) diff --git a/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv b/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv new file mode 100644 index 000000000..189765454 --- /dev/null +++ b/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv @@ -0,0 +1,31 @@ +Parameter,mean,sd +alpha,-4.73607,0.219781 +"alpha, alpha",2.76907,0.688682 +"alpha, shape",-0.383234,0.533813 +"alpha, t1",0.448772,1.57899 +"alpha, y0",0.700184,0.757452 +"alpha, y1",-0.0212652,0.222195 +shape,-0.681647,0.0690278 +"shape, alpha",-0.383234,0.533813 +"shape, shape",6.58223,2.3041 +"shape, t1",0.914755,2.42633 +"shape, y0",-2.45229,1.61395 +"shape, y1",-0.877117,0.319837 +t1,0.591297,0.100501 +"t1, alpha",0.448772,1.57899 +"t1, shape",0.914755,2.42633 +"t1, t1",20.3291,6.01563 +"t1, y0",3.25694,6.00627 +"t1, y1",0.0188795,0.473277 +y0,0.726466,0.0841371 +"y0, alpha",0.700184,0.757452 +"y0, shape",-2.45229,1.61395 +"y0, t1",3.25694,6.00627 +"y0, y0",13.2226,7.023 +"y0, y1",0.220216,0.552936 +y1,5.7489,0.348058 +"y1, alpha",-0.0212652,0.222195 +"y1, shape",-0.877117,0.319837 +"y1, t1",0.0188795,0.473277 +"y1, y0",0.220216,0.552936 +"y1, y1",0.681022,0.11074 diff --git a/tests/testthat/test-internal-popparams.R b/tests/testthat/test-internal-popparams.R new file mode 100644 index 000000000..2cdf1031b --- /dev/null +++ b/tests/testthat/test-internal-popparams.R @@ -0,0 +1,173 @@ +test_that("param_recode correctly recodes parameter indices", { + # Test valid parameter indices + expect_equal(serodynamics:::param_recode("1"), "y0") + expect_equal(serodynamics:::param_recode("2"), "y1") + expect_equal(serodynamics:::param_recode("3"), "t1") + expect_equal(serodynamics:::param_recode("4"), "alpha") + expect_equal(serodynamics:::param_recode("5"), "shape") + + # Test vector of valid indices + expect_equal( + serodynamics:::param_recode(c("1", "2", "3", "4", "5")), + c("y0", "y1", "t1", "alpha", "shape") + ) +}) + +test_that("unpack_jags handles factor Parameter column", { + # Create a simple ggs-like object with factor Parameter column + test_data <- tibble::tibble( + Iteration = rep(1:5, 3), + Chain = rep(1, 15), + Parameter = factor( + rep(c("mu.par[1,1]", "prec.par[1,1,2]", "y0[1,1]"), each = 5) + ), + value = rnorm(15) + ) + + # Should not error with factor column + result <- serodynamics:::unpack_jags(test_data) + + expect_true(is.data.frame(result)) + expect_true("Subject" %in% names(result)) + expect_true("Param" %in% names(result)) +}) + +test_that("unpack_jags correctly unpacks mu.par parameters", { + test_data <- tibble::tibble( + Iteration = rep(1:3, 2), + Chain = rep(1, 6), + Parameter = rep(c("mu.par[1,1]", "mu.par[1,2]"), each = 3), + value = rnorm(6) + ) + + result <- serodynamics:::unpack_jags(test_data) + + # Check that mu.par rows are present + mu_rows <- result[result$Subject == "mu.par", ] + expect_gt(nrow(mu_rows), 0) + + # Check Subject is correctly set + expect_true("mu.par" %in% result$Subject) + + # Check Param is correctly decoded + expect_true(all(mu_rows$Param %in% c("y0", "y1", "t1", "alpha", "shape"))) +}) + +test_that("unpack_jags correctly unpacks prec.par parameters", { + test_data <- tibble::tibble( + Iteration = rep(1:3, 2), + Chain = rep(1, 6), + Parameter = rep(c("prec.par[1,1,2]", "prec.par[1,2,3]"), each = 3), + value = rnorm(6) + ) + + result <- serodynamics:::unpack_jags(test_data) + + # Check that prec.par rows are present + prec_rows <- result[result$Subject == "prec.par", ] + expect_gt(nrow(prec_rows), 0) + + # Check Subject is correctly set + expect_true("prec.par" %in% result$Subject) + + # Check Param contains pairs (e.g., "y0, y1") + expect_true(any(grepl(",", prec_rows$Param))) +}) + +test_that("unpack_jags correctly unpacks prec.logy parameters", { + test_data <- tibble::tibble( + Iteration = rep(1:3, 2), + Chain = rep(1, 6), + Parameter = rep(c("prec.logy[1]", "prec.logy[2]"), each = 3), + value = rnorm(6) + ) + + result <- serodynamics:::unpack_jags(test_data) + + # Check that prec.logy rows are present + logy_rows <- result[result$Subject == "prec.logy", ] + expect_gt(nrow(logy_rows), 0) + + # Check Subject is correctly set + expect_true("prec.logy" %in% result$Subject) +}) + +test_that("unpack_jags correctly unpacks individual-level parameters", { + test_data <- tibble::tibble( + Iteration = rep(1:3, 2), + Chain = rep(1, 6), + Parameter = rep(c("y0[1,1]", "alpha[2,1]"), each = 3), + value = rnorm(6) + ) + + result <- serodynamics:::unpack_jags(test_data) + + # Check individual-level parameters are unpacked + expect_true("1" %in% result$Subject | "2" %in% result$Subject) + expect_true("y0" %in% result$Param | "alpha" %in% result$Param) +}) + +test_that("prep_popparams filters to population parameters only", { + test_data <- tibble::tibble( + Iteration = 1:10, + Chain = rep(1, 10), + Parameter = rep(c("y0", "mu.par"), each = 5), + Subject = rep(c("1", "mu.par"), each = 5), + value = rnorm(10) + ) + + result <- serodynamics:::prep_popparams(test_data) + + # Should only have population parameters + expect_true(all(result$Population_Parameter %in% + c("mu.par", "prec.par", "prec.logy"))) + + # Should rename Subject to Population_Parameter + expect_true("Population_Parameter" %in% names(result)) + expect_false("Subject" %in% names(result)) + + # Should have 5 rows (only mu.par rows) + expect_equal(nrow(result), 5) +}) + +test_that("ex_popparams excludes population parameters", { + test_data <- tibble::tibble( + Iteration = 1:10, + Chain = rep(1, 10), + Parameter = rep(c("y0", "mu.par"), each = 5), + Subject = rep(c("1", "mu.par"), each = 5), + value = rnorm(10) + ) + + result <- serodynamics:::ex_popparams(test_data) + + # Should not have any population parameters + expect_false(any(result$Subject %in% c("mu.par", "prec.par", "prec.logy"))) + + # Should have 5 rows (only y0 rows) + expect_equal(nrow(result), 5) + + # Should keep original structure + expect_equal(names(result), names(test_data)) +}) + +test_that("prep_popparams and ex_popparams are complementary", { + test_data <- tibble::tibble( + Iteration = rep(1:5, 4), + Chain = rep(1, 20), + Parameter = rep(c("y0", "mu.par", "prec.par", "prec.logy"), each = 5), + Subject = rep(c("1", "mu.par", "prec.par", "prec.logy"), each = 5), + value = rnorm(20) + ) + + pop_params <- serodynamics:::prep_popparams(test_data) + individual_params <- serodynamics:::ex_popparams(test_data) + + # Together they should account for all rows + expect_equal(nrow(pop_params) + nrow(individual_params), nrow(test_data)) + + # No overlap in subjects + # Note: pop_params has Population_Parameter column, not Subject + expect_false(any(individual_params$Subject %in% + c("mu.par", "prec.par", "prec.logy"))) +}) diff --git a/tests/testthat/test-run_mod.R b/tests/testthat/test-run_mod.R index 2d5c6ce34..891869406 100644 --- a/tests/testthat/test-run_mod.R +++ b/tests/testthat/test-run_mod.R @@ -3,6 +3,7 @@ test_that( code = { testthat::announce_snapshot_file("sim-strat-curve-params.csv") testthat::announce_snapshot_file("sim-strat-fitted_residuals.csv") + testthat::announce_snapshot_file("popparam-summary-stats.csv") withr::local_seed(1) strat1 <- serocalculator::typhoid_curves_nostrat_100 |> sim_case_data(n = 100, @@ -22,26 +23,49 @@ test_that( nmc = 10, niter = 10, # Number of iterations strat = "strat", # Variable to be stratified + with_pop_params = TRUE ) |> suppressWarnings() - - results |> - attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> - expect_snapshot_value(style = "deparse") - results |> expect_snapshot_data( "sim-strat-curve-params", variant = darwin_variant() ) + # Testing attributes + results |> + attributes() |> + names() |> + expect_setequal(c("names", "row.names", "class", "nChains", + "nParameters", "nIterations", "nBurnin", "nThin", + "description", "population_params", "priors", + "fitted_residuals")) + + # Verify class appears immediately after names and row.names + expect_equal( + names(attributes(results))[1:3], + c("names", "row.names", "class") + ) + attributes(results)$fitted_residuals |> expect_snapshot_data( "sim-strat-fitted_residuals", variant = darwin_variant() ) + + # Testing for population parameters + attributes(results)$population_params |> + dplyr::group_by(Parameter) |> + dplyr::summarise( + mean = mean(value), + sd = sd(value), + .groups = "drop" + ) |> + dplyr::arrange(Parameter) |> + expect_snapshot_data("popparam-summary-stats", + variant = darwin_variant() + ) } ) @@ -62,13 +86,13 @@ test_that( nburn = 10, # Number of unrecorded samples before sampling begins nmc = 100, niter = 100, # Number of iterations - strat = "bldculres", # Variable to be stratified + strat = "bldculres" # Variable to be stratified ) |> suppressWarnings() results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> + rlist::list.remove(c("row.names", "fitted_residuals")) |> expect_snapshot_value(style = "deparse") results |> @@ -82,6 +106,7 @@ test_that( "strat-fitted_residuals", variant = darwin_variant() ) + } ) @@ -101,13 +126,13 @@ test_that( nburn = 10, # Number of unrecorded samples before sampling begins nmc = 100, niter = 100, # Number of iterations - strat = NA, # Variable to be stratified + strat = NA # Variable to be stratified ) |> suppressWarnings() results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> + rlist::list.remove(c("row.names", "fitted_residuals")) |> expect_snapshot_value(style = "deparse") results |> @@ -144,12 +169,7 @@ test_that( with_post = TRUE ) |> suppressWarnings() - - results |> - attributes() |> - rlist::list.remove(c("row.names", "jags.post", "fitted_residuals", "population_params")) |> - expect_snapshot_value(style = "serialize") - + results |> expect_snapshot_data( "nostrat-curve-params-withpost", @@ -183,15 +203,11 @@ test_that( ) |> suppressWarnings() - results |> - attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals", "population_params")) |> - expect_snapshot_value(style = "serialize") - results |> expect_snapshot_data( "nostrat-curve-params-specpriors", variant = darwin_variant() ) + } ) From a7974e067cec5ddaef783175fd93e71e55d831e8 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Tue, 14 Apr 2026 07:38:24 +0000 Subject: [PATCH 04/15] Remove show_all_curves/alpha_samples params; update newperson description to predictive distribution Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/64eb25a1-7d2a-4ab5-b24a-5dc03686f3ee Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com> --- R/plot_serocurve.R | 61 +++---------------------- inst/examples/examples-plot_serocurve.R | 2 +- man/plot_serocurve.Rd | 18 ++------ 3 files changed, 11 insertions(+), 70 deletions(-) diff --git a/R/plot_serocurve.R b/R/plot_serocurve.R index d65a3b3fa..44a203f48 100644 --- a/R/plot_serocurve.R +++ b/R/plot_serocurve.R @@ -1,7 +1,7 @@ #' @title Plot Estimated Serodynamic Curves at the Population Level #' @description #' Plots the estimated antibody response curve derived from posterior samples -#' of population-level (`mu.par`) or "new person" parameters from a fitted +#' of population-level (`mu.par`) or the predictive distribution from a fitted #' [run_mod()] model. A median curve with an optional 95% credible interval #' ribbon is produced for each requested antigen-isotype and stratification #' combination. @@ -16,16 +16,10 @@ #' - `"population"` (default): uses population-level `mu.par` samples stored #' in `attr(model, "population_params")`. Requires the model to have been #' fitted with `run_mod(..., with_pop_params = TRUE)`. -#' - `"newperson"`: uses posterior samples for the `"newperson"` subject -#' (a subject with no observed data whose posterior is drawn entirely from -#' the population-level prior). +#' - `"newperson"`: uses the predictive distribution for a new individual +#' drawn from the population-level prior. #' @param show_ci [logical]; if [TRUE] (default), draws a 95% credible #' interval ribbon around the median curve. -#' @param show_all_curves [logical]; if [TRUE], overlays all individual -#' posterior-sample curves (can be slow for large numbers of samples). -#' Defaults to [FALSE]. -#' @param alpha_samples [numeric]; transparency level (0-1) for individual -#' sample curves when `show_all_curves = TRUE`. Defaults to `0.3`. #' @param log_y [logical]; if [TRUE], applies a [log10] transformation to the #' y-axis. Defaults to [FALSE]. #' @param log_x [logical]; if [TRUE], applies a pseudo-log10 transformation to @@ -51,8 +45,6 @@ plot_serocurve <- function( strat = unique(model$Stratification), param_source = "population", show_ci = TRUE, - show_all_curves = FALSE, - alpha_samples = 0.3, log_y = FALSE, log_x = FALSE, xlim = NULL, @@ -114,7 +106,8 @@ plot_serocurve <- function( ) antigen_iso_col <- "Iso_type" } else { - # "newperson": extract from the long-format sr_model tibble + # "newperson": predictive distribution for a new individual drawn from + # the population-level prior param_samples <- model |> dplyr::filter( .data$Subject == "newperson", @@ -138,15 +131,6 @@ plot_serocurve <- function( antigen_iso_col <- "Iso_type" } - # Add a unique sample identifier for line grouping - param_samples <- param_samples |> - dplyr::mutate( - sample_id = paste0( - .data$Chain, "_", .data$Iteration, "_", - .data[[antigen_iso_col]], "_", .data$Stratification - ) - ) - # ---- Compute predicted curves over a grid of time points --------------- tx <- seq(0, 1200, by = 5) @@ -156,7 +140,7 @@ plot_serocurve <- function( res = ab(.data$t, .data$y0, .data$y1, .data$t1, .data$alpha, .data$shape), .by = all_of( - c("Chain", "Iteration", antigen_iso_col, "Stratification", "sample_id") + c("Chain", "Iteration", antigen_iso_col, "Stratification") ) ) @@ -179,34 +163,6 @@ plot_serocurve <- function( ggplot2::labs(x = "Time since onset", y = "Assay result") + ggplot2::theme(legend.position = "bottom") - if (show_all_curves) { - if (multi_strat) { - p <- p + - ggplot2::geom_line( - data = serocourse_all, - ggplot2::aes( - x = .data$t, - y = .data$res, - group = .data$sample_id, - colour = .data$Stratification - ), - alpha = alpha_samples - ) - } else { - p <- p + - ggplot2::geom_line( - data = serocourse_all, - ggplot2::aes( - x = .data$t, - y = .data$res, - group = .data$sample_id, - colour = "samples" - ), - alpha = alpha_samples - ) - } - } - if (show_ci) { if (multi_strat) { p <- p + @@ -269,11 +225,6 @@ plot_serocurve <- function( color_vals <- c("median" = "red") color_labels <- c("median" = "Median") - if (show_all_curves) { - color_vals["samples"] <- "gray" - color_labels["samples"] <- "Posterior samples" - } - fill_vals <- c("ci" = "red") fill_labels <- c("ci" = "95% credible interval") diff --git a/inst/examples/examples-plot_serocurve.R b/inst/examples/examples-plot_serocurve.R index d532107ba..2825d3fdc 100644 --- a/inst/examples/examples-plot_serocurve.R +++ b/inst/examples/examples-plot_serocurve.R @@ -33,7 +33,7 @@ p4 <- plot_serocurve( ) print(p4) -# Using "newperson" posterior samples instead of mu.par +# Using the predictive distribution for a new individual (newperson posterior) p5 <- plot_serocurve( model = model, antigen_iso = "HlyE_IgA", diff --git a/man/plot_serocurve.Rd b/man/plot_serocurve.Rd index 7acaad11d..cec7088a0 100644 --- a/man/plot_serocurve.Rd +++ b/man/plot_serocurve.Rd @@ -10,8 +10,6 @@ plot_serocurve( strat = unique(model$Stratification), param_source = "population", show_ci = TRUE, - show_all_curves = FALSE, - alpha_samples = 0.3, log_y = FALSE, log_x = FALSE, xlim = NULL, @@ -35,21 +33,13 @@ curve. Options: \item \code{"population"} (default): uses population-level \code{mu.par} samples stored in \code{attr(model, "population_params")}. Requires the model to have been fitted with \code{run_mod(..., with_pop_params = TRUE)}. -\item \code{"newperson"}: uses posterior samples for the \code{"newperson"} subject -(a subject with no observed data whose posterior is drawn entirely from -the population-level prior). +\item \code{"newperson"}: uses the predictive distribution for a new individual +drawn from the population-level prior. }} \item{show_ci}{\link{logical}; if \link{TRUE} (default), draws a 95\% credible interval ribbon around the median curve.} -\item{show_all_curves}{\link{logical}; if \link{TRUE}, overlays all individual -posterior-sample curves (can be slow for large numbers of samples). -Defaults to \link{FALSE}.} - -\item{alpha_samples}{\link{numeric}; transparency level (0-1) for individual -sample curves when \code{show_all_curves = TRUE}. Defaults to \code{0.3}.} - \item{log_y}{\link{logical}; if \link{TRUE}, applies a \link{log10} transformation to the y-axis. Defaults to \link{FALSE}.} @@ -75,7 +65,7 @@ A \link[ggplot2:ggplot]{ggplot2::ggplot} object. } \description{ Plots the estimated antibody response curve derived from posterior samples -of population-level (\code{mu.par}) or "new person" parameters from a fitted +of population-level (\code{mu.par}) or the predictive distribution from a fitted \code{\link[=run_mod]{run_mod()}} model. A median curve with an optional 95\% credible interval ribbon is produced for each requested antigen-isotype and stratification combination. @@ -116,7 +106,7 @@ p4 <- plot_serocurve( ) print(p4) -# Using "newperson" posterior samples instead of mu.par +# Using the predictive distribution for a new individual (newperson posterior) p5 <- plot_serocurve( model = model, antigen_iso = "HlyE_IgA", From 5104edc04e38a6c8594d116b9734d2b37cfb3aac Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Thu, 7 May 2026 11:39:49 -0700 Subject: [PATCH 05/15] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- R/Run_Mod.R | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/R/Run_Mod.R b/R/Run_Mod.R index 48d202bf1..fb763c428 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -54,16 +54,20 @@ #' - `nBurnin`: Number of burn ins. #' - `nThin`: Thinning number (niter/nmc). #' - `population_params`: Optionally included modeled population parameters -#' indexed by -#' `Iteration`, -#' `Chain`, `Parameter`, `Iso_type`, and `Stratification`. Excluded as +#' indexed by +#' `Iteration`, +#' `Chain`, `Parameter`, `Iso_type`, and `Stratification`. Excluded as #' default. Includes the following modeled population parameters: -#' - `mu.par` = The population means of the host-specific model parameters -#' (on logarithmic scales). +#' - `mu.par` = The population means of the host-specific model parameters +#' on latent transformed scales. For these rows, `Parameter` values refer +#' to the underlying `par` components used in the model, not necessarily +#' to the observed-scale curve parameters used elsewhere in the package. +#' For example, `y1` corresponds to `log(y1 - y0)` and `shape` +#' corresponds to `log(shape - 1)`. #' - `prec.par` = The population precision matrix of the hyperparameters -#' (with diagonal elements equal to inverse variances). -#' - `prec.logy` = A vector of population precisions (inverse variances), -#' one per antigen/isotype combination. +#' (with diagonal elements equal to inverse variances). +#' - `prec.logy` = A vector of population precisions (inverse variances), +#' one per antigen/isotype combination. #' - `priors`: A [list] that summarizes the input priors, including: #' - `mu_hyp_param` #' - `prec_hyp_param` From d511f49b3ab98818475e97cba9222db60a6fe641 Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Thu, 7 May 2026 11:42:54 -0700 Subject: [PATCH 06/15] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 84fdadece..708b44803 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9048 +Version: 0.0.0.9050 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From bec1f993e765a7ce61402532bc3b0bbf987f9c9f Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Thu, 7 May 2026 11:48:09 -0700 Subject: [PATCH 07/15] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- NEWS.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 9fb1db318..32329f01c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,8 +6,10 @@ ribbons, stratified curves with colour or faceting, and multiple antigen-isotypes (#74). * `run_mod()` now monitors the `mu.par` hyperparameter and stores its - posterior samples (transformed to the original parameter scale) in a - `population_params` attribute of the returned `sr_model` object (#74). + posterior samples on the latent parameter scale in a + `population_params` attribute of the returned `sr_model` object; functions + such as `plot_serocurve()` apply transformations to the original parameter + scale when needed (#74). * Expanded `.github/copilot-instructions.md` with additional guidance on evidence-based claims, Quarto markdown/cross-reference conventions, R style practices, and phrase-level line-break formatting for source text. * Fixed `dplyr::as_tibble()` references to `tibble::as_tibble()` in `post_summ()` and `run_mod()`, since `as_tibble()` is exported from the `tibble` package, not `dplyr`. * Added R 4.5+ snapshot variants to handle the changed attribute ordering in From 68b133b18d668af119012229be7bfb2191b199a9 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 8 May 2026 14:16:49 +0000 Subject: [PATCH 08/15] fix: use all() in test assertions and idiomatic dplyr rename/select - Change | (OR) assertions to all() in test-internal-popparams.R so both subjects (1, 2) and both parameters (y0, alpha) must be present - Replace dplyr::rename(c("new" = "old")) with standard rename(new = "old") form in Run_Mod.R - Replace dplyr::select(!c(...)) with select(-all_of(c(...))) in Run_Mod.R Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/8de81669-134d-4ab9-b6ed-f52c75602afb Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com> --- R/Run_Mod.R | 14 +++++++++----- tests/testthat/test-internal-popparams.R | 4 ++-- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/R/Run_Mod.R b/R/Run_Mod.R index fb763c428..d7ef654a8 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -187,8 +187,10 @@ run_mod <- function(data, dplyr::mutate(Subject = as.character(dplyr::row_number())) jags_final <- dplyr::left_join(jags_unpacked, ids, by = "Subject") |> - dplyr::rename(c("Iso_type" = "attributes.longdata..antigens", - "Subject_mcmc" = "attr.longdata...ids..")) |> + dplyr::rename( + Iso_type = "attributes.longdata..antigens", + Subject_mcmc = "attr.longdata...ids.." + ) |> # Subject handling: # * For individual-level parameters, the left join above finds a row in # attr(longdata, "ids"), so Subject_mcmc contains the subject ID. @@ -208,9 +210,11 @@ run_mod <- function(data, # containing cleaned parameter names. # Drop the temporary Subject (now only used as a fallback for population # parameters) and rename Subject_mcmc back to Subject for downstream use. - dplyr::select(!c("Subnum", "Subject", "Parameter")) |> - dplyr::rename(c("Subject" = "Subject_mcmc", - "Parameter" = "Param")) + dplyr::select(-dplyr::all_of(c("Subnum", "Subject", "Parameter"))) |> + dplyr::rename( + Subject = "Subject_mcmc", + Parameter = "Param" + ) # Creating a label for the stratification, if there is one. # If not, will add in "None". diff --git a/tests/testthat/test-internal-popparams.R b/tests/testthat/test-internal-popparams.R index 2cdf1031b..bbcdfb113 100644 --- a/tests/testthat/test-internal-popparams.R +++ b/tests/testthat/test-internal-popparams.R @@ -103,8 +103,8 @@ test_that("unpack_jags correctly unpacks individual-level parameters", { result <- serodynamics:::unpack_jags(test_data) # Check individual-level parameters are unpacked - expect_true("1" %in% result$Subject | "2" %in% result$Subject) - expect_true("y0" %in% result$Param | "alpha" %in% result$Param) + expect_true(all(c("1", "2") %in% result$Subject)) + expect_true(all(c("y0", "alpha") %in% result$Param)) }) test_that("prep_popparams filters to population parameters only", { From cc5585b4839a46195bef2376103bd02a58eeb23d Mon Sep 17 00:00:00 2001 From: sschildhauer <sschildhauer@ucdavis.edu> Date: Fri, 29 May 2026 14:26:07 -0700 Subject: [PATCH 09/15] Merging with main --- .github/copilot-instructions.md | 21 +- .github/workflows/claude-code-review.yml | 164 + .github/workflows/claude.yml | 190 + .github/workflows/copilot-setup-steps.yml | 4 +- .github/workflows/lint-changed-files.yaml | 11 +- .github/workflows/test-coverage.yaml | 2 +- DESCRIPTION | 4 +- NEWS.md | 40 +- R/Run_Mod.R | 150 +- R/ex_popparams.R | 12 +- R/param_recode.R | 22 +- R/post_summ.R | 14 +- R/prep_strat_list.R | 58 + R/rebuild_sr_model_attributes.R | 32 + R/reconcile_subject_ids.R | 32 + R/relabel_preclogy_iso.R | 28 + R/unpack_jags.R | 40 +- inst/WORDLIST | 14 + man/ex_popparams.Rd | 4 + man/nepal_sees_jags_output.Rd | 2 +- man/param_recode.Rd | 8 +- man/plot_predicted_curve.Rd | 2 +- man/post_summ.Rd | 8 +- man/prep_popparams.Rd | 3 +- man/prep_strat_list.Rd | 32 + man/rebuild_sr_model_attributes.Rd | 32 + man/reconcile_subject_ids.Rd | 37 + man/relabel_preclogy_iso.Rd | 30 + man/run_mod.Rd | 51 +- man/serodynamics-package.Rd | 6 +- man/unpack_jags.Rd | 13 +- man/use_att_names.Rd | 2 +- .../run_mod/nostrat-curve-params-withpost.csv | 378001 --------------- .../popparam-nostrat-summary-stats.csv | 32 + .../darwin/run_mod/popparam-summary-stats.csv | 61 +- tests/testthat/_snaps/run_mod.md | 20 - .../run_mod/nostrat-curve-params-withpost.csv | 378001 --------------- .../popparam-nostrat-summary-stats.csv | 32 + .../_snaps/run_mod/popparam-summary-stats.csv | 61 +- tests/testthat/test-as_case_data.R | 4 +- tests/testthat/test-internal-popparams.R | 139 +- tests/testthat/test-run_mod.R | 119 +- 42 files changed, 1216 insertions(+), 756322 deletions(-) create mode 100644 .github/workflows/claude-code-review.yml create mode 100644 .github/workflows/claude.yml create mode 100644 R/prep_strat_list.R create mode 100644 R/rebuild_sr_model_attributes.R create mode 100644 R/reconcile_subject_ids.R create mode 100644 R/relabel_preclogy_iso.R create mode 100644 man/prep_strat_list.Rd create mode 100644 man/rebuild_sr_model_attributes.Rd create mode 100644 man/reconcile_subject_ids.Rd create mode 100644 man/relabel_preclogy_iso.Rd delete mode 100644 tests/testthat/_snaps/darwin/run_mod/nostrat-curve-params-withpost.csv create mode 100644 tests/testthat/_snaps/darwin/run_mod/popparam-nostrat-summary-stats.csv delete mode 100644 tests/testthat/_snaps/run_mod.md delete mode 100644 tests/testthat/_snaps/run_mod/nostrat-curve-params-withpost.csv create mode 100644 tests/testthat/_snaps/run_mod/popparam-nostrat-summary-stats.csv diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md index 4f377582a..0a877d14c 100644 --- a/.github/copilot-instructions.md +++ b/.github/copilot-instructions.md @@ -10,6 +10,24 @@ - **Key Dependencies**: runjags, rjags, JAGS 4.3.1, serocalculator, ggmcmc, dplyr, ggplot2 - **Lifecycle**: Experimental (under active development) +## Lab-Wide Guidance + +**Follow the guidance in the [UCD-SeRG Lab Manual](https://ucd-serg.github.io/lab-manual/)**, which provides comprehensive best practices for: +- Culture and conduct +- Communication +- Reproducibility +- Code repositories and version control +- Coding practices and style +- Working with big data +- Quarto and documentation +- GitHub workflows +- Reproducible environments +- Code and data publication +- AI tools usage +- And more + +If the web version is inaccessible, refer to the [source files on GitHub](https://github.com/UCD-SERG/lab-manual) for easier reading. + ## Critical Setup Requirements ### Copilot Setup Workflow (Automatic Environment Configuration) @@ -520,7 +538,8 @@ expect_false(has_missing_values(complete_data)) ## Code Style Guidelines -- **Follow tidyverse style guide**: https://style.tidyverse.org +- **Lab manual overrides tidyverse style**: Follow the [UCD-SeRG Lab Manual coding-style chapter](https://ucd-serg.github.io/lab-manual/coding-style.html) first; fall back to the [tidyverse style guide](https://style.tidyverse.org) only where the lab manual is silent. Where the two conflict, the lab manual wins. +- **Use explicit `return()` statements**: Per the [lab manual](https://ucd-serg.github.io/lab-manual/coding-style/function-structure-and-documentation.html#explicit-return-statements) (which follows the [Google R Style Guide](https://google.github.io/styleguide/Rguide.html#use-explicit-returns)), always end functions with `return(value)` rather than relying on R's implicit final-expression return. This overrides the tidyverse style guide. Note: `return_linter` is currently disabled in `.lintr.R` for flexibility on older code, but new code should use explicit returns. - **Use native pipe**: `|>` not `%>%` - **Avoid redundant logical comparisons**: Use logical values directly (e.g., `if (is_ready)` not `if (is_ready == TRUE)`) - **Naming**: snake_case, acronyms may be uppercase (e.g., `prep_IDs_data`) diff --git a/.github/workflows/claude-code-review.yml b/.github/workflows/claude-code-review.yml new file mode 100644 index 000000000..ab2f3d065 --- /dev/null +++ b/.github/workflows/claude-code-review.yml @@ -0,0 +1,164 @@ +name: Claude Code Review + +on: + pull_request: + types: [opened, synchronize, ready_for_review, reopened] + # Optional: Only run on specific file changes + # paths: + # - "src/**/*.ts" + # - "src/**/*.tsx" + # - "src/**/*.js" + # - "src/**/*.jsx" + +# Serialize runs per PR. The stash/restore reviewer dance below assumes +# only one run is mutating the PR's reviewer list at a time; without +# this, an overlapping second run reads an already-cleared list, stashes +# [], and on restore wipes the original reviewers permanently. Cancel +# the in-flight run on a new push so the freshest diff wins. +concurrency: + group: claude-review-${{ github.event.pull_request.number }} + cancel-in-progress: true + +jobs: + claude-review: + # Optional: Filter by PR author + # if: | + # github.event.pull_request.user.login == 'external-contributor' || + # github.event.pull_request.user.login == 'new-developer' || + # github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR' + + runs-on: ubuntu-latest + permissions: + contents: read + pull-requests: write + issues: write + id-token: write + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + fetch-depth: 1 + + # The reviewer stash/restore is a serialization signal: we clear the + # human reviewers before Claude runs so they aren't notified mid-run, + # then re-add them when Claude finishes so the re-add fires a fresh + # GitHub notification — letting the human see Claude's review before + # they start their own. We also snapshot the PR head SHA so the + # post-Claude step can detect whether Claude pushed any commits and + # route the re-request accordingly (human assignees vs. original + # reviewer set). The restore is load-bearing for the notification + # signal, so it must NOT silently swallow errors (see restore step + # below). + - name: Stash and clear reviewers; record starting head SHA + id: stash + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + REPO: ${{ github.repository }} + PR_NUMBER: ${{ github.event.pull_request.number }} + run: | + HEAD_SHA=$(gh api "repos/$REPO/pulls/$PR_NUMBER" --jq '.head.sha') + echo "head_before=$HEAD_SHA" >> "$GITHUB_OUTPUT" + echo "Starting PR head: $HEAD_SHA" + + REVIEWERS_JSON=$(gh api "repos/$REPO/pulls/$PR_NUMBER/requested_reviewers") + USERS=$(echo "$REVIEWERS_JSON" | jq -c '[.users[].login]') + TEAMS=$(echo "$REVIEWERS_JSON" | jq -c '[.teams[].slug]') + echo "users=$USERS" >> "$GITHUB_OUTPUT" + echo "teams=$TEAMS" >> "$GITHUB_OUTPUT" + echo "Stashed users: $USERS" + echo "Stashed teams: $TEAMS" + if [ "$USERS" != "[]" ] || [ "$TEAMS" != "[]" ]; then + # `|| true` is intentional and asymmetric with the restore step: + # a failed stash leaves reviewers in place, which only causes a + # mid-run notification (recoverable). A failed restore would + # silently drop them entirely (not recoverable) — see that step. + jq -n --argjson users "$USERS" --argjson teams "$TEAMS" \ + '{reviewers: $users, team_reviewers: $teams}' \ + | gh api -X DELETE \ + "repos/$REPO/pulls/$PR_NUMBER/requested_reviewers" \ + --input - || true + fi + + - name: Run Claude Code Review + id: claude-review + uses: anthropics/claude-code-action@v1 + with: + claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} + plugin_marketplaces: 'https://github.com/anthropics/claude-code.git' + plugins: 'code-review@claude-code-plugins' + prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}' + # Force tag mode (anthropics/claude-code-action src/modes/detector.ts). + # In the default agent mode for pull_request events, the action never + # posts any non-inline PR comment by itself (src/modes/agent/index.ts: + # "No tracking comment in agent mode", commentId: undefined). The + # code-review plugin will only post a top-level comment if it finds + # issues scoring >= 80, so silent runs are common on small/mechanical + # PRs. track_progress forces tag mode, which creates a tracking + # comment up front via createInitialComment() and updates it at the + # end — guaranteeing a PR comment regardless of plugin output. + track_progress: 'true' + # Bundle the tracking comment into a single sticky per PR rather than + # a new comment each run. (Only consulted in tag mode.) Each new run + # updates the same comment in place — the latest review is always + # visible, and prior reviews from `@claude review` invocations (which + # post as separate non-sticky comments) are left untouched. + use_sticky_comment: 'true' + # Also archive the formatted report to the Actions step summary page + # (does not affect PR comments). + display_report: 'true' + # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md + # or https://code.claude.com/docs/en/cli-reference for available options + + - name: Re-assign reviewers after Claude finishes + if: always() && steps.stash.outcome == 'success' + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + REPO: ${{ github.repository }} + PR_NUMBER: ${{ github.event.pull_request.number }} + HEAD_BEFORE: ${{ steps.stash.outputs.head_before }} + USERS_BEFORE: ${{ steps.stash.outputs.users }} + TEAMS_BEFORE: ${{ steps.stash.outputs.teams }} + run: | + PR_JSON=$(gh api "repos/$REPO/pulls/$PR_NUMBER") + HEAD_AFTER=$(echo "$PR_JSON" | jq -r '.head.sha') + echo "Head before Claude: $HEAD_BEFORE" + echo "Head after Claude: $HEAD_AFTER" + + if [ "$HEAD_AFTER" = "$HEAD_BEFORE" ]; then + # No new commits — restore the original reviewer set. + USERS=${USERS_BEFORE:-[]} + TEAMS=${TEAMS_BEFORE:-[]} + if [ "$USERS" = "[]" ] && [ "$TEAMS" = "[]" ]; then + echo "Claude made no commits and no reviewers were originally requested." + exit 0 + fi + echo "Claude made no commits; restoring original reviewers." + # Do NOT add `|| true` here. A failed restore means the human + # reviewer was silently dropped from the PR and never gets the + # post-Claude notification — fail loudly so it can be re-added + # manually instead of vanishing. + jq -n --argjson users "$USERS" --argjson teams "$TEAMS" \ + '{reviewers: $users, team_reviewers: $teams}' \ + | gh api -X POST \ + "repos/$REPO/pulls/$PR_NUMBER/requested_reviewers" \ + --input - + exit 0 + fi + + # Claude pushed commits: route the re-request to the PR's human + # assignees so they can review Claude's changes and delegate + # further reviews. Bot assignees (e.g. copilot-swe-agent) are + # filtered out. + ASSIGNEES=$(echo "$PR_JSON" | jq -c '[.assignees[] | select(.type == "User") | .login]') + echo "Human assignees: $ASSIGNEES" + if [ "$ASSIGNEES" = "[]" ]; then + echo "Claude added commits but PR has no human assignees; leaving reviewers cleared." + exit 0 + fi + # Same no-`|| true` rule as above — failure here drops the human + # assignee silently, so let it surface. + jq -n --argjson users "$ASSIGNEES" '{reviewers: $users}' \ + | gh api -X POST \ + "repos/$REPO/pulls/$PR_NUMBER/requested_reviewers" \ + --input - diff --git a/.github/workflows/claude.yml b/.github/workflows/claude.yml new file mode 100644 index 000000000..7828baac7 --- /dev/null +++ b/.github/workflows/claude.yml @@ -0,0 +1,190 @@ +name: Claude Code + +on: + issue_comment: + types: [created] + pull_request_review_comment: + types: [created] + issues: + types: [opened, assigned] + pull_request_review: + types: [submitted] + +jobs: + claude: + if: | + (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) || + (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) || + (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) || + (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude'))) + runs-on: ubuntu-latest + permissions: + contents: read + pull-requests: write + issues: write # so Claude can open follow-up issues for deferred work + id-token: write + actions: read # Required for Claude to read CI results on PRs + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + fetch-depth: 1 + + # R toolchain so Claude can run common package-maintenance commands + # (e.g. devtools::document(), styler::style_pkg(), pkgdown builds, + # spelling::spell_check_package(), lintr, R CMD check). + # Adds ~1–3 min when the dependency cache is warm; the first run after + # a lockfile change is slower. JAGS is required because `runjags` is in + # Imports and load-all/document needs the package to be loadable. + # System libs mirror copilot-setup-steps.yml so packages that source- + # build (textshaping, ragg, curl, xml2, ...) don't fail unpredictably. + - name: Install system dependencies (Ubuntu) + run: | + sudo apt-get update + sudo apt-get install -y \ + jags \ + libcurl4-openssl-dev \ + libssl-dev \ + libxml2-dev \ + libfontconfig1-dev \ + libharfbuzz-dev \ + libfribidi-dev \ + libfreetype6-dev \ + libpng-dev \ + libtiff5-dev \ + libjpeg-dev + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: | + any::devtools + any::roxygen2 + any::rjags + any::rmarkdown + any::lintr + any::spelling + any::rcmdcheck + needs: check + + - name: Resolve PR number (if any) + id: pr + env: + ISSUE_HAS_PR: ${{ github.event.issue.pull_request != null }} + run: | + case "${{ github.event_name }}" in + issue_comment) + if [ "$ISSUE_HAS_PR" = "true" ]; then + echo "number=${{ github.event.issue.number }}" >> "$GITHUB_OUTPUT" + fi + ;; + pull_request_review_comment|pull_request_review) + echo "number=${{ github.event.pull_request.number }}" >> "$GITHUB_OUTPUT" + ;; + esac + + - name: Stash and clear reviewers; record starting head SHA + id: stash + if: steps.pr.outputs.number != '' + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + PR_NUMBER: ${{ steps.pr.outputs.number }} + run: | + PR_JSON=$(gh api "repos/${{ github.repository }}/pulls/$PR_NUMBER") + HEAD_SHA=$(echo "$PR_JSON" | jq -r '.head.sha') + echo "head_before=$HEAD_SHA" >> "$GITHUB_OUTPUT" + echo "Starting PR head: $HEAD_SHA" + + REVIEWERS_JSON=$(gh api "repos/${{ github.repository }}/pulls/$PR_NUMBER/requested_reviewers") + USERS=$(echo "$REVIEWERS_JSON" | jq -c '[.users[].login]') + TEAMS=$(echo "$REVIEWERS_JSON" | jq -c '[.teams[].slug]') + echo "users=$USERS" >> "$GITHUB_OUTPUT" + echo "teams=$TEAMS" >> "$GITHUB_OUTPUT" + echo "Stashed users: $USERS" + echo "Stashed teams: $TEAMS" + if [ "$USERS" != "[]" ] || [ "$TEAMS" != "[]" ]; then + jq -n --argjson users "$USERS" --argjson teams "$TEAMS" \ + '{reviewers: $users, team_reviewers: $teams}' \ + | gh api -X DELETE \ + "repos/${{ github.repository }}/pulls/$PR_NUMBER/requested_reviewers" \ + --input - || true + fi + + - name: Run Claude Code + id: claude + uses: anthropics/claude-code-action@v1 + with: + claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} + + # This is an optional setting that allows Claude to read CI results on PRs + additional_permissions: | + actions: read + + # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it. + # prompt: 'Update the pull request description to include a summary of changes.' + + # Extend the Bash allowlist so Claude can: + # * run package-maintenance R commands (devtools::document(), + # styler::style_pkg(), R CMD ...) — toolchain is installed above; + # * file follow-up issues for work deferred out of the current PR + # (gh issue create / comment / edit / view / list). + # Pin the model explicitly: the action's default points at + # claude-sonnet-4-20250514, which is retired and returns 404 from + # the API. The 404 in turn manifests as the obfuscated AJV crash + # in sdk.mjs documented in upstream issue #892. Once that issue + # is resolved (or the action's default is bumped), --model here + # can be dropped. + claude_args: '--model claude-opus-4-7 --allowed-tools "Bash(Rscript:*)" "Bash(R:*)" "Bash(R CMD:*)" "Bash(gh issue:*)"' + + # Surface the spawned `claude` CLI's stderr in the Actions log so + # SDK init crashes (e.g. run 26144000481) show a real error + # instead of a minified-JS stack frame from sdk.mjs. + show_full_output: true + + - name: Re-assign reviewers after Claude finishes + if: always() && steps.stash.outcome == 'success' && steps.pr.outputs.number != '' + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + PR_NUMBER: ${{ steps.pr.outputs.number }} + HEAD_BEFORE: ${{ steps.stash.outputs.head_before }} + USERS_BEFORE: ${{ steps.stash.outputs.users }} + TEAMS_BEFORE: ${{ steps.stash.outputs.teams }} + run: | + PR_JSON=$(gh api "repos/${{ github.repository }}/pulls/$PR_NUMBER") + HEAD_AFTER=$(echo "$PR_JSON" | jq -r '.head.sha') + echo "Head before Claude: $HEAD_BEFORE" + echo "Head after Claude: $HEAD_AFTER" + + if [ "$HEAD_AFTER" = "$HEAD_BEFORE" ]; then + # No new commits — restore the original reviewer set. + USERS=${USERS_BEFORE:-[]} + TEAMS=${TEAMS_BEFORE:-[]} + if [ "$USERS" = "[]" ] && [ "$TEAMS" = "[]" ]; then + echo "Claude made no commits and no reviewers were originally requested." + exit 0 + fi + echo "Claude made no commits; restoring original reviewers." + jq -n --argjson users "$USERS" --argjson teams "$TEAMS" \ + '{reviewers: $users, team_reviewers: $teams}' \ + | gh api -X POST \ + "repos/${{ github.repository }}/pulls/$PR_NUMBER/requested_reviewers" \ + --input - || true + exit 0 + fi + + # Claude added commits — request review only from human assignees. + ASSIGNEES=$(echo "$PR_JSON" | jq -c '[.assignees[] | select(.type == "User") | .login]') + echo "Human assignees: $ASSIGNEES" + if [ "$ASSIGNEES" = "[]" ]; then + echo "Claude added commits but PR has no human assignees; leaving reviewers cleared." + exit 0 + fi + jq -n --argjson users "$ASSIGNEES" '{reviewers: $users}' \ + | gh api -X POST \ + "repos/${{ github.repository }}/pulls/$PR_NUMBER/requested_reviewers" \ + --input - || true diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml index 251368ad7..b8a98e92d 100644 --- a/.github/workflows/copilot-setup-steps.yml +++ b/.github/workflows/copilot-setup-steps.yml @@ -102,7 +102,7 @@ jobs: withr::local_options(warn = 2) library(rjags) library(runjags) - runjags::findJAGS() + runjags::findjags() runjags::testjags() shell: Rscript {0} @@ -119,7 +119,7 @@ jobs: Rscript -e 'cat("runjags version:", as.character(packageVersion("runjags")), "\n")' echo "" echo "JAGS location (from runjags):" - Rscript -e 'print(runjags::findJAGS())' + Rscript -e 'print(runjags::findjags())' echo "" echo "Running JAGS test:" Rscript -e 'runjags::testjags()' diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml index 04580529a..7cd95e9d7 100644 --- a/.github/workflows/lint-changed-files.yaml +++ b/.github/workflows/lint-changed-files.yaml @@ -10,8 +10,6 @@ permissions: read-all jobs: lint-changed-files: runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v4 @@ -37,11 +35,18 @@ jobs: - name: Extract and lint files changed by this PR run: | - files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files") + Sys.unsetenv("GITHUB_PAT") + + files <- gh::gh( + "GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files", + .token = Sys.getenv("GITHUB_TOKEN") + ) + changed_files <- purrr::map_chr(files, "filename") all_files <- list.files(recursive = TRUE) exclusions_list <- as.list(setdiff(all_files, changed_files)) lintr::lint_package(exclusions = exclusions_list) shell: Rscript {0} env: + GITHUB_TOKEN: ${{ github.token }} LINTR_ERROR_ON_LINT: true diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 702425567..f493a2bbf 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -57,7 +57,7 @@ jobs: withr::local_options(warn = 2) library(rjags) library(runjags) - runjags::findJAGS() + runjags::findjags() runjags::testjags() shell: Rscript {0} diff --git a/DESCRIPTION b/DESCRIPTION index 708b44803..e17794e0b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,11 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9050 +Version: 0.0.0.9055 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), person("Samuel", "Schildhauer", , "sschildhauer@ucdavis.edu", role = c("aut", "cre")), - person("Kwan Ho", "Lee", , "ksjlee@ucdavis.edu", role = "ctb"), + person("Kwan Ho", "Lee", , "ksjlee@ucdavis.edu", role = "aut"), person("Kristen", "Aiemjoy", , "kaiemjoy@ucdavis.edu", role = "aut"), person("Douglas Ezra", "Morrison", , "demorrison@ucdavis.edu", role = "aut") ) diff --git a/NEWS.md b/NEWS.md index 32329f01c..47b33d4e8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,11 +5,39 @@ (or optionally the "newperson" subject). Supports 95% credible interval ribbons, stratified curves with colour or faceting, and multiple antigen-isotypes (#74). -* `run_mod()` now monitors the `mu.par` hyperparameter and stores its - posterior samples on the latent parameter scale in a - `population_params` attribute of the returned `sr_model` object; functions - such as `plot_serocurve()` apply transformations to the original parameter - scale when needed (#74). +* Clarified Code Style Guidelines in `.github/copilot-instructions.md`: + the UCD-SeRG Lab Manual takes precedence over the tidyverse style + guide where they conflict, and functions should end with an explicit + `return()` call per the lab manual / Google R Style Guide. This + closes a gap where `@claude` reviews were flagging explicit returns + as non-conforming. +* Expanded what the `Claude Code` (`@claude`) workflow can do: + - Install the full R toolchain (R, JAGS, pandoc, the apt system libs + mirrored from `copilot-setup-steps.yml`, plus `devtools`, `roxygen2`, + `rmarkdown`, `lintr`, `spelling`, `rcmdcheck`) and allow `Rscript`, + `R`, and `R CMD` invocations, so requests that need package- + maintenance commands (`devtools::document()`, + `spelling::spell_check_package()`, `R CMD check`, vignette rebuilds) + succeed instead of being patched by hand. + - Grant `issues: write` and allow `gh issue` invocations so Claude + can file follow-up issues for work deferred out of the current PR + instead of burying it in a comment. +* Standardized `runjags::findjags()` casing across `test-coverage.yaml` + and `copilot-setup-steps.yml` to match the `R-CMD-check.yaml` form + arriving with the 0.1.0 release (#207 advisory). +* Re-assign reviewers to a PR's human assignees (filtered via + `type == "User"`) when Claude pushes commits during a `@claude` or + `Claude Code Review` run; if Claude makes no commits, the original + reviewer set is restored as before. Detected by comparing the PR's + head SHA before and after the Claude step (#210). +* Stopped deleting prior Claude review comments at the start of each + `Claude Code Review` run, so reviews posted by `@claude review` invocations + are preserved across subsequent pushes instead of being wiped when the + review step fails its bot-actor gate (#217). +* Hardened the Claude code-review workflow against races and silent failures: + serialized concurrent runs per PR, made reviewer restore fail loudly instead + of silently dropping reviewers, and cleaned up all stale Claude top-level + comments per run (#216). * Expanded `.github/copilot-instructions.md` with additional guidance on evidence-based claims, Quarto markdown/cross-reference conventions, R style practices, and phrase-level line-break formatting for source text. * Fixed `dplyr::as_tibble()` references to `tibble::as_tibble()` in `post_summ()` and `run_mod()`, since `as_tibble()` is exported from the `tibble` package, not `dplyr`. * Added R 4.5+ snapshot variants to handle the changed attribute ordering in @@ -19,6 +47,7 @@ Workspace sessions much faster. * Reorganized pkgdown documentation with new "Getting Started" guide demonstrating main API workflow, organized articles into "Get started" and "Developer Notes" sections (#73). * Added `.github/workflows/copilot-setup-steps.yml` GitHub Actions workflow to automate environment setup for GitHub Copilot coding agent, preinstalling R, JAGS, and all dependencies. +* Added reference to UCD-SeRG Lab Manual in copilot-instructions for lab-wide best practices guidance. * Consolidated OS-specific snapshot variants: removed redundant Linux and Windows snapshot directories (which were identical), keeping only base snapshots and @@ -29,6 +58,7 @@ ## New features +* Including optional population parameters as attributes in run_mod output. (#141) * Made "newperson" optional in `prep_data()` (#73) * Including fitted and residual values as data frame in run_mod output. (#101) * Added `plot_predicted_curve()` with support for faceting by multiple IDs (#68) diff --git a/R/Run_Mod.R b/R/Run_Mod.R index d7ef654a8..7cc6c6d1a 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -22,20 +22,27 @@ #' @param strat A [character] string specifying the stratification variable, #' entered in quotes. #' @param with_post A [logical] value specifying whether a raw `jags.post` -#' component -#' should be included as an element of the [list] object returned by `run_mod()` +#' object should be included as an optional `"jags.post"` attribute on the +#' returned `sr_model` tibble #' (see `Value` section below for details). #' Note: These objects can be large. -#' @param with_pop_params A [logical] value specifying whether population -#' level parameters should be included as an attribute entitled -#' `population_params`. Excluded as default. +#' @param with_pop_params A [logical] value specifying whether population +#' level parameters should be included as an attribute entitled +#' `population_params`. Excluded by default. #' Note: These objects can be large. +#' @param preclogy_per_iso A [logical] value. When `TRUE` and `with_pop_params` +#' is also `TRUE`, the `Parameter` column for `prec.logy` rows in +#' `population_params` will contain the antigen/isotype label (e.g., +#' `"HlyE_IgA"`) rather than the constant `"prec.logy"`. This allows grouping +#' by `Parameter` to obtain per-isotype precision estimates directly. Default +#' is `FALSE` (all `prec.logy` rows share `Parameter = "prec.logy"`; the +#' `Iso_type` column distinguishes isotypes). #' @returns An `sr_model` class object: a subclass of [tibble::tbl_df] that #' contains MCMC samples from the joint posterior distribution of the model #' parameters, conditional on the provided input `data`, #' including the following: -#' - `iteration` = Number of sampling iterations -#' - `chain` = Number of MCMC chains run; between 1 and 4 +#' - `Iteration` = Number of sampling iterations +#' - `Chain` = Number of MCMC chains run; between 1 and 4 #' - `Parameter` = Parameter being estimated. Includes the following: #' - `y0` = Posterior estimate of baseline antibody concentration #' - `y1` = Posterior estimate of peak antibody concentration @@ -48,26 +55,26 @@ #' - `value` = Estimated value of the parameter #' - The following [attributes] are included in the output: #' - `class`: Class of the output object. -#' - `nChain`: Number of chains run. +#' - `nChains`: Number of chains run. #' - `nParameters`: The amount of parameters estimated in the model. #' - `nIterations`: Number of iteration specified. #' - `nBurnin`: Number of burn ins. #' - `nThin`: Thinning number (niter/nmc). -#' - `population_params`: Optionally included modeled population parameters -#' indexed by -#' `Iteration`, -#' `Chain`, `Parameter`, `Iso_type`, and `Stratification`. Excluded as -#' default. Includes the following modeled population parameters: -#' - `mu.par` = The population means of the host-specific model parameters -#' on latent transformed scales. For these rows, `Parameter` values refer -#' to the underlying `par` components used in the model, not necessarily -#' to the observed-scale curve parameters used elsewhere in the package. -#' For example, `y1` corresponds to `log(y1 - y0)` and `shape` -#' corresponds to `log(shape - 1)`. -#' - `prec.par` = The population precision matrix of the hyperparameters -#' (with diagonal elements equal to inverse variances). -#' - `prec.logy` = A vector of population precisions (inverse variances), -#' one per antigen/isotype combination. +#' - `population_params`: Optionally included modeled population parameters, +#' returned as a [data.frame] and excluded by default. +#' Columns include +#' `Iteration`, `Chain`, `Parameter`, `Iso_type`, `Stratification`, +#' `Population_Parameter`, and `value`. +#' - `Population_Parameter` identifies which modeled population parameter +#' is represented: +#' - `mu.par` = The population means of the host-specific model +#' parameters (on logarithmic scales). Note: y1 and shape are transformed. +#' - `prec.par` = The population precision matrix of the +#' hyperparameters (with diagonal elements equal to inverse variances). +#' The two parameters listed (separated by commas) represent the pairwise +#' precision relationship between specified parameters. +#' - `prec.logy` = A vector of population precisions (inverse +#' variances), one per antigen/isotype combination. #' - `priors`: A [list] that summarizes the input priors, including: #' - `mu_hyp_param` #' - `prec_hyp_param` @@ -91,13 +98,10 @@ run_mod <- function(data, strat = NA, with_post = FALSE, with_pop_params = FALSE, + preclogy_per_iso = FALSE, ...) { - ## Conditionally creating a stratification list to loop through - if (is.na(strat)) { - strat_list <- "None" - } else { - strat_list <- unique(data[[strat]]) - } + ## Build and validate the stratification list to loop through. + strat_list <- prep_strat_list(data, strat) ## Creating a shell to output results jags_out <- tibble::tibble( @@ -130,10 +134,7 @@ run_mod <- function(data, # inputs for jags model nchains <- nchain # nr of MC chains to run simultaneously - nadapt <- nadapt # nr of iterations for adaptation nburnin <- nburn # nr of iterations to use for burn-in - nmc <- nmc # nr of samples in posterior chains - niter <- niter # nr of iterations for posterior sample nthin <- round(niter / nmc) # thinning needed to produce nmc from niter tomonitor <- c("y0", "y1", "t1", "alpha", "shape") @@ -159,7 +160,7 @@ run_mod <- function(data, # Assigning the raw jags output to a list. # This object will include a raw output for the jags.post for each # stratification and will only be included if specified. - jags_post_final[[i]] <- jags_post + jags_post_final[[as.character(i)]] <- jags_post # Unpacking and cleaning MCMC output. jags_packed <- ggmcmc::ggs(jags_post[["mcmc"]]) @@ -168,54 +169,35 @@ run_mod <- function(data, mod_atts <- attributes(jags_packed) # Select necessary attributes by name for robustness across platforms mod_atts <- mod_atts[c("nChains", "nParameters", "nIterations", - "nBurnin", "nThin", "description")] + "nBurnin", "nThin")] # extracting antigen-iso combinations to correctly number # them by the order they are estimated by the program. - iso_dat <- data.frame(attributes(longdata)$antigens) - iso_dat <- iso_dat |> dplyr::mutate(Subnum = row.names(iso_dat)) + iso_dat <- tibble::tibble( + Iso_type = attr(longdata, "antigens"), + Subnum = as.character(seq_along(attr(longdata, "antigens"))) + ) # Unpacking the mcmc object jags_unpacked <- unpack_jags(jags_packed) - # Merging isodat in to ensure we are classifying antigen_iso. - jags_unpacked <- dplyr::left_join(jags_unpacked, iso_dat, + # Merging isodat in to ensure we are classifying antigen_iso. + jags_unpacked <- dplyr::left_join(jags_unpacked, iso_dat, by = "Subnum") - + + # Optionally relabel prec.logy Parameter by isotype so that grouping by + # Parameter in population_params distinguishes per-isotype precision. + if (with_pop_params && preclogy_per_iso) { + jags_unpacked <- relabel_preclogy_iso(jags_unpacked) + } + # Adding in ID name - ids <- data.frame(attr(longdata, "ids")) |> - dplyr::mutate(Subject = as.character(dplyr::row_number())) - jags_final <- dplyr::left_join(jags_unpacked, ids, - by = "Subject") |> - dplyr::rename( - Iso_type = "attributes.longdata..antigens", - Subject_mcmc = "attr.longdata...ids.." - ) |> - # Subject handling: - # * For individual-level parameters, the left join above finds a row in - # attr(longdata, "ids"), so Subject_mcmc contains the subject ID. - # * For population-level parameters (e.g., mu.par, prec.par, prec.logy), - # there is no matching ID, so Subject_mcmc is NA. In that case we - # intentionally keep the original Subject value from unpack_jags, - # which holds the parameter name and serves as the identifier. - dplyr::mutate(Subject_mcmc = ifelse(is.na(.data$Subject_mcmc), - .data$Subject, - .data$Subject_mcmc)) |> - # At this point, jags_unpacked contains: - # * Parameter: original JAGS parameter names (e.g., "y0[1,2]") - # * Param: cleaned parameter names used elsewhere in the package. - # We drop the original JAGS-style Parameter column and keep the - # cleaned names, then rename Param back to Parameter so that all - # downstream code consistently uses a single "Parameter" column - # containing cleaned parameter names. - # Drop the temporary Subject (now only used as a fallback for population - # parameters) and rename Subject_mcmc back to Subject for downstream use. - dplyr::select(-dplyr::all_of(c("Subnum", "Subject", "Parameter"))) |> - dplyr::rename( - Subject = "Subject_mcmc", - Parameter = "Param" - ) - + ids <- tibble::tibble( + Subject_mcmc = as.character(attr(longdata, "ids")), + Subject = as.character(seq_along(attr(longdata, "ids"))) + ) + jags_final <- reconcile_subject_ids(jags_unpacked, ids) + # Creating a label for the stratification, if there is one. # If not, will add in "None". jags_final$Stratification <- i @@ -239,26 +221,9 @@ run_mod <- function(data, # Making output a tibble and restructuring. jags_out <- jags_out[, c("Iteration", "Chain", "Parameter", "Iso_type", "Stratification", "Subject", "value")] - current_atts <- attributes(jags_out) - # Explicitly build the attribute list in the correct order to ensure that - # `class` appears immediately after `names` and `row.names`. - # The dplyr operations above can carry ggmcmc attributes (nChains, etc.) - # from jags_packed into jags_out, placing `class` at the end. We use - # mod_atts (named selection from jags_packed) as the authoritative source - # for the ggmcmc-style metadata attributes. - new_atts <- list( - names = current_atts$names, - row.names = current_atts$row.names, - class = union("sr_model", current_atts$class), - nChains = mod_atts$nChains, - nParameters = mod_atts$nParameters, - nIterations = mod_atts$nIterations, - nBurnin = mod_atts$nBurnin, - nThin = mod_atts$nThin, - description = mod_atts$description - ) - attributes(jags_out) <- new_atts - + + jags_out <- rebuild_sr_model_attributes(jags_out, mod_atts) + # Adding population parameters optionally and priors in as attributes if (with_pop_params) { jags_out <- jags_out |> @@ -268,7 +233,6 @@ run_mod <- function(data, structure(priors = attributes(priorspec)$used_priors) # Calculating fitted and residuals - # Renaming columns using attributes from as_case_data fit_res <- calc_fit_mod(modeled_dat = jags_out, original_data = dl_sub) jags_out <- jags_out |> diff --git a/R/ex_popparams.R b/R/ex_popparams.R index 7a565776e..f0cf7b97b 100644 --- a/R/ex_popparams.R +++ b/R/ex_popparams.R @@ -3,11 +3,11 @@ #' @description #' `ex_popparams` excludes estimated population parameters from final output #' [data.frame]. -#' @param x A [data.frame] with a `Subject` variable. +#' @param x A [data.frame] with a `.is_population_parameter` variable. #' @returns A filtered [data.frame] excluding population parameters. #' @keywords internal -ex_popparams <- function(x) { - x <- x |> - dplyr::filter(!(.data$Subject %in% c("mu.par", "prec.par", "prec.logy"))) - return(x) -} +ex_popparams <- function(x) { + x |> + dplyr::filter(!.data$.is_population_parameter) |> + dplyr::select(-c(".is_population_parameter")) +} diff --git a/R/param_recode.R b/R/param_recode.R index de05454b5..18b1b4c74 100644 --- a/R/param_recode.R +++ b/R/param_recode.R @@ -1,17 +1,17 @@ #' @title Parameter recode #' @author Sam Schildhauer #' @description -#' `param_recode` recodes character numbers as their corresponding parameter. -#' @param x A [vector] of character numbers that represent parameters. -#' @returns A [vector] with recoded values. +#' `param_recode()` recodes JAGS curve-parameter indices (1-5) as their +#' log-scale parameter labels (e.g., `"log(y0)"`, `"log(alpha)"`). +#' @param x A [vector] of character numbers ("1"-"5") that represent +#' parameters. +#' @returns A [vector] of log-scale parameter labels. #' @keywords internal param_recode <- function(x) { - dplyr::recode( - x, - "1" = "y0", - "2" = "y1", - "3" = "t1", - "4" = "alpha", - "5" = "shape" - ) + map <- c("1" = "log(y0)", + "2" = "log(y1 - y0)", + "3" = "log(t1)", + "4" = "log(alpha)", + "5" = "log(shape - 1)") + unname(map[as.character(x)]) } diff --git a/R/post_summ.R b/R/post_summ.R index f45baf933..f18ecb727 100644 --- a/R/post_summ.R +++ b/R/post_summ.R @@ -2,7 +2,7 @@ #' @title Summary Table of Jags Posterior Estimates #' @author Sam Schildhauer #' @description -#' `post_summ()` takes a [list] output from [run_mod] +#' `post_summ()` takes an `sr_model` tibble returned by [run_mod] #' to summary table for parameter, antigen/antibody, and stratification #' combination. #' Defaults will produce every combination of antigen/antibody, parameters, @@ -12,16 +12,16 @@ #' - y0 = baseline antibody concentration #' - y1 = peak antibody concentration #' - t1 = time to peak -#' - r = shape parameter +#' - shape = shape parameter #' - alpha = decay rate -#' @param data A [list] outputted from [run_mod]. +#' @param data An `sr_model` tibble returned by [run_mod]. #' @param iso Specify [character] string to produce tables of only a #' specific antigen/antibody combination, entered with quotes. Default outputs #' all antigen/antibody combinations. #' @param param Specify [character] string to produce tables of only a #' specific parameter, entered with quotes. Options include: #' - `alpha` = posterior estimate of decay rate -#' - `r` = posterior estimate of shape parameter +#' - `shape` = posterior estimate of shape parameter #' - `t1` = posterior estimate of time to peak #' - `y0` = posterior estimate of baseline antibody concentration #' - `y1` = posterior estimate of peak antibody concentration @@ -39,9 +39,9 @@ post_summ <- function(data, strat = unique(data$Stratification)) { summarize_jags <- data |> - filter(.data$Iso_type %in% iso) |> - filter(.data$Parameter %in% param) |> - filter(.data$Stratification %in% strat) |> + dplyr::filter(.data$Iso_type %in% iso) |> + dplyr::filter(.data$Parameter %in% param) |> + dplyr::filter(.data$Stratification %in% strat) |> dplyr::filter(.data$Subject == "newperson") summarize_jags <- summarize_jags |> diff --git a/R/prep_strat_list.R b/R/prep_strat_list.R new file mode 100644 index 000000000..65d25e7d2 --- /dev/null +++ b/R/prep_strat_list.R @@ -0,0 +1,58 @@ +#' @title Prepare and validate a stratification list +#' @author Sam Schildhauer +#' @description +#' `prep_strat_list()` builds the vector of stratum labels that [run_mod()] +#' iterates over. +#' When `strat` is `NA`, a single pseudo-stratum (`"None"`) is returned so the +#' model runs once on the full data set. +#' Otherwise the unique values of `data[[strat]]` are returned, with factor +#' columns coerced to their character labels so the loop iterates over labels +#' rather than the underlying integer codes. +#' Rows with a missing stratification value are dropped with a warning, since +#' they cannot be assigned to a stratum. +#' @param data A [base::data.frame()] containing the stratification column. +#' @param strat A [character] string naming the stratification column, or `NA` +#' to run the model without stratification. +#' @returns A vector of stratum labels to loop over. +#' @keywords internal +prep_strat_list <- function(data, strat) { + if (is.na(strat)) { + return("None") + } + + # The stratification variable must be an existing column. + if (!strat %in% names(data)) { + cli::cli_abort(c( + "Can't stratify by {.field {strat}}.", + "x" = "Column {.field {strat}} was not found in {.arg data}." + )) + } + + strat_list <- if (is.factor(data[[strat]])) { + as.character(unique(data[[strat]])) # factor -> character labels + } else { + unique(data[[strat]]) # preserve character/numeric type + } + + # Warn about and drop rows whose stratification value is missing. + if (anyNA(strat_list)) { + cli::cli_warn(c( + "!" = "The stratification variable {.field {strat}} contains \\ + {.val {NA}} value{?s}.", + "i" = "Rows with a missing stratification value are dropped and \\ + not modeled." + )) + strat_list <- strat_list |> + purrr::discard(is.na) + } + + # Once missing values are removed there must be something left to model. + if (length(strat_list) == 0) { + cli::cli_abort(c( + "Can't stratify by {.field {strat}}.", + "x" = "Column {.field {strat}} contains no non-missing values." + )) + } + + strat_list +} diff --git a/R/rebuild_sr_model_attributes.R b/R/rebuild_sr_model_attributes.R new file mode 100644 index 000000000..a1c047785 --- /dev/null +++ b/R/rebuild_sr_model_attributes.R @@ -0,0 +1,32 @@ +#' @title Rebuild `sr_model` output attributes in a stable order +#' @author Sam Schildhauer +#' @description +#' `rebuild_sr_model_attributes()` reconstructs the attribute list of the +#' combined [run_mod()] output in a fixed order, ensuring `class` appears +#' immediately after `names` and `row.names`. +#' The `dplyr` operations used to assemble the output can carry `ggmcmc` +#' attributes (`nChains`, etc.) into the result and push `class` to the end, +#' so this helper rebuilds the attributes explicitly. `mod_atts` (a named +#' selection from the `ggmcmc::ggs()` object) is the authoritative source for +#' the `ggmcmc`-style metadata attributes. +#' @param x A [data.frame] / [tibble::tbl_df] of combined MCMC output. +#' @param mod_atts A named [list] of `ggmcmc` metadata attributes, containing +#' `nChains`, `nParameters`, `nIterations`, `nBurnin`, and `nThin`. +#' @returns `x` with its attributes rebuilt in a stable order and the +#' `sr_model` class prepended. +#' @keywords internal +rebuild_sr_model_attributes <- function(x, mod_atts) { + current_atts <- attributes(x) + new_atts <- list( + names = current_atts$names, + row.names = current_atts$row.names, + class = union("sr_model", current_atts$class), + nChains = mod_atts$nChains, + nParameters = mod_atts$nParameters, + nIterations = mod_atts$nIterations, + nBurnin = mod_atts$nBurnin, + nThin = mod_atts$nThin + ) + attributes(x) <- new_atts + x +} diff --git a/R/reconcile_subject_ids.R b/R/reconcile_subject_ids.R new file mode 100644 index 000000000..0f26b4e18 --- /dev/null +++ b/R/reconcile_subject_ids.R @@ -0,0 +1,32 @@ +#' @title Reconcile MCMC subject indices with subject IDs +#' @author Sam Schildhauer +#' @description +#' `reconcile_subject_ids()` joins unpacked MCMC output to the subject ID +#' lookup table and resolves a single `Subject` identifier for every row. +#' - Individual-level parameters match a row in `ids`, so they receive the +#' original subject ID. +#' - Population-level parameters (e.g., `mu.par`, `prec.par`, `prec.logy`) +#' have no matching ID, so they retain the parameter name produced by +#' [unpack_jags()] as their identifier. +#' The temporary index columns are then dropped and the cleaned parameter +#' names (`Param`) are promoted to `Parameter` for downstream use. +#' @param jags_unpacked A [tibble::tbl_df] returned by [unpack_jags()] +#' (after the `Iso_type` join), containing `Subject`, `Subnum`, `Param`, +#' and `Parameter` columns. +#' @param ids A [tibble::tbl_df] with a `Subject_mcmc` column (the subject ID) +#' and a `Subject` column (the MCMC index as a character string). +#' @returns A [tibble::tbl_df] with a single resolved `Subject` column and a +#' `Parameter` column holding the cleaned parameter name. +#' @keywords internal +reconcile_subject_ids <- function(jags_unpacked, ids) { + dplyr::left_join(jags_unpacked, ids, by = "Subject") |> + dplyr::mutate( + Subject_mcmc = dplyr::if_else( + is.na(.data$Subject_mcmc), + .data$Subject, + .data$Subject_mcmc + ) + ) |> + dplyr::select(-c("Subnum", "Subject", "Parameter")) |> + dplyr::rename("Subject" = "Subject_mcmc", "Parameter" = "Param") +} diff --git a/R/relabel_preclogy_iso.R b/R/relabel_preclogy_iso.R new file mode 100644 index 000000000..9cfd00a87 --- /dev/null +++ b/R/relabel_preclogy_iso.R @@ -0,0 +1,28 @@ +#' @title Relabel `prec.logy` population parameters by isotype +#' @author Sam Schildhauer +#' @description +#' `relabel_preclogy_iso()` replaces the `Param` label of `prec.logy` +#' population-parameter rows with their antigen/isotype label (`Iso_type`). +#' This lets callers group `population_params` by `Parameter` to obtain +#' per-isotype precision estimates, rather than collapsing all isotypes into a +#' single `"prec.logy"` group. +#' Rows that are not `prec.logy` population parameters, and rows lacking an +#' `Iso_type` (e.g., the scalar/unindexed case), are left unchanged. +#' @param jags_unpacked A [tibble::tbl_df] returned by [unpack_jags()] after +#' the `Iso_type` join, containing `.is_population_parameter`, `Subject`, +#' `Iso_type`, and `Param` columns. +#' @returns The input with `Param` relabeled to `Iso_type` for `prec.logy` +#' population-parameter rows. +#' @keywords internal +relabel_preclogy_iso <- function(jags_unpacked) { + jags_unpacked |> + dplyr::mutate( + Param = dplyr::if_else( + .data$.is_population_parameter & + .data$Subject == "prec.logy" & + !is.na(.data$Iso_type), + .data$Iso_type, + .data$Param + ) + ) +} diff --git a/R/unpack_jags.R b/R/unpack_jags.R index 84bef9c7c..4b1d1ed2c 100644 --- a/R/unpack_jags.R +++ b/R/unpack_jags.R @@ -9,11 +9,12 @@ #' usually `ggmcmc::ggs(jags_post[["mcmc"]])` where `jags_post` comes from #' [run_mod]. Must contain at least `Iteration`, `Chain`, `Parameter`, #' and `value` columns. -#' @returns A [tibble::tbl_df] that -#' contains MCMC samples from the joint posterior distribution of the model -#' with unpacked individual-level parameters (e.g., `y0`, `y1`, `t1`, -#' `alpha`, `shape`) and population-level parameters (e.g., `mu.par`, -#' `prec.par`, `prec.logy`), along with isotypes and subjects. +#' @returns A [tibble::tbl_df] containing MCMC samples from the joint +#' posterior distribution of the model with unpacked individual-level +#' parameters (e.g., `y0`, `y1`, `t1`, `alpha`, `shape`) and +#' population-level parameters (e.g., `mu.par`, `prec.par`, `prec.logy`), +#' along with subject-related fields such as `Subject` and `Subnum`. +#' Isotype names are not added by `unpack_jags()` itself. #' @keywords internal unpack_jags <- function(data) { @@ -25,10 +26,21 @@ unpack_jags <- function(data) { unpack_with_pattern <- function(data, filter_pattern, regex_pattern, subject_repl, subnum_repl, param_fun) { data |> - dplyr::filter(startsWith(.data$Parameter, paste0(filter_pattern, "["))) |> + dplyr::filter( + startsWith(.data$Parameter, paste0(filter_pattern, "[")) | + .data$Parameter == filter_pattern + ) |> dplyr::mutate( - Subject = gsub(regex_pattern, subject_repl, .data$Parameter), - Subnum = gsub(regex_pattern, subnum_repl, .data$Parameter), + Subject = dplyr::if_else( + .data$Parameter == filter_pattern, + filter_pattern, + gsub(regex_pattern, subject_repl, .data$Parameter) + ), + Subnum = dplyr::if_else( + .data$Parameter == filter_pattern, + "1", + gsub(regex_pattern, subnum_repl, .data$Parameter) + ), Param = param_fun(.data$Parameter, regex_pattern) ) } @@ -88,13 +100,13 @@ unpack_jags <- function(data) { ) |> dplyr::filter(.data$Param %in% c("y0", "y1", "t1", "alpha", "shape")) - # Putting data frame together + # Putting data frame together, marking population-parameter rows explicitly jags_unpack_bind <- dplyr::bind_rows( - jags_unpack_params, - jags_mupar, - jags_precpar, - jags_preclogy + dplyr::mutate(jags_unpack_params, .is_population_parameter = FALSE), + dplyr::mutate(jags_mupar, .is_population_parameter = TRUE), + dplyr::mutate(jags_precpar, .is_population_parameter = TRUE), + dplyr::mutate(jags_preclogy, .is_population_parameter = TRUE) ) - return(jags_unpack_bind) + jags_unpack_bind } diff --git a/inst/WORDLIST b/inst/WORDLIST index 802b628d0..95895593c 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -6,15 +6,21 @@ HlyE IgA IgG Iso +Isotype JAGS's JAGs Lifecycle MSVC +PR's Postprocess Rhat +SHA +SeRG TSI +UCD Vectorization Wasserstein +assignees behaviour biomarker biomarkers @@ -35,12 +41,14 @@ iso isotype isotypes libm +libs linux mcmc mitre newperson nmc onwards +pandoc params pkgdown prec @@ -54,6 +62,12 @@ strat stratifications tbl testthat +tibble +tidyverse +toolchain +unindexed unstratified vh wishdf +SeRG +UCD diff --git a/man/ex_popparams.Rd b/man/ex_popparams.Rd index b389d8358..62d09b8c7 100644 --- a/man/ex_popparams.Rd +++ b/man/ex_popparams.Rd @@ -7,7 +7,11 @@ ex_popparams(x) } \arguments{ +<<<<<<< HEAD \item{x}{A \link{data.frame} with a \code{Subject} variable.} +======= +\item{x}{A \link{data.frame} with a \code{.is_population_parameter} variable.} +>>>>>>> ba9ae9868709bb0b019067d1304c63f2dd15a4c9 } \value{ A filtered \link{data.frame} excluding population parameters. diff --git a/man/nepal_sees_jags_output.Rd b/man/nepal_sees_jags_output.Rd index 809166d7a..4c9d4981d 100644 --- a/man/nepal_sees_jags_output.Rd +++ b/man/nepal_sees_jags_output.Rd @@ -5,7 +5,7 @@ \alias{nepal_sees_jags_output} \title{SEES Typhoid run_mod jags output} \format{ -An S3 object of class \code{sr_model}: A \link[tibble:tbl_df-class]{tibble::tbl_df} that contains +An S3 object of class \code{sr_model}: A \link[tibble:tbl_df]{tibble::tbl_df} that contains the posterior predictive distribution of the person-specific parameters for a "new person" with no observed data (\code{Subject = "newperson"}) and posterior diff --git a/man/param_recode.Rd b/man/param_recode.Rd index 60e648b01..427cd5051 100644 --- a/man/param_recode.Rd +++ b/man/param_recode.Rd @@ -7,13 +7,15 @@ param_recode(x) } \arguments{ -\item{x}{A \link{vector} of character numbers that represent parameters.} +\item{x}{A \link{vector} of character numbers ("1"-"5") that represent +parameters.} } \value{ -A \link{vector} with recoded values. +A \link{vector} of log-scale parameter labels. } \description{ -\code{param_recode} recodes character numbers as their corresponding parameter. +\code{param_recode()} recodes JAGS curve-parameter indices (1-5) as their +log-scale parameter labels (e.g., \code{"log(y0)"}, \code{"log(alpha)"}). } \author{ Sam Schildhauer diff --git a/man/plot_predicted_curve.Rd b/man/plot_predicted_curve.Rd index 0bb77d835..25873e25b 100644 --- a/man/plot_predicted_curve.Rd +++ b/man/plot_predicted_curve.Rd @@ -31,7 +31,7 @@ samples from the posterior distribution of the model parameters.} \item{antigen_iso}{The antigen isotype to plot; for example, "HlyE_IgA" or "HlyE_IgG".} -\item{dataset}{(Optional) A \link[tibble:tbl_df-class]{tibble::tbl_df} with observed antibody response +\item{dataset}{(Optional) A \link[tibble:tbl_df]{tibble::tbl_df} with observed antibody response data. Must contain: \itemize{ diff --git a/man/post_summ.Rd b/man/post_summ.Rd index 239faa1bc..a7678fcf6 100644 --- a/man/post_summ.Rd +++ b/man/post_summ.Rd @@ -12,7 +12,7 @@ post_summ( ) } \arguments{ -\item{data}{A \link{list} outputted from \link{run_mod}.} +\item{data}{An \code{sr_model} tibble returned by \link{run_mod}.} \item{iso}{Specify \link{character} string to produce tables of only a specific antigen/antibody combination, entered with quotes. Default outputs @@ -22,7 +22,7 @@ all antigen/antibody combinations.} specific parameter, entered with quotes. Options include: \itemize{ \item \code{alpha} = posterior estimate of decay rate -\item \code{r} = posterior estimate of shape parameter +\item \code{shape} = posterior estimate of shape parameter \item \code{t1} = posterior estimate of time to peak \item \code{y0} = posterior estimate of baseline antibody concentration \item \code{y1} = posterior estimate of peak antibody concentration @@ -36,7 +36,7 @@ A \link{data.frame} summarizing estimate mean, standard deviation (SD), median, and quantiles (2.5\%, 25.0\%, 50.0\%, 75.0\%, 97.5\%). } \description{ -\code{post_summ()} takes a \link{list} output from \link{run_mod} +\code{post_summ()} takes an \code{sr_model} tibble returned by \link{run_mod} to summary table for parameter, antigen/antibody, and stratification combination. Defaults will produce every combination of antigen/antibody, parameters, @@ -47,7 +47,7 @@ The antibody dynamic curve includes the following parameters: \item y0 = baseline antibody concentration \item y1 = peak antibody concentration \item t1 = time to peak -\item r = shape parameter +\item shape = shape parameter \item alpha = decay rate } } diff --git a/man/prep_popparams.Rd b/man/prep_popparams.Rd index b4f4d3d26..e9f29b02c 100644 --- a/man/prep_popparams.Rd +++ b/man/prep_popparams.Rd @@ -7,7 +7,8 @@ prep_popparams(x) } \arguments{ -\item{x}{A \link{data.frame} with a \code{Subject} variable.} +\item{x}{A \link{data.frame} with \code{Subject} and \code{.is_population_parameter} +variables.} } \value{ A filtered \link{data.frame} with the \code{Subject} variable renamed to diff --git a/man/prep_strat_list.Rd b/man/prep_strat_list.Rd new file mode 100644 index 000000000..8370cb9b0 --- /dev/null +++ b/man/prep_strat_list.Rd @@ -0,0 +1,32 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/prep_strat_list.R +\name{prep_strat_list} +\alias{prep_strat_list} +\title{Prepare and validate a stratification list} +\usage{ +prep_strat_list(data, strat) +} +\arguments{ +\item{data}{A \code{\link[base:data.frame]{base::data.frame()}} containing the stratification column.} + +\item{strat}{A \link{character} string naming the stratification column, or \code{NA} +to run the model without stratification.} +} +\value{ +A vector of stratum labels to loop over. +} +\description{ +\code{prep_strat_list()} builds the vector of stratum labels that \code{\link[=run_mod]{run_mod()}} +iterates over. +When \code{strat} is \code{NA}, a single pseudo-stratum (\code{"None"}) is returned so the +model runs once on the full data set. +Otherwise the unique values of \code{data[[strat]]} are returned, with factor +columns coerced to their character labels so the loop iterates over labels +rather than the underlying integer codes. +Rows with a missing stratification value are dropped with a warning, since +they cannot be assigned to a stratum. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/rebuild_sr_model_attributes.Rd b/man/rebuild_sr_model_attributes.Rd new file mode 100644 index 000000000..dd9ada8b3 --- /dev/null +++ b/man/rebuild_sr_model_attributes.Rd @@ -0,0 +1,32 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/rebuild_sr_model_attributes.R +\name{rebuild_sr_model_attributes} +\alias{rebuild_sr_model_attributes} +\title{Rebuild \code{sr_model} output attributes in a stable order} +\usage{ +rebuild_sr_model_attributes(x, mod_atts) +} +\arguments{ +\item{x}{A \link{data.frame} / \link[tibble:tbl_df]{tibble::tbl_df} of combined MCMC output.} + +\item{mod_atts}{A named \link{list} of \code{ggmcmc} metadata attributes, containing +\code{nChains}, \code{nParameters}, \code{nIterations}, \code{nBurnin}, and \code{nThin}.} +} +\value{ +\code{x} with its attributes rebuilt in a stable order and the +\code{sr_model} class prepended. +} +\description{ +\code{rebuild_sr_model_attributes()} reconstructs the attribute list of the +combined \code{\link[=run_mod]{run_mod()}} output in a fixed order, ensuring \code{class} appears +immediately after \code{names} and \code{row.names}. +The \code{dplyr} operations used to assemble the output can carry \code{ggmcmc} +attributes (\code{nChains}, etc.) into the result and push \code{class} to the end, +so this helper rebuilds the attributes explicitly. \code{mod_atts} (a named +selection from the \code{ggmcmc::ggs()} object) is the authoritative source for +the \code{ggmcmc}-style metadata attributes. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/reconcile_subject_ids.Rd b/man/reconcile_subject_ids.Rd new file mode 100644 index 000000000..548abd5a8 --- /dev/null +++ b/man/reconcile_subject_ids.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/reconcile_subject_ids.R +\name{reconcile_subject_ids} +\alias{reconcile_subject_ids} +\title{Reconcile MCMC subject indices with subject IDs} +\usage{ +reconcile_subject_ids(jags_unpacked, ids) +} +\arguments{ +\item{jags_unpacked}{A \link[tibble:tbl_df]{tibble::tbl_df} returned by \code{\link[=unpack_jags]{unpack_jags()}} +(after the \code{Iso_type} join), containing \code{Subject}, \code{Subnum}, \code{Param}, +and \code{Parameter} columns.} + +\item{ids}{A \link[tibble:tbl_df]{tibble::tbl_df} with a \code{Subject_mcmc} column (the subject ID) +and a \code{Subject} column (the MCMC index as a character string).} +} +\value{ +A \link[tibble:tbl_df]{tibble::tbl_df} with a single resolved \code{Subject} column and a +\code{Parameter} column holding the cleaned parameter name. +} +\description{ +\code{reconcile_subject_ids()} joins unpacked MCMC output to the subject ID +lookup table and resolves a single \code{Subject} identifier for every row. +\itemize{ +\item Individual-level parameters match a row in \code{ids}, so they receive the +original subject ID. +\item Population-level parameters (e.g., \code{mu.par}, \code{prec.par}, \code{prec.logy}) +have no matching ID, so they retain the parameter name produced by +\code{\link[=unpack_jags]{unpack_jags()}} as their identifier. +The temporary index columns are then dropped and the cleaned parameter +names (\code{Param}) are promoted to \code{Parameter} for downstream use. +} +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/relabel_preclogy_iso.Rd b/man/relabel_preclogy_iso.Rd new file mode 100644 index 000000000..ded65b7ae --- /dev/null +++ b/man/relabel_preclogy_iso.Rd @@ -0,0 +1,30 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/relabel_preclogy_iso.R +\name{relabel_preclogy_iso} +\alias{relabel_preclogy_iso} +\title{Relabel \code{prec.logy} population parameters by isotype} +\usage{ +relabel_preclogy_iso(jags_unpacked) +} +\arguments{ +\item{jags_unpacked}{A \link[tibble:tbl_df]{tibble::tbl_df} returned by \code{\link[=unpack_jags]{unpack_jags()}} after +the \code{Iso_type} join, containing \code{.is_population_parameter}, \code{Subject}, +\code{Iso_type}, and \code{Param} columns.} +} +\value{ +The input with \code{Param} relabeled to \code{Iso_type} for \code{prec.logy} +population-parameter rows. +} +\description{ +\code{relabel_preclogy_iso()} replaces the \code{Param} label of \code{prec.logy} +population-parameter rows with their antigen/isotype label (\code{Iso_type}). +This lets callers group \code{population_params} by \code{Parameter} to obtain +per-isotype precision estimates, rather than collapsing all isotypes into a +single \code{"prec.logy"} group. +Rows that are not \code{prec.logy} population parameters, and rows lacking an +\code{Iso_type} (e.g., the scalar/unindexed case), are left unchanged. +} +\author{ +Sam Schildhauer +} +\keyword{internal} diff --git a/man/run_mod.Rd b/man/run_mod.Rd index 0d0aff085..13d8d6809 100644 --- a/man/run_mod.Rd +++ b/man/run_mod.Rd @@ -15,6 +15,7 @@ run_mod( strat = NA, with_post = FALSE, with_pop_params = FALSE, + preclogy_per_iso = FALSE, ... ) } @@ -38,16 +39,24 @@ the number of MCMC chains to be run per jags model.} entered in quotes.} \item{with_post}{A \link{logical} value specifying whether a raw \code{jags.post} -component -should be included as an element of the \link{list} object returned by \code{run_mod()} +object should be included as an optional \code{"jags.post"} attribute on the +returned \code{sr_model} tibble (see \code{Value} section below for details). Note: These objects can be large.} \item{with_pop_params}{A \link{logical} value specifying whether population level parameters should be included as an attribute entitled -\code{population_params}. Excluded as default. +\code{population_params}. Excluded by default. Note: These objects can be large.} +\item{preclogy_per_iso}{A \link{logical} value. When \code{TRUE} and \code{with_pop_params} +is also \code{TRUE}, the \code{Parameter} column for \code{prec.logy} rows in +\code{population_params} will contain the antigen/isotype label (e.g., +\code{"HlyE_IgA"}) rather than the constant \code{"prec.logy"}. This allows grouping +by \code{Parameter} to obtain per-isotype precision estimates directly. Default +is \code{FALSE} (all \code{prec.logy} rows share \code{Parameter = "prec.logy"}; the +\code{Iso_type} column distinguishes isotypes).} + \item{...}{ Arguments passed on to \code{\link{prep_priors}} \describe{ @@ -99,13 +108,13 @@ If specified, must be 2 values long: }} } \value{ -An \code{sr_model} class object: a subclass of \link[tibble:tbl_df-class]{tibble::tbl_df} that +An \code{sr_model} class object: a subclass of \link[tibble:tbl_df]{tibble::tbl_df} that contains MCMC samples from the joint posterior distribution of the model parameters, conditional on the provided input \code{data}, including the following: \itemize{ -\item \code{iteration} = Number of sampling iterations -\item \code{chain} = Number of MCMC chains run; between 1 and 4 +\item \code{Iteration} = Number of sampling iterations +\item \code{Chain} = Number of MCMC chains run; between 1 and 4 \item \code{Parameter} = Parameter being estimated. Includes the following: \itemize{ \item \code{y0} = Posterior estimate of baseline antibody concentration @@ -121,23 +130,29 @@ including the following: \item The following \link{attributes} are included in the output: \itemize{ \item \code{class}: Class of the output object. -\item \code{nChain}: Number of chains run. +\item \code{nChains}: Number of chains run. \item \code{nParameters}: The amount of parameters estimated in the model. \item \code{nIterations}: Number of iteration specified. \item \code{nBurnin}: Number of burn ins. \item \code{nThin}: Thinning number (niter/nmc). -\item \code{population_params}: Optionally included modeled population parameters -indexed by -\code{Iteration}, -\code{Chain}, \code{Parameter}, \code{Iso_type}, and \code{Stratification}. Excluded as -default. Includes the following modeled population parameters: +\item \code{population_params}: Optionally included modeled population parameters, +returned as a \link{data.frame} and excluded by default. +Columns include +\code{Iteration}, \code{Chain}, \code{Parameter}, \code{Iso_type}, \code{Stratification}, +\code{Population_Parameter}, and \code{value}. +\itemize{ +\item \code{Population_Parameter} identifies which modeled population parameter +is represented: \itemize{ -\item \code{mu.par} = The population means of the host-specific model parameters -(on logarithmic scales). -\item \code{prec.par} = The population precision matrix of the hyperparameters -(with diagonal elements equal to inverse variances). -\item \code{prec.logy} = A vector of population precisions (inverse variances), -one per antigen/isotype combination. +\item \code{mu.par} = The population means of the host-specific model +parameters (on logarithmic scales). Note: y1 and shape are transformed. +\item \code{prec.par} = The population precision matrix of the +hyperparameters (with diagonal elements equal to inverse variances). +The two parameters listed (separated by commas) represent the pairwise +precision relationship between specified parameters. +\item \code{prec.logy} = A vector of population precisions (inverse +variances), one per antigen/isotype combination. +} } \item \code{priors}: A \link{list} that summarizes the input priors, including: \itemize{ diff --git a/man/serodynamics-package.Rd b/man/serodynamics-package.Rd index 0eb607209..42c64b98e 100644 --- a/man/serodynamics-package.Rd +++ b/man/serodynamics-package.Rd @@ -24,14 +24,10 @@ Authors: \itemize{ \item Samuel Schildhauer \email{sschildhauer@ucdavis.edu} \item Peter Teunis \email{p.teunis@emory.edu} (Author of the method and original code.) [copyright holder] + \item Kwan Ho Lee \email{ksjlee@ucdavis.edu} \item Kristen Aiemjoy \email{kaiemjoy@ucdavis.edu} \item Douglas Ezra Morrison \email{demorrison@ucdavis.edu} } -Other contributors: -\itemize{ - \item Kwan Ho Lee \email{ksjlee@ucdavis.edu} [contributor] -} - } \keyword{internal} diff --git a/man/unpack_jags.Rd b/man/unpack_jags.Rd index f4a41c482..00677dad7 100644 --- a/man/unpack_jags.Rd +++ b/man/unpack_jags.Rd @@ -7,17 +7,18 @@ unpack_jags(data) } \arguments{ -\item{data}{A \link[tibble:tbl_df-class]{tibble::tbl_df} in \code{\link[ggmcmc:ggs]{ggmcmc::ggs()}} / MCMC-long format, +\item{data}{A \link[tibble:tbl_df]{tibble::tbl_df} in \code{\link[ggmcmc:ggs]{ggmcmc::ggs()}} / MCMC-long format, usually \code{ggmcmc::ggs(jags_post[["mcmc"]])} where \code{jags_post} comes from \link{run_mod}. Must contain at least \code{Iteration}, \code{Chain}, \code{Parameter}, and \code{value} columns.} } \value{ -A \link[tibble:tbl_df-class]{tibble::tbl_df} that -contains MCMC samples from the joint posterior distribution of the model -with unpacked individual-level parameters (e.g., \code{y0}, \code{y1}, \code{t1}, -\code{alpha}, \code{shape}) and population-level parameters (e.g., \code{mu.par}, -\code{prec.par}, \code{prec.logy}), along with isotypes and subjects. +A \link[tibble:tbl_df]{tibble::tbl_df} containing MCMC samples from the joint +posterior distribution of the model with unpacked individual-level +parameters (e.g., \code{y0}, \code{y1}, \code{t1}, \code{alpha}, \code{shape}) and +population-level parameters (e.g., \code{mu.par}, \code{prec.par}, \code{prec.logy}), +along with subject-related fields such as \code{Subject} and \code{Subnum}. +Isotype names are not added by \code{unpack_jags()} itself. } \description{ \code{unpack_jags()} takes a long-format MCMC sample (typically created by diff --git a/man/use_att_names.Rd b/man/use_att_names.Rd index 5367bf7fe..03a87619c 100644 --- a/man/use_att_names.Rd +++ b/man/use_att_names.Rd @@ -16,7 +16,7 @@ The input \link{data.frame} with columns named after attributes. \description{ \code{use_att_names} takes prepared longitudinal data for antibody kinetic modeling and names columns using attribute values to allow merging -with a modeled \link{run_mod} output \link[tibble:tbl_df-class]{tibble::tbl_df}. The column names include +with a modeled \link{run_mod} output \link[tibble:tbl_df]{tibble::tbl_df}. The column names include \code{Subject}, \code{Iso_type}, \code{t}, and \code{result}. } \keyword{internal} diff --git a/tests/testthat/_snaps/darwin/run_mod/nostrat-curve-params-withpost.csv b/tests/testthat/_snaps/darwin/run_mod/nostrat-curve-params-withpost.csv deleted file mode 100644 index 61c3bd24b..000000000 --- a/tests/testthat/_snaps/darwin/run_mod/nostrat-curve-params-withpost.csv +++ /dev/null @@ -1,378001 +0,0 @@ -Iteration,Chain,Parameter,Iso_type,Stratification,Subject,value -1,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -2,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -3,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -4,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -5,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -6,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -7,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -8,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -9,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -10,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -11,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -12,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -13,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -14,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -15,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -16,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -17,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -18,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -19,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -20,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -21,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -22,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -23,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -24,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -25,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -26,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -27,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -28,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -29,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -30,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -31,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -32,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -33,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -34,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -35,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -36,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -37,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -38,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -39,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -40,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -41,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -42,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -43,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -44,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -45,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -46,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -47,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -48,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -49,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -50,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -51,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -52,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -53,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -54,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -55,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -56,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -57,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -58,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -59,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -60,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -61,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -62,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -63,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -64,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -65,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -66,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -67,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -68,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -69,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -70,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -71,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -72,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -73,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -74,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -75,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -76,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -77,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -78,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -79,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -80,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -81,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -82,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -83,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -84,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -85,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -86,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -87,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -88,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -89,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -90,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -91,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -92,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -93,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -94,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -95,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -96,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -97,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -98,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -99,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -100,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -1,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -2,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -3,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -4,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -5,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -6,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -7,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -8,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -9,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -10,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -11,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -12,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -13,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -14,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -15,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 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-52,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -53,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -54,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -55,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -56,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -57,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -58,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -59,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -60,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -61,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -62,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -63,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -64,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -65,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -66,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -67,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -68,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -69,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -70,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -71,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -72,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -73,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -74,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -75,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -76,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -77,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -78,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -79,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -80,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -81,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -82,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -83,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -84,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -85,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -86,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -87,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -88,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -89,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -90,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -91,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -92,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -93,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -94,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -95,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -96,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -97,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -98,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -99,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -100,1,y1,HlyE_IgA,None,sees_npl_23,1099.35 -1,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -2,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -3,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -4,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -5,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -6,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -7,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -8,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -9,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -10,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -11,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -12,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -13,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -14,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -15,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -16,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -17,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -18,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -19,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -20,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -21,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -22,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -23,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -24,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -25,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -26,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -27,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -28,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -29,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -30,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -31,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -32,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -33,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -34,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -35,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -36,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -37,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -38,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -39,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -40,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -41,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -42,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -43,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -44,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -45,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -46,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -47,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -48,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -49,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -50,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -51,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -52,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -53,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -54,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -55,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -56,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -57,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -58,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -59,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -60,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -61,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -62,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -63,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -64,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -65,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -66,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -67,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -68,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -69,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -70,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -71,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -72,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -73,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -74,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -75,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -76,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -77,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -78,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -79,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -80,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -81,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -82,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -83,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -84,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -85,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -86,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -87,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -88,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -89,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -90,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -91,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -92,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -93,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -94,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -95,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -96,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -97,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -98,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -99,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -100,2,y1,HlyE_IgA,None,sees_npl_23,1099.35 -1,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -2,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -3,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -4,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -5,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -6,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -7,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -8,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -9,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -10,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -11,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -12,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -13,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -14,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -15,1,y1,HlyE_IgG,None,sees_npl_23,123.526 -16,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -17,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -18,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -19,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -20,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -21,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -22,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -23,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -24,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -25,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -26,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -27,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -28,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -29,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -30,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -31,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -32,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -33,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -34,1,y1,HlyE_IgG,None,sees_npl_23,223.876 -35,1,y1,HlyE_IgG,None,sees_npl_23,223.876 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-30,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -31,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -32,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -33,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -34,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -35,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -36,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -37,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -38,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -39,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -40,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -41,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -42,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -43,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -44,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -45,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -46,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -47,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -48,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -49,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -50,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -51,2,y1,HlyE_IgA,None,sees_npl_74,330.373 -52,2,y1,HlyE_IgA,None,sees_npl_74,330.373 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-99,2,y1,HlyE_IgA,None,sees_npl_74,1115.54 -100,2,y1,HlyE_IgA,None,sees_npl_74,1115.54 -1,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -2,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -3,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -4,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -5,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -6,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -7,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -8,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -9,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -10,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -11,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -12,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -13,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -14,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -15,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -16,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -17,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -18,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -19,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -20,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -21,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 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-45,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -46,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -47,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -48,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -49,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -50,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -51,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -52,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -53,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -54,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -55,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -56,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -57,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -58,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -59,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -60,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -61,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -62,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -63,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -64,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -65,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -66,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -67,1,y1,HlyE_IgG,None,sees_npl_74,995.963 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-64,2,y1,HlyE_IgA,None,newperson,518.717 -65,2,y1,HlyE_IgA,None,newperson,1077.09 -66,2,y1,HlyE_IgA,None,newperson,216.224 -67,2,y1,HlyE_IgA,None,newperson,601.883 -68,2,y1,HlyE_IgA,None,newperson,220.39 -69,2,y1,HlyE_IgA,None,newperson,1377.07 -70,2,y1,HlyE_IgA,None,newperson,539.473 -71,2,y1,HlyE_IgA,None,newperson,635.829 -72,2,y1,HlyE_IgA,None,newperson,1036.58 -73,2,y1,HlyE_IgA,None,newperson,436.814 -74,2,y1,HlyE_IgA,None,newperson,535.929 -75,2,y1,HlyE_IgA,None,newperson,2349.41 -76,2,y1,HlyE_IgA,None,newperson,783.778 -77,2,y1,HlyE_IgA,None,newperson,773.946 -78,2,y1,HlyE_IgA,None,newperson,1184.38 -79,2,y1,HlyE_IgA,None,newperson,1140.55 -80,2,y1,HlyE_IgA,None,newperson,931.255 -81,2,y1,HlyE_IgA,None,newperson,1125.8 -82,2,y1,HlyE_IgA,None,newperson,2328.05 -83,2,y1,HlyE_IgA,None,newperson,736.718 -84,2,y1,HlyE_IgA,None,newperson,1675.35 -85,2,y1,HlyE_IgA,None,newperson,563.714 -86,2,y1,HlyE_IgA,None,newperson,644.42 -87,2,y1,HlyE_IgA,None,newperson,394.363 -88,2,y1,HlyE_IgA,None,newperson,3702.41 -89,2,y1,HlyE_IgA,None,newperson,1756.72 -90,2,y1,HlyE_IgA,None,newperson,1134.79 -91,2,y1,HlyE_IgA,None,newperson,466.016 -92,2,y1,HlyE_IgA,None,newperson,3036.75 -93,2,y1,HlyE_IgA,None,newperson,3802.85 -94,2,y1,HlyE_IgA,None,newperson,314.371 -95,2,y1,HlyE_IgA,None,newperson,806.2 -96,2,y1,HlyE_IgA,None,newperson,809.85 -97,2,y1,HlyE_IgA,None,newperson,2876.44 -98,2,y1,HlyE_IgA,None,newperson,1516.01 -99,2,y1,HlyE_IgA,None,newperson,1079.27 -100,2,y1,HlyE_IgA,None,newperson,408.166 -1,1,y1,HlyE_IgG,None,newperson,1943.35 -2,1,y1,HlyE_IgG,None,newperson,1056.7 -3,1,y1,HlyE_IgG,None,newperson,103.257 -4,1,y1,HlyE_IgG,None,newperson,1128.8 -5,1,y1,HlyE_IgG,None,newperson,1428.74 -6,1,y1,HlyE_IgG,None,newperson,439.598 -7,1,y1,HlyE_IgG,None,newperson,1120.49 -8,1,y1,HlyE_IgG,None,newperson,741.308 -9,1,y1,HlyE_IgG,None,newperson,1264.34 -10,1,y1,HlyE_IgG,None,newperson,1312.79 -11,1,y1,HlyE_IgG,None,newperson,946.232 -12,1,y1,HlyE_IgG,None,newperson,1824.17 -13,1,y1,HlyE_IgG,None,newperson,938.513 -14,1,y1,HlyE_IgG,None,newperson,1812.43 -15,1,y1,HlyE_IgG,None,newperson,1399.33 -16,1,y1,HlyE_IgG,None,newperson,4632.53 -17,1,y1,HlyE_IgG,None,newperson,1814.58 -18,1,y1,HlyE_IgG,None,newperson,3116.66 -19,1,y1,HlyE_IgG,None,newperson,205.14 -20,1,y1,HlyE_IgG,None,newperson,7390.38 -21,1,y1,HlyE_IgG,None,newperson,1349.85 -22,1,y1,HlyE_IgG,None,newperson,1229.66 -23,1,y1,HlyE_IgG,None,newperson,5306.18 -24,1,y1,HlyE_IgG,None,newperson,4332.39 -25,1,y1,HlyE_IgG,None,newperson,467.417 -26,1,y1,HlyE_IgG,None,newperson,528.994 -27,1,y1,HlyE_IgG,None,newperson,506.216 -28,1,y1,HlyE_IgG,None,newperson,363.522 -29,1,y1,HlyE_IgG,None,newperson,2149.77 -30,1,y1,HlyE_IgG,None,newperson,2496.44 -31,1,y1,HlyE_IgG,None,newperson,727.606 -32,1,y1,HlyE_IgG,None,newperson,1844.28 -33,1,y1,HlyE_IgG,None,newperson,16353.3 -34,1,y1,HlyE_IgG,None,newperson,1340.36 -35,1,y1,HlyE_IgG,None,newperson,905.059 -36,1,y1,HlyE_IgG,None,newperson,2635.83 -37,1,y1,HlyE_IgG,None,newperson,2795.01 -38,1,y1,HlyE_IgG,None,newperson,453.734 -39,1,y1,HlyE_IgG,None,newperson,11326.7 -40,1,y1,HlyE_IgG,None,newperson,871.138 -41,1,y1,HlyE_IgG,None,newperson,292.092 -42,1,y1,HlyE_IgG,None,newperson,2890.82 -43,1,y1,HlyE_IgG,None,newperson,768.985 -44,1,y1,HlyE_IgG,None,newperson,439.264 -45,1,y1,HlyE_IgG,None,newperson,437.172 -46,1,y1,HlyE_IgG,None,newperson,886.979 -47,1,y1,HlyE_IgG,None,newperson,5011.49 -48,1,y1,HlyE_IgG,None,newperson,16321.6 -49,1,y1,HlyE_IgG,None,newperson,400.302 -50,1,y1,HlyE_IgG,None,newperson,297.814 -51,1,y1,HlyE_IgG,None,newperson,5099.21 -52,1,y1,HlyE_IgG,None,newperson,1540.57 -53,1,y1,HlyE_IgG,None,newperson,611.081 -54,1,y1,HlyE_IgG,None,newperson,446.672 -55,1,y1,HlyE_IgG,None,newperson,672.312 -56,1,y1,HlyE_IgG,None,newperson,463.413 -57,1,y1,HlyE_IgG,None,newperson,557.519 -58,1,y1,HlyE_IgG,None,newperson,116.305 -59,1,y1,HlyE_IgG,None,newperson,9951.99 -60,1,y1,HlyE_IgG,None,newperson,1091.1 -61,1,y1,HlyE_IgG,None,newperson,2174.5 -62,1,y1,HlyE_IgG,None,newperson,1380.6 -63,1,y1,HlyE_IgG,None,newperson,2890.35 -64,1,y1,HlyE_IgG,None,newperson,2067.14 -65,1,y1,HlyE_IgG,None,newperson,1640.39 -66,1,y1,HlyE_IgG,None,newperson,497.773 -67,1,y1,HlyE_IgG,None,newperson,1179.07 -68,1,y1,HlyE_IgG,None,newperson,2637.91 -69,1,y1,HlyE_IgG,None,newperson,1895.84 -70,1,y1,HlyE_IgG,None,newperson,3342.14 -71,1,y1,HlyE_IgG,None,newperson,4427.42 -72,1,y1,HlyE_IgG,None,newperson,3778 -73,1,y1,HlyE_IgG,None,newperson,12140.4 -74,1,y1,HlyE_IgG,None,newperson,3842.84 -75,1,y1,HlyE_IgG,None,newperson,2420.84 -76,1,y1,HlyE_IgG,None,newperson,3203.7 -77,1,y1,HlyE_IgG,None,newperson,2095.23 -78,1,y1,HlyE_IgG,None,newperson,3904.98 -79,1,y1,HlyE_IgG,None,newperson,3695.59 -80,1,y1,HlyE_IgG,None,newperson,1358.74 -81,1,y1,HlyE_IgG,None,newperson,1505.57 -82,1,y1,HlyE_IgG,None,newperson,1863.25 -83,1,y1,HlyE_IgG,None,newperson,149.956 -84,1,y1,HlyE_IgG,None,newperson,1073.76 -85,1,y1,HlyE_IgG,None,newperson,676.876 -86,1,y1,HlyE_IgG,None,newperson,402.712 -87,1,y1,HlyE_IgG,None,newperson,1202.35 -88,1,y1,HlyE_IgG,None,newperson,1415.97 -89,1,y1,HlyE_IgG,None,newperson,1045.81 -90,1,y1,HlyE_IgG,None,newperson,766.477 -91,1,y1,HlyE_IgG,None,newperson,706.955 -92,1,y1,HlyE_IgG,None,newperson,833.313 -93,1,y1,HlyE_IgG,None,newperson,1588.54 -94,1,y1,HlyE_IgG,None,newperson,980.301 -95,1,y1,HlyE_IgG,None,newperson,243.406 -96,1,y1,HlyE_IgG,None,newperson,2683.9 -97,1,y1,HlyE_IgG,None,newperson,1251.35 -98,1,y1,HlyE_IgG,None,newperson,1526.77 -99,1,y1,HlyE_IgG,None,newperson,675.34 -100,1,y1,HlyE_IgG,None,newperson,1031.13 -1,2,y1,HlyE_IgG,None,newperson,225.481 -2,2,y1,HlyE_IgG,None,newperson,3446.08 -3,2,y1,HlyE_IgG,None,newperson,496.46 -4,2,y1,HlyE_IgG,None,newperson,287.766 -5,2,y1,HlyE_IgG,None,newperson,587.11 -6,2,y1,HlyE_IgG,None,newperson,1486.71 -7,2,y1,HlyE_IgG,None,newperson,4391.26 -8,2,y1,HlyE_IgG,None,newperson,612.548 -9,2,y1,HlyE_IgG,None,newperson,2256.12 -10,2,y1,HlyE_IgG,None,newperson,1603.02 -11,2,y1,HlyE_IgG,None,newperson,1278.47 -12,2,y1,HlyE_IgG,None,newperson,4726.13 -13,2,y1,HlyE_IgG,None,newperson,2675.74 -14,2,y1,HlyE_IgG,None,newperson,1322.05 -15,2,y1,HlyE_IgG,None,newperson,6951.96 -16,2,y1,HlyE_IgG,None,newperson,4098.81 -17,2,y1,HlyE_IgG,None,newperson,79.6868 -18,2,y1,HlyE_IgG,None,newperson,218.601 -19,2,y1,HlyE_IgG,None,newperson,334.071 -20,2,y1,HlyE_IgG,None,newperson,293.336 -21,2,y1,HlyE_IgG,None,newperson,2929.06 -22,2,y1,HlyE_IgG,None,newperson,3715 -23,2,y1,HlyE_IgG,None,newperson,1902.36 -24,2,y1,HlyE_IgG,None,newperson,888.618 -25,2,y1,HlyE_IgG,None,newperson,223.095 -26,2,y1,HlyE_IgG,None,newperson,463.761 -27,2,y1,HlyE_IgG,None,newperson,1168.22 -28,2,y1,HlyE_IgG,None,newperson,445.309 -29,2,y1,HlyE_IgG,None,newperson,1108.68 -30,2,y1,HlyE_IgG,None,newperson,997.142 -31,2,y1,HlyE_IgG,None,newperson,622.13 -32,2,y1,HlyE_IgG,None,newperson,472.211 -33,2,y1,HlyE_IgG,None,newperson,3749.69 -34,2,y1,HlyE_IgG,None,newperson,3150.01 -35,2,y1,HlyE_IgG,None,newperson,665.677 -36,2,y1,HlyE_IgG,None,newperson,979.954 -37,2,y1,HlyE_IgG,None,newperson,474.641 -38,2,y1,HlyE_IgG,None,newperson,292.682 -39,2,y1,HlyE_IgG,None,newperson,2871.66 -40,2,y1,HlyE_IgG,None,newperson,191.761 -41,2,y1,HlyE_IgG,None,newperson,777.589 -42,2,y1,HlyE_IgG,None,newperson,949.111 -43,2,y1,HlyE_IgG,None,newperson,471.657 -44,2,y1,HlyE_IgG,None,newperson,432.629 -45,2,y1,HlyE_IgG,None,newperson,348.568 -46,2,y1,HlyE_IgG,None,newperson,686.684 -47,2,y1,HlyE_IgG,None,newperson,174.059 -48,2,y1,HlyE_IgG,None,newperson,2442.09 -49,2,y1,HlyE_IgG,None,newperson,856.649 -50,2,y1,HlyE_IgG,None,newperson,2746.71 -51,2,y1,HlyE_IgG,None,newperson,1627.92 -52,2,y1,HlyE_IgG,None,newperson,1146.35 -53,2,y1,HlyE_IgG,None,newperson,1342.76 -54,2,y1,HlyE_IgG,None,newperson,135.427 -55,2,y1,HlyE_IgG,None,newperson,1920.96 -56,2,y1,HlyE_IgG,None,newperson,267.317 -57,2,y1,HlyE_IgG,None,newperson,542.034 -58,2,y1,HlyE_IgG,None,newperson,1988.6 -59,2,y1,HlyE_IgG,None,newperson,2788.69 -60,2,y1,HlyE_IgG,None,newperson,1420.23 -61,2,y1,HlyE_IgG,None,newperson,559.84 -62,2,y1,HlyE_IgG,None,newperson,769.351 -63,2,y1,HlyE_IgG,None,newperson,1008.91 -64,2,y1,HlyE_IgG,None,newperson,280.789 -65,2,y1,HlyE_IgG,None,newperson,687.073 -66,2,y1,HlyE_IgG,None,newperson,737.836 -67,2,y1,HlyE_IgG,None,newperson,2958.17 -68,2,y1,HlyE_IgG,None,newperson,2739.06 -69,2,y1,HlyE_IgG,None,newperson,756.505 -70,2,y1,HlyE_IgG,None,newperson,679.761 -71,2,y1,HlyE_IgG,None,newperson,1510.23 -72,2,y1,HlyE_IgG,None,newperson,4332.79 -73,2,y1,HlyE_IgG,None,newperson,917.108 -74,2,y1,HlyE_IgG,None,newperson,1260.66 -75,2,y1,HlyE_IgG,None,newperson,2544.96 -76,2,y1,HlyE_IgG,None,newperson,479.541 -77,2,y1,HlyE_IgG,None,newperson,253.026 -78,2,y1,HlyE_IgG,None,newperson,1795.34 -79,2,y1,HlyE_IgG,None,newperson,118.751 -80,2,y1,HlyE_IgG,None,newperson,3822.38 -81,2,y1,HlyE_IgG,None,newperson,27.8291 -82,2,y1,HlyE_IgG,None,newperson,1047.64 -83,2,y1,HlyE_IgG,None,newperson,77.8833 -84,2,y1,HlyE_IgG,None,newperson,4282.08 -85,2,y1,HlyE_IgG,None,newperson,200.7 -86,2,y1,HlyE_IgG,None,newperson,733.883 -87,2,y1,HlyE_IgG,None,newperson,1470.34 -88,2,y1,HlyE_IgG,None,newperson,23.9 -89,2,y1,HlyE_IgG,None,newperson,194.65 -90,2,y1,HlyE_IgG,None,newperson,4088.92 -91,2,y1,HlyE_IgG,None,newperson,657.126 -92,2,y1,HlyE_IgG,None,newperson,865.124 -93,2,y1,HlyE_IgG,None,newperson,88.9675 -94,2,y1,HlyE_IgG,None,newperson,4773.51 -95,2,y1,HlyE_IgG,None,newperson,220.485 -96,2,y1,HlyE_IgG,None,newperson,347.584 -97,2,y1,HlyE_IgG,None,newperson,1988.19 -98,2,y1,HlyE_IgG,None,newperson,691.887 -99,2,y1,HlyE_IgG,None,newperson,895.466 -100,2,y1,HlyE_IgG,None,newperson,1254.34 diff --git a/tests/testthat/_snaps/darwin/run_mod/popparam-nostrat-summary-stats.csv b/tests/testthat/_snaps/darwin/run_mod/popparam-nostrat-summary-stats.csv new file mode 100644 index 000000000..7dd609f3e --- /dev/null +++ b/tests/testthat/_snaps/darwin/run_mod/popparam-nostrat-summary-stats.csv @@ -0,0 +1,32 @@ +Parameter,mean,sd +log(alpha),-4.37383,0.338902 +"log(alpha), log(alpha)",5.63916,2.54057 +"log(alpha), log(shape - 1)",-2.13651,1.57126 +"log(alpha), log(t1)",2.33993,2.35205 +"log(alpha), log(y0)",-0.422569,2.19764 +"log(alpha), log(y1 - y0)",-0.0684156,0.302793 +log(shape - 1),-1.12932,0.116991 +"log(shape - 1), log(alpha)",-2.13651,1.57126 +"log(shape - 1), log(shape - 1)",21.4911,8.11084 +"log(shape - 1), log(t1)",-3.20605,11.4274 +"log(shape - 1), log(y0)",-5.30339,3.95788 +"log(shape - 1), log(y1 - y0)",-0.516525,1.00039 +log(t1),1.05253,0.0531201 +"log(t1), log(alpha)",2.33993,2.35205 +"log(t1), log(shape - 1)",-3.20605,11.4274 +"log(t1), log(t1)",32.0067,26.8567 +"log(t1), log(y0)",-0.798223,10.1937 +"log(t1), log(y1 - y0)",-0.643067,0.986963 +log(y0),0.968397,0.0372532 +"log(y0), log(alpha)",-0.422569,2.19764 +"log(y0), log(shape - 1)",-5.30339,3.95788 +"log(y0), log(t1)",-0.798223,10.1937 +"log(y0), log(y0)",45.9769,28.863 +"log(y0), log(y1 - y0)",-0.596065,0.876996 +log(y1 - y0),6.91163,0.143855 +"log(y1 - y0), log(alpha)",-0.0684156,0.302793 +"log(y1 - y0), log(shape - 1)",-0.516525,1.00039 +"log(y1 - y0), log(t1)",-0.643067,0.986963 +"log(y1 - y0), log(y0)",-0.596065,0.876996 +"log(y1 - y0), log(y1 - y0)",1.74642,0.666081 +prec.logy,0.212787,0.122624 diff --git a/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv b/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv index 8a7b29a59..aebe21c7f 100644 --- a/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv +++ b/tests/testthat/_snaps/darwin/run_mod/popparam-summary-stats.csv @@ -1,31 +1,32 @@ Parameter,mean,sd -alpha,-4.8276,0.200665 -"alpha, alpha",2.56363,0.368743 -"alpha, shape",-0.610002,0.872237 -"alpha, t1",0.253244,0.910382 -"alpha, y0",-0.269962,0.623738 -"alpha, y1",-0.052442,0.187775 -shape,-0.627015,0.0691708 -"shape, alpha",-0.610002,0.872237 -"shape, shape",9.52829,2.70326 -"shape, t1",4.04278,3.12409 -"shape, y0",-2.43068,3.82725 -"shape, y1",-1.03352,0.430277 -t1,0.463903,0.0405599 -"t1, alpha",0.253244,0.910382 -"t1, shape",4.04278,3.12409 -"t1, t1",18.8339,5.49919 -"t1, y0",0.778855,4.44261 -"t1, y1",0.0564977,0.659988 -y0,0.78573,0.110742 -"y0, alpha",-0.269962,0.623738 -"y0, shape",-2.43068,3.82725 -"y0, t1",0.778855,4.44261 -"y0, y0",11.1517,4.71125 -"y0, y1",0.230998,0.401854 -y1,5.87676,0.185882 -"y1, alpha",-0.052442,0.187775 -"y1, shape",-1.03352,0.430277 -"y1, t1",0.0564977,0.659988 -"y1, y0",0.230998,0.401854 -"y1, y1",0.706827,0.126534 +log(alpha),-4.8276,0.200665 +"log(alpha), log(alpha)",2.56363,0.368743 +"log(alpha), log(shape - 1)",-0.610002,0.872237 +"log(alpha), log(t1)",0.253244,0.910382 +"log(alpha), log(y0)",-0.269962,0.623738 +"log(alpha), log(y1 - y0)",-0.052442,0.187775 +log(shape - 1),-0.627015,0.0691708 +"log(shape - 1), log(alpha)",-0.610002,0.872237 +"log(shape - 1), log(shape - 1)",9.52829,2.70326 +"log(shape - 1), log(t1)",4.04278,3.12409 +"log(shape - 1), log(y0)",-2.43068,3.82725 +"log(shape - 1), log(y1 - y0)",-1.03352,0.430277 +log(t1),0.463903,0.0405599 +"log(t1), log(alpha)",0.253244,0.910382 +"log(t1), log(shape - 1)",4.04278,3.12409 +"log(t1), log(t1)",18.8339,5.49919 +"log(t1), log(y0)",0.778855,4.44261 +"log(t1), log(y1 - y0)",0.0564977,0.659988 +log(y0),0.78573,0.110742 +"log(y0), log(alpha)",-0.269962,0.623738 +"log(y0), log(shape - 1)",-2.43068,3.82725 +"log(y0), log(t1)",0.778855,4.44261 +"log(y0), log(y0)",11.1517,4.71125 +"log(y0), log(y1 - y0)",0.230998,0.401854 +log(y1 - y0),5.87676,0.185882 +"log(y1 - y0), log(alpha)",-0.052442,0.187775 +"log(y1 - y0), log(shape - 1)",-1.03352,0.430277 +"log(y1 - y0), log(t1)",0.0564977,0.659988 +"log(y1 - y0), log(y0)",0.230998,0.401854 +"log(y1 - y0), log(y1 - y0)",0.706827,0.126534 +prec.logy,1.65554,0.3125 diff --git a/tests/testthat/_snaps/run_mod.md b/tests/testthat/_snaps/run_mod.md deleted file mode 100644 index 7a53344b9..000000000 --- a/tests/testthat/_snaps/run_mod.md +++ /dev/null @@ -1,20 +0,0 @@ -# results are consistent with SEES data - - list(names = c("Iteration", "Chain", "Parameter", "Iso_type", - "Stratification", "Subject", "value"), class = c("sr_model", - "tbl_df", "tbl", "data.frame"), nChains = 2L, nParameters = 440L, - nIterations = 100L, nBurnin = 20, nThin = 1, description = "jags_post[[\"mcmc\"]]", - priors = list(mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, - 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), wishdf_param = 20, - prec_logy_hyp_param = c(4, 1))) - -# results are consistent with unstratified SEES data - - list(names = c("Iteration", "Chain", "Parameter", "Iso_type", - "Stratification", "Subject", "value"), class = c("sr_model", - "tbl_df", "tbl", "data.frame"), nChains = 2L, nParameters = 1890L, - nIterations = 100L, nBurnin = 20, nThin = 1, description = "jags_post[[\"mcmc\"]]", - priors = list(mu_hyp_param = c(1, 7, 1, -4, -1), prec_hyp_param = c(1, - 1e-05, 1, 0.001, 1), omega_param = c(1, 50, 1, 10, 1), wishdf_param = 20, - prec_logy_hyp_param = c(4, 1))) - diff --git a/tests/testthat/_snaps/run_mod/nostrat-curve-params-withpost.csv b/tests/testthat/_snaps/run_mod/nostrat-curve-params-withpost.csv deleted file mode 100644 index b3b73f1cf..000000000 --- a/tests/testthat/_snaps/run_mod/nostrat-curve-params-withpost.csv +++ /dev/null @@ -1,378001 +0,0 @@ -Iteration,Chain,Parameter,Iso_type,Stratification,Subject,value -1,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -2,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -3,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -4,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -5,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -6,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -7,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -8,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -9,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -10,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -11,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -12,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -13,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -14,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -15,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -16,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -17,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -18,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -19,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -20,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -21,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -22,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -23,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -24,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -25,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -26,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -27,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -28,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -29,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -30,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -31,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -32,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -33,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -34,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -35,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -36,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -37,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -38,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -39,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -40,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -41,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -42,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -43,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -44,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -45,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -46,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -47,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -48,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -49,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -50,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -51,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -52,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -53,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -54,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -55,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -56,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -57,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -58,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -59,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -60,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -61,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -62,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -63,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -64,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -65,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -66,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -67,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -68,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -69,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -70,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -71,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -72,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -73,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -74,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -75,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -76,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -77,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -78,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -79,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -80,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -81,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -82,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -83,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -84,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -85,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -86,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -87,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -88,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -89,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -90,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -91,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -92,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -93,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -94,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -95,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -96,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -97,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -98,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -99,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -100,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -1,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -2,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -3,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -4,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -5,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -6,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -7,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -8,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -9,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -10,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -11,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -12,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -13,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -14,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -15,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -16,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -17,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -18,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -19,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -20,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -21,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -22,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -23,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -24,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -25,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -26,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -27,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -28,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -29,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -30,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -31,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -32,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -33,2,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 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-99,2,y1,HlyE_IgA,None,sees_npl_12,1099.35 -100,2,y1,HlyE_IgA,None,sees_npl_12,1099.35 -1,1,y1,HlyE_IgG,None,sees_npl_12,303.747 -2,1,y1,HlyE_IgG,None,sees_npl_12,289.077 -3,1,y1,HlyE_IgG,None,sees_npl_12,289.077 -4,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -5,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -6,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -7,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -8,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -9,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -10,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -11,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -12,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -13,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -14,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -15,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -16,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -17,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -18,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -19,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -20,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -21,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -22,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -23,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -24,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -25,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -26,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -27,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -28,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -29,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -30,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -31,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -32,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -33,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -34,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -35,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -36,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -37,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -38,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -39,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -40,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -41,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -42,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -43,1,y1,HlyE_IgG,None,sees_npl_12,244.213 -44,1,y1,HlyE_IgG,None,sees_npl_12,244.213 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-91,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -92,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -93,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -94,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -95,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -96,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -97,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -98,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -99,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -100,2,y1,HlyE_IgA,None,sees_npl_18,1099.35 -1,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -2,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -3,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -4,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -5,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -6,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -7,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -8,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -9,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -10,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -11,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -12,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -13,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -14,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -15,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -16,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -17,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -18,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -19,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -20,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -21,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -22,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -23,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -24,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -25,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -26,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -27,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -28,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -29,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -30,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -31,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -32,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -33,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -34,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -35,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -36,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -37,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -38,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -39,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -40,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -41,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -42,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -43,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -44,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -45,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -46,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -47,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -48,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -49,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -50,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -51,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -52,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -53,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -54,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -55,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -56,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -57,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -58,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -59,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -60,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -61,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -62,1,y1,HlyE_IgG,None,sees_npl_18,1525.51 -63,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -64,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -65,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -66,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -67,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -68,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -69,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -70,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -71,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -72,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -73,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -74,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -75,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -76,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -77,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -78,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -79,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -80,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -81,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -82,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -83,1,y1,HlyE_IgG,None,sees_npl_18,2262.56 -84,1,y1,HlyE_IgG,None,sees_npl_18,1074.61 -85,1,y1,HlyE_IgG,None,sees_npl_18,2193.89 -86,1,y1,HlyE_IgG,None,sees_npl_18,2193.89 -87,1,y1,HlyE_IgG,None,sees_npl_18,2193.89 -88,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -89,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -90,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -91,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -92,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -93,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -94,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -95,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -96,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -97,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -98,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -99,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -100,1,y1,HlyE_IgG,None,sees_npl_18,2441.12 -1,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -2,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -3,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -4,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -5,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -6,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -7,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -8,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -9,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -10,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -11,2,y1,HlyE_IgG,None,sees_npl_18,1099.35 -12,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -13,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -14,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -15,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -16,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -17,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -18,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -19,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -20,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -21,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -22,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -23,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -24,2,y1,HlyE_IgG,None,sees_npl_18,1084.13 -25,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -26,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -27,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -28,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -29,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -30,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -31,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -32,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -33,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -34,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -35,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -36,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -37,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -38,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -39,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -40,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -41,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -42,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -43,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -44,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -45,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -46,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -47,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -48,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -49,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -50,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -51,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -52,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -53,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -54,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -55,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -56,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -57,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -58,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -59,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -60,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -61,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -62,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -63,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -64,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -65,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -66,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -67,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -68,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -69,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -70,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -71,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -72,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -73,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -74,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -75,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -76,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -77,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -78,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -79,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -80,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -81,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -82,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -83,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -84,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -85,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -86,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -87,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -88,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -89,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -90,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -91,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -92,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -93,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -94,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -95,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -96,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -97,2,y1,HlyE_IgG,None,sees_npl_18,1581.92 -98,2,y1,HlyE_IgG,None,sees_npl_18,344.47 -99,2,y1,HlyE_IgG,None,sees_npl_18,344.47 -100,2,y1,HlyE_IgG,None,sees_npl_18,344.47 -1,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -2,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -3,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -4,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -5,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -6,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -7,1,y1,HlyE_IgA,None,sees_npl_19,1099.35 -8,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -9,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -10,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -11,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -12,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -13,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -14,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -15,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -16,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -17,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -18,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -19,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -20,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -21,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -22,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -23,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -24,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -25,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -26,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -27,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -28,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -29,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -30,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -31,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -32,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -33,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -34,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -35,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -36,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -37,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -38,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -39,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -40,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -41,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -42,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -43,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -44,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -45,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -46,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -47,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -48,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -49,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -50,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -51,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -52,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -53,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -54,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -55,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -56,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -57,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -58,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -59,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -60,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -61,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -62,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -63,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -64,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -65,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -66,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -67,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -68,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -69,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -70,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -71,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -72,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -73,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -74,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -75,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -76,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -77,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -78,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -79,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -80,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -81,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -82,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -83,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -84,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -85,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -86,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -87,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -88,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -89,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -90,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -91,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -92,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -93,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -94,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -95,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -96,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -97,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -98,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -99,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -100,1,y1,HlyE_IgA,None,sees_npl_19,573.114 -1,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -2,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -3,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -4,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -5,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -6,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -7,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -8,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -9,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -10,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -11,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -12,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -13,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -14,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -15,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -16,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -17,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -18,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -19,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -20,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -21,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -22,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -23,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -24,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -25,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -26,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -27,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -28,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -29,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -30,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -31,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -32,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -33,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -34,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -35,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -36,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -37,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -38,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -39,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -40,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -41,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -42,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -43,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -44,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -45,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -46,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -47,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -48,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -49,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -50,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -51,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -52,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -53,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -54,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -55,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -56,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -57,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -58,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -59,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -60,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -61,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -62,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -63,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -64,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -65,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -66,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -67,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -68,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -69,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -70,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -71,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -72,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -73,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -74,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -75,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -76,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -77,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -78,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -79,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -80,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -81,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -82,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -83,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -84,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -85,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -86,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -87,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -88,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -89,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -90,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -91,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -92,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -93,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -94,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -95,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -96,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -97,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -98,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -99,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -100,2,y1,HlyE_IgA,None,sees_npl_19,1099.35 -1,1,y1,HlyE_IgG,None,sees_npl_19,1099.35 -2,1,y1,HlyE_IgG,None,sees_npl_19,1099.35 -3,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -4,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -5,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -6,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -7,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -8,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -9,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -10,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -11,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -12,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -13,1,y1,HlyE_IgG,None,sees_npl_19,1479.96 -14,1,y1,HlyE_IgG,None,sees_npl_19,1806.93 -15,1,y1,HlyE_IgG,None,sees_npl_19,1806.93 -16,1,y1,HlyE_IgG,None,sees_npl_19,1806.93 -17,1,y1,HlyE_IgG,None,sees_npl_19,1806.93 -18,1,y1,HlyE_IgG,None,sees_npl_19,1806.93 -19,1,y1,HlyE_IgG,None,sees_npl_19,1806.93 -20,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -21,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -22,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -23,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -24,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -25,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -26,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -27,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -28,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -29,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -30,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -31,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -32,1,y1,HlyE_IgG,None,sees_npl_19,1312.76 -33,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -34,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -35,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -36,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -37,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -38,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -39,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -40,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -41,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -42,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -43,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -44,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -45,1,y1,HlyE_IgG,None,sees_npl_19,5271.74 -46,1,y1,HlyE_IgG,None,sees_npl_19,5086.68 -47,1,y1,HlyE_IgG,None,sees_npl_19,5086.68 -48,1,y1,HlyE_IgG,None,sees_npl_19,5086.68 -49,1,y1,HlyE_IgG,None,sees_npl_19,5086.68 -50,1,y1,HlyE_IgG,None,sees_npl_19,5086.68 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-15,1,y1,HlyE_IgG,None,sees_npl_23,123.551 -16,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -17,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -18,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -19,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -20,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -21,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -22,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -23,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -24,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -25,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -26,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -27,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -28,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -29,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -30,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -31,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -32,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -33,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -34,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -35,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -36,1,y1,HlyE_IgG,None,sees_npl_23,223.896 -37,1,y1,HlyE_IgG,None,sees_npl_23,223.896 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-47,1,y1,HlyE_IgG,None,sees_npl_45,3603.82 -48,1,y1,HlyE_IgG,None,sees_npl_45,3603.82 -49,1,y1,HlyE_IgG,None,sees_npl_45,3603.82 -50,1,y1,HlyE_IgG,None,sees_npl_45,1119.32 -51,1,y1,HlyE_IgG,None,sees_npl_45,1119.32 -52,1,y1,HlyE_IgG,None,sees_npl_45,1119.32 -53,1,y1,HlyE_IgG,None,sees_npl_45,1119.32 -54,1,y1,HlyE_IgG,None,sees_npl_45,1119.32 -55,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -56,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -57,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -58,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -59,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -60,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -61,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -62,1,y1,HlyE_IgG,None,sees_npl_45,753.106 -63,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -64,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -65,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -66,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -67,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -68,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -69,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -70,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -71,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -72,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -73,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -74,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -75,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -76,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -77,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -78,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -79,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -80,1,y1,HlyE_IgG,None,sees_npl_45,304.19 -81,1,y1,HlyE_IgG,None,sees_npl_45,332.241 -82,1,y1,HlyE_IgG,None,sees_npl_45,332.241 -83,1,y1,HlyE_IgG,None,sees_npl_45,332.241 -84,1,y1,HlyE_IgG,None,sees_npl_45,332.241 -85,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -86,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -87,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -88,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -89,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -90,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -91,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -92,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -93,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -94,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -95,1,y1,HlyE_IgG,None,sees_npl_45,579.968 -96,1,y1,HlyE_IgG,None,sees_npl_45,430.81 -97,1,y1,HlyE_IgG,None,sees_npl_45,430.81 -98,1,y1,HlyE_IgG,None,sees_npl_45,430.81 -99,1,y1,HlyE_IgG,None,sees_npl_45,430.81 -100,1,y1,HlyE_IgG,None,sees_npl_45,430.81 -1,2,y1,HlyE_IgG,None,sees_npl_45,1099.35 -2,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -3,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -4,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -5,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -6,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -7,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -8,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -9,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -10,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -11,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -12,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -13,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -14,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -15,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -16,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -17,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -18,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -19,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -20,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -21,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -22,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -23,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -24,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -25,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -26,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -27,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -28,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -29,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -30,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -31,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -32,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -33,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -34,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -35,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -36,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -37,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -38,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -39,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -40,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -41,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -42,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -43,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -44,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -45,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -46,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -47,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -48,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -49,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -50,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -51,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -52,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -53,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -54,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -55,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -56,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -57,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -58,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -59,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -60,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -61,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -62,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -63,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -64,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -65,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -66,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -67,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -68,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -69,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -70,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -71,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -72,2,y1,HlyE_IgG,None,sees_npl_45,616.596 -73,2,y1,HlyE_IgG,None,sees_npl_45,441.733 -74,2,y1,HlyE_IgG,None,sees_npl_45,441.733 -75,2,y1,HlyE_IgG,None,sees_npl_45,441.733 -76,2,y1,HlyE_IgG,None,sees_npl_45,441.733 -77,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -78,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -79,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -80,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -81,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -82,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -83,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -84,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -85,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -86,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -87,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -88,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -89,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -90,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -91,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -92,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -93,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -94,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -95,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -96,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -97,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -98,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -99,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -100,2,y1,HlyE_IgG,None,sees_npl_45,768.254 -1,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 -2,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 -3,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 -4,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 -5,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 -6,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 -7,1,y1,HlyE_IgA,None,sees_npl_46,2353.74 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-64,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -65,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -66,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -67,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -68,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -69,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -70,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -71,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -72,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -73,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -74,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -75,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -76,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -77,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -78,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -79,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -80,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -81,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -82,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -83,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -84,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -85,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -86,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -87,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -88,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -89,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -90,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -91,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -92,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -93,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -94,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -95,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -96,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -97,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -98,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -99,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -100,1,y1,HlyE_IgA,None,sees_npl_114,1099.35 -1,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -2,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -3,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -4,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -5,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -6,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -7,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -8,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -9,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -10,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -11,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -12,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -13,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -14,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -15,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -16,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -17,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -18,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -19,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -20,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -21,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -22,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -23,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -24,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -25,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -26,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -27,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -28,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -29,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -30,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -31,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -32,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -33,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -34,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -35,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -36,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -37,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -38,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -39,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -40,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -41,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -42,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -43,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -44,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -45,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -46,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -47,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -48,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -49,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -50,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -51,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -52,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -53,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -54,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -55,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -56,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -57,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -58,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -59,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -60,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -61,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -62,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -63,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -64,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -65,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -66,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -67,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -68,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -69,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -70,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -71,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -72,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -73,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -74,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -75,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -76,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -77,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -78,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -79,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -80,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -81,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -82,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -83,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -84,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -85,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -86,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -87,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -88,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -89,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -90,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -91,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -92,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -93,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -94,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -95,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -96,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -97,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -98,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -99,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -100,2,y1,HlyE_IgA,None,sees_npl_114,1099.35 -1,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -2,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -3,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -4,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -5,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -6,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -7,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -8,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -9,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -10,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -11,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -12,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -13,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -14,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -15,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -16,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -17,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -18,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -19,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -20,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -21,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -22,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -23,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -24,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -25,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -26,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -27,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -28,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -29,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -30,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -31,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -32,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -33,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -34,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -35,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -36,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -37,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -38,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 -39,1,y1,HlyE_IgG,None,sees_npl_114,1099.35 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-86,2,y1,HlyE_IgG,None,newperson,718.03 -87,2,y1,HlyE_IgG,None,newperson,431.711 -88,2,y1,HlyE_IgG,None,newperson,19513.9 -89,2,y1,HlyE_IgG,None,newperson,2637.58 -90,2,y1,HlyE_IgG,None,newperson,3631.18 -91,2,y1,HlyE_IgG,None,newperson,751.65 -92,2,y1,HlyE_IgG,None,newperson,458.362 -93,2,y1,HlyE_IgG,None,newperson,134.765 -94,2,y1,HlyE_IgG,None,newperson,149.461 -95,2,y1,HlyE_IgG,None,newperson,253.166 -96,2,y1,HlyE_IgG,None,newperson,1287.99 -97,2,y1,HlyE_IgG,None,newperson,1762.17 -98,2,y1,HlyE_IgG,None,newperson,562.91 -99,2,y1,HlyE_IgG,None,newperson,545.354 -100,2,y1,HlyE_IgG,None,newperson,399.049 diff --git a/tests/testthat/_snaps/run_mod/popparam-nostrat-summary-stats.csv b/tests/testthat/_snaps/run_mod/popparam-nostrat-summary-stats.csv new file mode 100644 index 000000000..7b75f3adb --- /dev/null +++ b/tests/testthat/_snaps/run_mod/popparam-nostrat-summary-stats.csv @@ -0,0 +1,32 @@ +Parameter,mean,sd +log(alpha),-4.36295,0.322479 +"log(alpha), log(alpha)",5.66746,2.43334 +"log(alpha), log(shape - 1)",-1.49385,2.82031 +"log(alpha), log(t1)",2.17162,2.44217 +"log(alpha), log(y0)",-0.831427,1.96462 +"log(alpha), log(y1 - y0)",-0.103803,0.3206 +log(shape - 1),-1.12482,0.128093 +"log(shape - 1), log(alpha)",-1.49385,2.82031 +"log(shape - 1), log(shape - 1)",28.6476,16.8063 +"log(shape - 1), log(t1)",0.278906,7.1988 +"log(shape - 1), log(y0)",-6.14469,5.60768 +"log(shape - 1), log(y1 - y0)",-0.952284,1.64387 +log(t1),1.0439,0.0377371 +"log(t1), log(alpha)",2.17162,2.44217 +"log(t1), log(shape - 1)",0.278906,7.1988 +"log(t1), log(t1)",28.6348,22.4761 +"log(t1), log(y0)",-1.21827,9.45396 +"log(t1), log(y1 - y0)",-0.619606,0.977868 +log(y0),0.969232,0.0422494 +"log(y0), log(alpha)",-0.831427,1.96462 +"log(y0), log(shape - 1)",-6.14469,5.60768 +"log(y0), log(t1)",-1.21827,9.45396 +"log(y0), log(y0)",36.7869,19.762 +"log(y0), log(y1 - y0)",-0.805015,0.843427 +log(y1 - y0),6.91882,0.145896 +"log(y1 - y0), log(alpha)",-0.103803,0.3206 +"log(y1 - y0), log(shape - 1)",-0.952284,1.64387 +"log(y1 - y0), log(t1)",-0.619606,0.977868 +"log(y1 - y0), log(y0)",-0.805015,0.843427 +"log(y1 - y0), log(y1 - y0)",1.81331,0.694315 +prec.logy,0.204595,0.0971737 diff --git a/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv b/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv index 189765454..2750def14 100644 --- a/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv +++ b/tests/testthat/_snaps/run_mod/popparam-summary-stats.csv @@ -1,31 +1,32 @@ Parameter,mean,sd -alpha,-4.73607,0.219781 -"alpha, alpha",2.76907,0.688682 -"alpha, shape",-0.383234,0.533813 -"alpha, t1",0.448772,1.57899 -"alpha, y0",0.700184,0.757452 -"alpha, y1",-0.0212652,0.222195 -shape,-0.681647,0.0690278 -"shape, alpha",-0.383234,0.533813 -"shape, shape",6.58223,2.3041 -"shape, t1",0.914755,2.42633 -"shape, y0",-2.45229,1.61395 -"shape, y1",-0.877117,0.319837 -t1,0.591297,0.100501 -"t1, alpha",0.448772,1.57899 -"t1, shape",0.914755,2.42633 -"t1, t1",20.3291,6.01563 -"t1, y0",3.25694,6.00627 -"t1, y1",0.0188795,0.473277 -y0,0.726466,0.0841371 -"y0, alpha",0.700184,0.757452 -"y0, shape",-2.45229,1.61395 -"y0, t1",3.25694,6.00627 -"y0, y0",13.2226,7.023 -"y0, y1",0.220216,0.552936 -y1,5.7489,0.348058 -"y1, alpha",-0.0212652,0.222195 -"y1, shape",-0.877117,0.319837 -"y1, t1",0.0188795,0.473277 -"y1, y0",0.220216,0.552936 -"y1, y1",0.681022,0.11074 +log(alpha),-4.73607,0.219781 +"log(alpha), log(alpha)",2.76907,0.688682 +"log(alpha), log(shape - 1)",-0.383234,0.533813 +"log(alpha), log(t1)",0.448772,1.57899 +"log(alpha), log(y0)",0.700184,0.757452 +"log(alpha), log(y1 - y0)",-0.0212652,0.222195 +log(shape - 1),-0.681647,0.0690278 +"log(shape - 1), log(alpha)",-0.383234,0.533813 +"log(shape - 1), log(shape - 1)",6.58223,2.3041 +"log(shape - 1), log(t1)",0.914755,2.42633 +"log(shape - 1), log(y0)",-2.45229,1.61395 +"log(shape - 1), log(y1 - y0)",-0.877117,0.319837 +log(t1),0.591297,0.100501 +"log(t1), log(alpha)",0.448772,1.57899 +"log(t1), log(shape - 1)",0.914755,2.42633 +"log(t1), log(t1)",20.3291,6.01563 +"log(t1), log(y0)",3.25694,6.00627 +"log(t1), log(y1 - y0)",0.0188795,0.473277 +log(y0),0.726466,0.0841371 +"log(y0), log(alpha)",0.700184,0.757452 +"log(y0), log(shape - 1)",-2.45229,1.61395 +"log(y0), log(t1)",3.25694,6.00627 +"log(y0), log(y0)",13.2226,7.023 +"log(y0), log(y1 - y0)",0.220216,0.552936 +log(y1 - y0),5.7489,0.348058 +"log(y1 - y0), log(alpha)",-0.0212652,0.222195 +"log(y1 - y0), log(shape - 1)",-0.877117,0.319837 +"log(y1 - y0), log(t1)",0.0188795,0.473277 +"log(y1 - y0), log(y0)",0.220216,0.552936 +"log(y1 - y0), log(y1 - y0)",0.681022,0.11074 +prec.logy,1.71057,0.432721 diff --git a/tests/testthat/test-as_case_data.R b/tests/testthat/test-as_case_data.R index 018fff478..7de8fd2c5 100644 --- a/tests/testthat/test-as_case_data.R +++ b/tests/testthat/test-as_case_data.R @@ -9,7 +9,7 @@ test_that( sim_case_data(n = 5) } ) - + test_obj <- test_obj |> as_case_data( id_var = "id", @@ -17,7 +17,7 @@ test_that( time_in_days = "timeindays", value_var = "value" ) - + test_obj |> attributes() |> rlist::list.remove("row.names") |> diff --git a/tests/testthat/test-internal-popparams.R b/tests/testthat/test-internal-popparams.R index bbcdfb113..3bfa329fe 100644 --- a/tests/testthat/test-internal-popparams.R +++ b/tests/testthat/test-internal-popparams.R @@ -1,19 +1,21 @@ test_that("param_recode correctly recodes parameter indices", { # Test valid parameter indices - expect_equal(serodynamics:::param_recode("1"), "y0") - expect_equal(serodynamics:::param_recode("2"), "y1") - expect_equal(serodynamics:::param_recode("3"), "t1") - expect_equal(serodynamics:::param_recode("4"), "alpha") - expect_equal(serodynamics:::param_recode("5"), "shape") + expect_equal(serodynamics:::param_recode("1"), "log(y0)") + expect_equal(serodynamics:::param_recode("2"), "log(y1 - y0)") + expect_equal(serodynamics:::param_recode("3"), "log(t1)") + expect_equal(serodynamics:::param_recode("4"), "log(alpha)") + expect_equal(serodynamics:::param_recode("5"), "log(shape - 1)") # Test vector of valid indices expect_equal( serodynamics:::param_recode(c("1", "2", "3", "4", "5")), - c("y0", "y1", "t1", "alpha", "shape") + c("log(y0)", "log(y1 - y0)", "log(t1)", + "log(alpha)", "log(shape - 1)") ) }) test_that("unpack_jags handles factor Parameter column", { + withr::local_seed(42) # Create a simple ggs-like object with factor Parameter column test_data <- tibble::tibble( Iteration = rep(1:5, 3), @@ -33,6 +35,7 @@ test_that("unpack_jags handles factor Parameter column", { }) test_that("unpack_jags correctly unpacks mu.par parameters", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = rep(1:3, 2), Chain = rep(1, 6), @@ -50,10 +53,12 @@ test_that("unpack_jags correctly unpacks mu.par parameters", { expect_true("mu.par" %in% result$Subject) # Check Param is correctly decoded - expect_true(all(mu_rows$Param %in% c("y0", "y1", "t1", "alpha", "shape"))) + expect_true(all(mu_rows$Param %in% c("log(y0)", "log(y1 - y0)", "log(t1)", + "log(alpha)", "log(shape - 1)"))) }) test_that("unpack_jags correctly unpacks prec.par parameters", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = rep(1:3, 2), Chain = rep(1, 6), @@ -75,6 +80,7 @@ test_that("unpack_jags correctly unpacks prec.par parameters", { }) test_that("unpack_jags correctly unpacks prec.logy parameters", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = rep(1:3, 2), Chain = rep(1, 6), @@ -92,7 +98,24 @@ test_that("unpack_jags correctly unpacks prec.logy parameters", { expect_true("prec.logy" %in% result$Subject) }) +test_that("unpack_jags correctly unpacks scalar prec.logy parameters", { + withr::local_seed(42) + test_data <- tibble::tibble( + Iteration = 1:3, + Chain = rep(1, 3), + Parameter = rep("prec.logy", 3), + value = rnorm(3) + ) + + result <- serodynamics:::unpack_jags(test_data) + + expect_true(all(result$Subject == "prec.logy")) + expect_true(all(result$Subnum == "1")) + expect_true(all(result$Param == "prec.logy")) +}) + test_that("unpack_jags correctly unpacks individual-level parameters", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = rep(1:3, 2), Chain = rep(1, 6), @@ -108,12 +131,14 @@ test_that("unpack_jags correctly unpacks individual-level parameters", { }) test_that("prep_popparams filters to population parameters only", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = 1:10, Chain = rep(1, 10), Parameter = rep(c("y0", "mu.par"), each = 5), Subject = rep(c("1", "mu.par"), each = 5), - value = rnorm(10) + value = rnorm(10), + .is_population_parameter = rep(c(FALSE, TRUE), each = 5) ) result <- serodynamics:::prep_popparams(test_data) @@ -126,17 +151,22 @@ test_that("prep_popparams filters to population parameters only", { expect_true("Population_Parameter" %in% names(result)) expect_false("Subject" %in% names(result)) + # .is_population_parameter column should be removed + expect_false(".is_population_parameter" %in% names(result)) + # Should have 5 rows (only mu.par rows) expect_equal(nrow(result), 5) }) test_that("ex_popparams excludes population parameters", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = 1:10, Chain = rep(1, 10), Parameter = rep(c("y0", "mu.par"), each = 5), Subject = rep(c("1", "mu.par"), each = 5), - value = rnorm(10) + value = rnorm(10), + .is_population_parameter = rep(c(FALSE, TRUE), each = 5) ) result <- serodynamics:::ex_popparams(test_data) @@ -147,27 +177,106 @@ test_that("ex_popparams excludes population parameters", { # Should have 5 rows (only y0 rows) expect_equal(nrow(result), 5) - # Should keep original structure - expect_equal(names(result), names(test_data)) + # .is_population_parameter column should be removed + expect_false(".is_population_parameter" %in% names(result)) +}) + +test_that("preclogy_per_iso relabels prec.logy Parameter by Iso_type", { + withr::local_seed(42) + # Simulate the data shape that exists in Run_Mod.R after the iso_dat join + # but before the rename of Param → Parameter. + mock_unpacked <- tibble::tibble( + Iteration = rep(1:3, 4), + Chain = 1L, + Param = c( + rep("prec.logy", 3), rep("prec.logy", 3), + rep("y0", 3), rep("y0", 3) + ), + Subject = c( + rep("prec.logy", 3), rep("prec.logy", 3), + rep("1", 3), rep("2", 3) + ), + Iso_type = c( + rep("HlyE_IgA", 3), rep("HlyE_IgG", 3), + rep("HlyE_IgA", 3), rep("HlyE_IgA", 3) + ), + value = rnorm(12), + .is_population_parameter = c(rep(TRUE, 6), rep(FALSE, 6)) + ) + + # Apply the preclogy_per_iso transformation via the extracted helper + result <- serodynamics:::relabel_preclogy_iso(mock_unpacked) + + preclogy_rows <- result[result$.is_population_parameter, ] + # Each prec.logy row should now carry its isotype as the Param label + expect_setequal(unique(preclogy_rows$Param), c("HlyE_IgA", "HlyE_IgG")) + + # Individual-level rows are unchanged + ind_rows <- result[!result$.is_population_parameter, ] + expect_true(all(ind_rows$Param == "y0")) }) test_that("prep_popparams and ex_popparams are complementary", { + withr::local_seed(42) test_data <- tibble::tibble( Iteration = rep(1:5, 4), Chain = rep(1, 20), Parameter = rep(c("y0", "mu.par", "prec.par", "prec.logy"), each = 5), Subject = rep(c("1", "mu.par", "prec.par", "prec.logy"), each = 5), - value = rnorm(20) + value = rnorm(20), + .is_population_parameter = rep(c(FALSE, TRUE, TRUE, TRUE), each = 5) ) pop_params <- serodynamics:::prep_popparams(test_data) individual_params <- serodynamics:::ex_popparams(test_data) - + # Together they should account for all rows expect_equal(nrow(pop_params) + nrow(individual_params), nrow(test_data)) - + # No overlap in subjects # Note: pop_params has Population_Parameter column, not Subject - expect_false(any(individual_params$Subject %in% + expect_false(any(individual_params$Subject %in% c("mu.par", "prec.par", "prec.logy"))) }) + +test_that("prep_strat_list returns 'None' when strat is NA", { + data <- tibble::tibble(x = 1:3, grp = c("a", "b", "a")) + expect_equal(serodynamics:::prep_strat_list(data, NA), "None") +}) + +test_that("prep_strat_list returns character labels for factor columns", { + # Factor columns must iterate over labels, not the underlying integer codes + data <- tibble::tibble(x = 1:4, grp = factor(c("b", "a", "b", "a"))) + result <- serodynamics:::prep_strat_list(data, "grp") + expect_type(result, "character") + expect_setequal(result, c("a", "b")) +}) + +test_that("prep_strat_list aborts when the strat column is missing", { + data <- tibble::tibble(x = 1:3, grp = c("a", "b", "a")) + expect_error( + serodynamics:::prep_strat_list(data, "not_a_column"), + "was not found" + ) +}) + +test_that("prep_strat_list aborts when no non-missing strata remain", { + data <- tibble::tibble( + x = 1:3, + grp = c(NA_character_, NA_character_, NA_character_) + ) + expect_error( + suppressWarnings(serodynamics:::prep_strat_list(data, "grp")), + "no non-missing values" + ) +}) + +test_that("prep_strat_list warns about and drops missing stratum values", { + data <- tibble::tibble(x = 1:3, grp = c("a", NA, "b")) + expect_warning( + result <- serodynamics:::prep_strat_list(data, "grp"), + "missing" + ) + expect_setequal(result, c("a", "b")) + expect_false(anyNA(result)) +}) diff --git a/tests/testthat/test-run_mod.R b/tests/testthat/test-run_mod.R index 891869406..074fefde4 100644 --- a/tests/testthat/test-run_mod.R +++ b/tests/testthat/test-run_mod.R @@ -16,7 +16,7 @@ test_that( dataset <- dplyr::bind_rows(strat1, strat2) results <- run_mod( data = dataset, # The data set input - file_mod = fs::path_package("serodynamics", "extdata/model.jags"), + file_mod = serodynamics_example("model.jags"), nchain = 2, # Number of mcmc chains to run nadapt = 100, # Number of adaptations to run nburn = 100, # Number of unrecorded samples before sampling begins @@ -33,21 +33,20 @@ test_that( variant = darwin_variant() ) + # Testing exact order of attributes + expect_equal(names(attributes(results))[1:3], + c("names", "row.names", "class")) + # Testing attributes results |> attributes() |> names() |> expect_setequal(c("names", "row.names", "class", "nChains", "nParameters", "nIterations", "nBurnin", "nThin", - "description", "population_params", "priors", + "population_params", "priors", "fitted_residuals")) - # Verify class appears immediately after names and row.names - expect_equal( - names(attributes(results))[1:3], - c("names", "row.names", "class") - ) - + attributes(results)$fitted_residuals |> expect_snapshot_data( "sim-strat-fitted_residuals", @@ -66,6 +65,15 @@ test_that( expect_snapshot_data("popparam-summary-stats", variant = darwin_variant() ) + pop_params <- attributes(results)$population_params + expect_s3_class(pop_params, "data.frame") + expect_true(all(c("Population_Parameter", "value") %in% names(pop_params))) + + expect_setequal( + unique(pop_params$Population_Parameter), + c("mu.par", "prec.par", "prec.logy") + ) + expect_true(all(is.finite(pop_params$value))) } ) @@ -90,10 +98,13 @@ test_that( ) |> suppressWarnings() + # Testing attributes results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals")) |> - expect_snapshot_value(style = "deparse") + names() |> + expect_setequal(c("names", "row.names", "class", "nChains", "nParameters", + "nIterations", "nBurnin", "nThin", "priors", + "fitted_residuals")) results |> expect_snapshot_data( @@ -106,15 +117,18 @@ test_that( "strat-fitted_residuals", variant = darwin_variant() ) - + expect_null(attr(results, "population_params")) } ) test_that( - desc = "results are consistent with unstratified SEES data", + desc = "results are consistent with unstratified SEES data with population + parameters", code = { announce_snapshot_file("nostrat-curve-params.csv") announce_snapshot_file("nostrat-fitted_residuals.csv") + announce_snapshot_file("popparam-nostrat-summary-stats.csv") + withr::local_seed(1) dataset <- serodynamics::nepal_sees @@ -126,14 +140,18 @@ test_that( nburn = 10, # Number of unrecorded samples before sampling begins nmc = 100, niter = 100, # Number of iterations - strat = NA # Variable to be stratified + strat = NA, # Variable to be stratified + with_pop_params = TRUE ) |> suppressWarnings() + # Testing attributes results |> attributes() |> - rlist::list.remove(c("row.names", "fitted_residuals")) |> - expect_snapshot_value(style = "deparse") + names() |> + expect_setequal(c("names", "row.names", "class", "nChains", "nParameters", + "nIterations", "nBurnin", "nThin", "population_params", + "priors", "fitted_residuals")) results |> expect_snapshot_data( @@ -146,41 +164,60 @@ test_that( "nostrat-fitted_residuals", variant = darwin_variant() ) + + # Testing for population parameters + attributes(results)$population_params |> + dplyr::group_by(Parameter) |> + dplyr::summarise( + mean = mean(value), + sd = sd(value), + .groups = "drop" + ) |> + dplyr::arrange(Parameter) |> + expect_snapshot_data( + "popparam-nostrat-summary-stats", + variant = darwin_variant() + ) } ) test_that( - desc = "results are consistent with unstratified SEES data with jags.post - included", + desc = "preclogy_per_iso relabels prec.logy Parameter by isotype in run_mod", code = { - announce_snapshot_file("nostrat-curve-params-withpost.csv") withr::local_seed(1) - dataset <- serodynamics::nepal_sees - - results <- run_mod( - data = dataset, # The data set input - file_mod = serodynamics_example("model.jags"), - nchain = 2, # Number of mcmc chains to run - nadapt = 10, # Number of adaptations to run - nburn = 10, # Number of unrecorded samples before sampling begins - nmc = 100, - niter = 100, # Number of iterations - strat = NA, # Variable to be stratified - with_post = TRUE - ) |> - suppressWarnings() + dataset <- serodynamics::nepal_sees - results |> - expect_snapshot_data( - "nostrat-curve-params-withpost", - variant = darwin_variant() + results <- suppressWarnings( + run_mod( + data = dataset, + file_mod = serodynamics_example("model.jags"), + nchain = 2, + nadapt = 10, + nburn = 10, + nmc = 100, + niter = 100, + strat = NA, + with_pop_params = TRUE, + preclogy_per_iso = TRUE ) + ) + + pop_params <- attr(results, "population_params") + expect_s3_class(pop_params, "data.frame") + + preclogy_row <- pop_params[pop_params$Population_Parameter == "prec.logy", ] + expect_gt(nrow(preclogy_row), 0) + + # With preclogy_per_iso = TRUE, Parameter should be the isotype label, + # not the constant "prec.logy" + expect_false(all(preclogy_row$Parameter == "prec.logy")) + expect_true(all(preclogy_row$Parameter %in% unique(pop_params$Iso_type))) } ) test_that( - desc = "results are consistent with unstratified SEES data with modified - priors", + desc = "results are consistent with unstratified SEES data with modified + priors and post", code = { announce_snapshot_file("nostrat-curve-params-specpriors.csv") withr::local_seed(1) @@ -195,6 +232,7 @@ test_that( nmc = 100, niter = 100, # Number of iterations strat = NA, # Variable to be stratified + with_post = TRUE, mu_hyp_param = c(1, 4, 1, -3, -1), prec_hyp_param = c(0.01, 0.0001, 0.01, 0.001, 0.01), omega_param = c(1, 20, 1, 10, 1), @@ -209,5 +247,10 @@ test_that( variant = darwin_variant() ) + jags_post <- attributes(results)$jags.post + expect_false(is.null(jags_post)) + expect_type(jags_post, "list") + expect_true("None" %in% names(jags_post)) + expect_s3_class(jags_post$None$mcmc, "mcmc.list") } ) From b88afeead94e502562d94ca34acc5f3b879d761c Mon Sep 17 00:00:00 2001 From: sschildhauer <sschildhauer@ucdavis.edu> Date: Fri, 29 May 2026 14:26:40 -0700 Subject: [PATCH 10/15] Merging with main --- R/prep_popparams.R | 15 ++++++++------- man/ex_popparams.Rd | 4 ---- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/R/prep_popparams.R b/R/prep_popparams.R index 8ecb6751b..d41cc3f60 100644 --- a/R/prep_popparams.R +++ b/R/prep_popparams.R @@ -3,13 +3,14 @@ #' @description #' `prep_popparams` filters a [data.frame] to only include population #' parameters and renames the `Subject` variable as `Population_Parameter`. -#' @param x A [data.frame] with a `Subject` variable. +#' @param x A [data.frame] with `Subject` and `.is_population_parameter` +#' variables. #' @returns A filtered [data.frame] with the `Subject` variable renamed to #' `Population_Parameter`. #' @keywords internal -prep_popparams <- function(x) { - x <- x |> - dplyr::filter(.data$Subject %in% c("mu.par", "prec.par", "prec.logy")) |> - dplyr::rename(Population_Parameter = "Subject") - return(x) -} +prep_popparams <- function(x) { + x |> + dplyr::filter(.data$.is_population_parameter) |> + dplyr::rename("Population_Parameter" = "Subject") |> + dplyr::select(-c(".is_population_parameter")) +} diff --git a/man/ex_popparams.Rd b/man/ex_popparams.Rd index 62d09b8c7..15c3f3011 100644 --- a/man/ex_popparams.Rd +++ b/man/ex_popparams.Rd @@ -7,11 +7,7 @@ ex_popparams(x) } \arguments{ -<<<<<<< HEAD -\item{x}{A \link{data.frame} with a \code{Subject} variable.} -======= \item{x}{A \link{data.frame} with a \code{.is_population_parameter} variable.} ->>>>>>> ba9ae9868709bb0b019067d1304c63f2dd15a4c9 } \value{ A filtered \link{data.frame} excluding population parameters. From 96e06239fd6c53c9dfe2b3069ab4b57a88164800 Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Sat, 30 May 2026 18:00:55 +0000 Subject: [PATCH 11/15] fix: address failing CI checks - bump version 0.0.0.9055 -> 0.0.0.9056 to satisfy version-check - add Serodynamic/serodynamic to WORDLIST to clear spellcheck - add plot_serocurve to pkgdown reference index - update as_case_data r45 snapshot to match current attribute order Co-authored-by: Samuel Hisaji Schildhauer <sschildhauer@users.noreply.github.com> --- DESCRIPTION | 2 +- inst/WORDLIST | 2 ++ pkgdown/_pkgdown.yml | 3 +++ tests/testthat/_snaps/r45/as_case_data.md | 6 +++--- 4 files changed, 9 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e17794e0b..bdd312fea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9055 +Version: 0.0.0.9056 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), diff --git a/inst/WORDLIST b/inst/WORDLIST index 95895593c..f4b9d4fe9 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -70,4 +70,6 @@ unstratified vh wishdf SeRG +Serodynamic UCD +serodynamic diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 61c982025..1be0fa9df 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -36,6 +36,9 @@ reference: - plot_jags_trace - plot_jags_effect - plot_predicted_curve +- title: Visualize model results + contents: + - plot_serocurve - title: Postprocess JAGS output contents: - postprocess_jags_output diff --git a/tests/testthat/_snaps/r45/as_case_data.md b/tests/testthat/_snaps/r45/as_case_data.md index efd6396b1..44130b207 100644 --- a/tests/testthat/_snaps/r45/as_case_data.md +++ b/tests/testthat/_snaps/r45/as_case_data.md @@ -1,9 +1,9 @@ # results are consistent with simulated data list(names = c("id", "visit_num", "timeindays", "iter", "antigen_iso", - "y0", "y1", "t1", "alpha", "r", "value"), id_var = "id", biomarker_var = "antigen_iso", - timeindays = "timeindays", value_var = "value", class = c("case_data", - "tbl_df", "tbl", "data.frame")) + "y0", "y1", "t1", "alpha", "r", "value"), class = c("case_data", + "tbl_df", "tbl", "data.frame"), id_var = "id", biomarker_var = "antigen_iso", + timeindays = "timeindays", value_var = "value") # results are consistent with SEES data From edc91ce933ebd23b7fcfc916fedff6be025e6071 Mon Sep 17 00:00:00 2001 From: sschildhauer <sschildhauer@ucdavis.edu> Date: Mon, 1 Jun 2026 14:19:13 -0700 Subject: [PATCH 12/15] Reverting as_case_data --- R/as_case_data.R | 26 ++++++-------------------- 1 file changed, 6 insertions(+), 20 deletions(-) diff --git a/R/as_case_data.R b/R/as_case_data.R index 80dfbffb1..eb55b1409 100644 --- a/R/as_case_data.R +++ b/R/as_case_data.R @@ -51,24 +51,10 @@ as_case_data <- function( visit_num = dplyr::row_number() ) |> serocalculator::set_id_var(id_var) |> - (\(x) { - current_atts <- attributes(x) - # Explicitly order attributes so that class comes immediately after - # names and row.names, which is the expected position for tibble - # subclasses. tibble::as_tibble() on a subclass can reorder - # standard attributes, so we rebuild them in the correct order. - # Use current_atts$id_var to preserve any standardization done by - # serocalculator::set_id_var (e.g., renaming the ID column to "id"). - new_atts <- list( - names = current_atts$names, - row.names = current_atts$row.names, - class = union("case_data", class(data)), - id_var = current_atts$id_var, - biomarker_var = biomarker_var, - timeindays = time_in_days, - value_var = value_var - ) - attributes(x) <- new_atts - x - })() + structure( + class = union("case_data", class(data)), + biomarker_var = biomarker_var, + timeindays = time_in_days, + value_var = value_var + ) } From bf221e279ad1cfb7e9ffb3c8581c7535eada8d66 Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 01:50:02 +0000 Subject: [PATCH 13/15] test: sync r45 as_case_data snapshot with main The snapshot on this branch had `class` reordered to position 2, but main's snapshot keeps `class` last (matching the current as_case_data.R behavior). Aligning with main so the as_case_data test passes again. Co-authored-by: Samuel Hisaji Schildhauer <sschildhauer@users.noreply.github.com> --- tests/testthat/_snaps/r45/as_case_data.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/testthat/_snaps/r45/as_case_data.md b/tests/testthat/_snaps/r45/as_case_data.md index 44130b207..efd6396b1 100644 --- a/tests/testthat/_snaps/r45/as_case_data.md +++ b/tests/testthat/_snaps/r45/as_case_data.md @@ -1,9 +1,9 @@ # results are consistent with simulated data list(names = c("id", "visit_num", "timeindays", "iter", "antigen_iso", - "y0", "y1", "t1", "alpha", "r", "value"), class = c("case_data", - "tbl_df", "tbl", "data.frame"), id_var = "id", biomarker_var = "antigen_iso", - timeindays = "timeindays", value_var = "value") + "y0", "y1", "t1", "alpha", "r", "value"), id_var = "id", biomarker_var = "antigen_iso", + timeindays = "timeindays", value_var = "value", class = c("case_data", + "tbl_df", "tbl", "data.frame")) # results are consistent with SEES data From 54d5fe770dc41901d8dd513cb6963db87453c240 Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 04:18:20 +0000 Subject: [PATCH 14/15] fix(plot_serocurve): suppress fill scale warning when show_ci = FALSE MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Move `scale_fill_manual()` inside an `if (show_ci)` guard so it is only added when a CI ribbon is actually drawn. Previously the fill scale was applied unconditionally for single-stratification plots, producing "No shared levels found between names(values) of the manual scale and the data's fill values" when show_ci was FALSE — which triggered an R CMD check failure on the `serocurve-population-no-ci` test. Co-authored-by: Samuel Hisaji Schildhauer <sschildhauer@users.noreply.github.com> --- R/plot_serocurve.R | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/R/plot_serocurve.R b/R/plot_serocurve.R index 44a203f48..1e19f823f 100644 --- a/R/plot_serocurve.R +++ b/R/plot_serocurve.R @@ -225,22 +225,26 @@ plot_serocurve <- function( color_vals <- c("median" = "red") color_labels <- c("median" = "Median") - fill_vals <- c("ci" = "red") - fill_labels <- c("ci" = "95% credible interval") - p <- p + ggplot2::scale_color_manual( name = "", values = color_vals, labels = color_labels, guide = ggplot2::guide_legend(override.aes = list(shape = NA)) - ) + - ggplot2::scale_fill_manual( - name = "", - values = fill_vals, - labels = fill_labels, - guide = ggplot2::guide_legend(override.aes = list(color = NA)) ) + + if (show_ci) { + fill_vals <- c("ci" = "red") + fill_labels <- c("ci" = "95% credible interval") + + p <- p + + ggplot2::scale_fill_manual( + name = "", + values = fill_vals, + labels = fill_labels, + guide = ggplot2::guide_legend(override.aes = list(color = NA)) + ) + } } # ---- Faceting ---------------------------------------------------------- From f543317c6f17c4cf8911be8234e9226d4daaec62 Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 18:09:24 +0000 Subject: [PATCH 15/15] refactor(plot_serocurve): apply review polish - Add empty-result guard for newperson param_source that errors with an actionable message when no newperson rows match the requested antigen- isotype/stratification, instead of silently producing an empty plot. - Clamp the tx time grid to xlim when supplied, avoiding unnecessary computation outside the visible range. - Lift duplicated antigen_iso_col assignment above the if/else. - Document the antigen_iso/strat default-source asymmetry (defaults come from the subject-level draws while population samples come from the population_params attribute). - Move plot_predicted_curve into the "Visualize model results" pkgdown reference section so plot_serocurve is no longer an orphaned entry. Co-authored-by: Samuel Hisaji Schildhauer <sschildhauer@users.noreply.github.com> --- R/plot_serocurve.R | 41 ++++++++++++++++++++++++++++++++++------- man/plot_serocurve.Rd | 8 ++++++-- pkgdown/_pkgdown.yml | 2 +- 3 files changed, 41 insertions(+), 10 deletions(-) diff --git a/R/plot_serocurve.R b/R/plot_serocurve.R index 1e19f823f..a10e3ddbe 100644 --- a/R/plot_serocurve.R +++ b/R/plot_serocurve.R @@ -8,9 +8,13 @@ #' #' @param model An `sr_model` object returned by [run_mod()]. #' @param antigen_iso A [character] vector of antigen-isotype combinations to -#' plot. Defaults to all antigen-isotypes present in `model`. +#' plot. Defaults to all antigen-isotypes present in the subject-level +#' draws of `model` (`model$Iso_type`); in normal usage these match the +#' levels available in `attr(model, "population_params")`. #' @param strat A [character] vector of stratification levels to include. -#' Defaults to all stratification levels present in `model`. +#' Defaults to all stratification levels present in the subject-level +#' draws of `model` (`model$Stratification`); in normal usage these match +#' the levels available in `attr(model, "population_params")`. #' @param param_source [character]; which posterior samples to use for the #' curve. Options: #' - `"population"` (default): uses population-level `mu.par` samples stored @@ -54,6 +58,8 @@ plot_serocurve <- function( param_source <- match.arg(param_source, c("population", "newperson")) + antigen_iso_col <- "Iso_type" + # ---- Retrieve posterior samples of curve parameters -------------------- if (param_source == "population") { pop_params <- attr(model, "population_params") @@ -104,16 +110,32 @@ plot_serocurve <- function( Iso_type = factor(.data$Iso_type), Stratification = factor(.data$Stratification) ) - antigen_iso_col <- "Iso_type" } else { # "newperson": predictive distribution for a new individual drawn from # the population-level prior - param_samples <- model |> + newperson_rows <- model |> dplyr::filter( .data$Subject == "newperson", .data$Iso_type %in% .env$antigen_iso, .data$Stratification %in% .env$strat - ) |> + ) + + if (nrow(newperson_rows) == 0) { + cli::cli_abort( + c( + paste0( + "No {.val newperson} subject found in {.arg model} for the ", + "requested {.arg antigen_iso}/{.arg strat}." + ), + "i" = paste0( + "Ensure the model was fit with a {.val newperson} subject ", + "included." + ) + ) + ) + } + + param_samples <- newperson_rows |> dplyr::select( all_of( c("Chain", "Iteration", "Parameter", "Iso_type", "Stratification", @@ -128,11 +150,16 @@ plot_serocurve <- function( Iso_type = factor(.data$Iso_type), Stratification = factor(.data$Stratification) ) - antigen_iso_col <- "Iso_type" } # ---- Compute predicted curves over a grid of time points --------------- - tx <- seq(0, 1200, by = 5) + # Clamp the grid to `xlim` when supplied to avoid unnecessary computation + # outside the visible range. + if (!is.null(xlim)) { + tx <- seq(xlim[1], xlim[2], by = 5) + } else { + tx <- seq(0, 1200, by = 5) + } serocourse_all <- param_samples |> dplyr::reframe( diff --git a/man/plot_serocurve.Rd b/man/plot_serocurve.Rd index cec7088a0..53b53a210 100644 --- a/man/plot_serocurve.Rd +++ b/man/plot_serocurve.Rd @@ -22,10 +22,14 @@ plot_serocurve( \item{model}{An \code{sr_model} object returned by \code{\link[=run_mod]{run_mod()}}.} \item{antigen_iso}{A \link{character} vector of antigen-isotype combinations to -plot. Defaults to all antigen-isotypes present in \code{model}.} +plot. Defaults to all antigen-isotypes present in the subject-level +draws of \code{model} (\code{model$Iso_type}); in normal usage these match the +levels available in \code{attr(model, "population_params")}.} \item{strat}{A \link{character} vector of stratification levels to include. -Defaults to all stratification levels present in \code{model}.} +Defaults to all stratification levels present in the subject-level +draws of \code{model} (\code{model$Stratification}); in normal usage these match +the levels available in \code{attr(model, "population_params")}.} \item{param_source}{\link{character}; which posterior samples to use for the curve. Options: diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 1be0fa9df..b56b3bdb5 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -35,9 +35,9 @@ reference: - plot_jags_Rhat - plot_jags_trace - plot_jags_effect - - plot_predicted_curve - title: Visualize model results contents: + - plot_predicted_curve - plot_serocurve - title: Postprocess JAGS output contents: