Merge pull request #440 from UCD-SERG/feat/issue439/revert-to-est_seroincidence_by-2

Update estimate_scr to est_seroincidence_by

Author: d-morrison

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.3.0.9046
+Version: 1.3.0.9047
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

NAMESPACE

@@ -24,7 +24,7 @@ export(count_strata)
 export(est.incidence)
 export(est.incidence.by)
 export(est_seroincidence)
-export(estimate_scr_by)
+export(est_seroincidence_by)
 export(f_dev)
 export(f_dev0)
 export(fdev)

NEWS.md

@@ -2,6 +2,7 @@
 
 ## New features
 
+* Rename `estimate_scr()` to `est_seroincidence_by()` (#439)
 * Rename `estimate_scr()` to `est_seroincidence()` (#432)
 * Rename argument `curve_params` to `sr_params` (#424)
 * added documentation for `count_strata()` (#431)

R/autoplot.seroincidence.by.R

@@ -1,10 +1,10 @@
 #' Plot `seroincidence.by` log-likelihoods
 #' @description
 #' Plots log-likelihood curves by stratum, for `seroincidence.by` objects
-#' @param object a '"seroincidence.by"' object (from [estimate_scr_by()])
+#' @param object a '"seroincidence.by"' object (from [est_seroincidence_by()])
 #' @param ncol number of columns to use for panel of plots
 #' @inheritDotParams autoplot.seroincidence
-#' @return an object of class `"ggarrange"`, which is a [ggplot2::ggplot()] or a [list()] of [ggplot2::ggplot()]s.
+#' @return a `"ggarrange"` object: a single or [list()] of [ggplot2::ggplot()]s
 #' @export
 #' @examples
 #'\donttest{
@@ -21,7 +21,7 @@
 #' noise <-
 #'   example_noise_params_pk
 #'
-#' est2 <- estimate_scr_by(
+#' est2 <- est_seroincidence_by(
 #'   strata = c("catchment"),
 #'   pop_data = xs_data,
 #'   curve_params = curve,
@@ -36,7 +36,7 @@
 #' # Plot the log-likelihood curve
 #' autoplot(est2)
 #'}
-autoplot.seroincidence.by = function(
+autoplot.seroincidence.by <- function(
     object,
     ncol = min(3, length(object)),
     ...) {
@@ -47,16 +47,15 @@ autoplot.seroincidence.by = function(
   if (!attr(object, "graphs_included")) {
     stop(
       "Graphs cannot be extracted; ",
-      "`build_graph` was not `TRUE` in the call to `estimate_scr_by()`"
+      "`build_graph` was not `TRUE` in the call to `est_seroincidence_by()`"
     )
     figure <- NULL
   }
 
   labels <- names(object)
   figs <- lapply(object, FUN = autoplot.seroincidence, ...)
 
-  for (i in 1:length(figs))
-  {
+  for (i in seq_along(figs)){
     figs[[i]] <- figs[[i]] + ggplot2::ggtitle(labels[i])
   }
 

R/autoplot.summary.seroincidence.by.R

@@ -3,7 +3,7 @@
 #' @param object
 #' a `summary.seroincidence.by` object
 #' (generated by applying the `summary()`
-#' method to the output of [estimate_scr_by()]).
+#' method to the output of [est_seroincidence_by()]).
 #' @param type
 #' [character] string indicating which type of plot to generate.
 #' The implemented options are:
@@ -29,7 +29,7 @@
 #' noise <-
 #'   example_noise_params_pk
 #'
-#' est2 <- estimate_scr_by(
+#' est2 <- est_seroincidence_by(
 #'   strata = c("catchment", "ageCat"),
 #'   pop_data = xs_data,
 #'   curve_params = curve,

R/check_parallel_cores.R

@@ -11,7 +11,7 @@ check_parallel_cores <- function(num_cores) {
       c(
         "This computer appears to have
         {parallel::detectCores()} cores available.
-        `estimate_scr_by()` has reduced its
+        `est_seroincidence_by()` has reduced its
         `num_cores` argument to {num_cores}
         to avoid destabilizing the computer."
       )

R/estimate_scr_by.R R/est_seroincidence_by.RR/estimate_scr_by.R renamed to R/est_seroincidence_by.R

@@ -23,7 +23,7 @@
 #' If `strata` is left empty, a warning will be produced,
 #' recommending that you use [est_seroincidence()] for unstratified analyses,
 #' and then the data will be passed to [est_seroincidence()].
-#' If for some reason you want to use [estimate_scr_by()]
+#' If for some reason you want to use [est_seroincidence_by()]
 #' with no strata instead of calling [est_seroincidence()],
 #' you may use `NA`, `NULL`, or `""` as the `strata`
 #' argument to avoid that warning.
@@ -57,7 +57,7 @@
 #' noise <-
 #'   example_noise_params_pk
 #'
-#' est2 <- estimate_scr_by(
+#' est2 <- est_seroincidence_by(
 #'   strata = "catchment",
 #'   pop_data = xs_data,
 #'   curve_params = curve,
@@ -69,7 +69,7 @@
 #' print(est2)
 #' summary(est2)
 #'
-estimate_scr_by <- function(
+est_seroincidence_by <- function(
     pop_data,
     curve_params,
     noise_params,
@@ -275,14 +275,15 @@ estimate_scr_by <- function(
 #' @description
 #' `r lifecycle::badge("deprecated")`
 #'
-#' `est.incidence.by()` was renamed to [estimate_scr_by()] to create a more
+#' `est.incidence.by()` was renamed to [est_seroincidence_by()] to create a more
 #' consistent API.
 #' @keywords internal
 #' @export
 est.incidence.by <- function( # nolint: object_name_linter
     ...) {
-  lifecycle::deprecate_soft("1.3.1", "est.incidence.by()", "estimate_scr_by()")
-  estimate_scr_by(
+  lifecycle::deprecate_soft("1.4.0", "est.incidence.by()",
+                            "est_seroincidence_by()")
+  est_seroincidence_by(
     ...
   )
 }

R/print.seroincidence.by.R

@@ -3,9 +3,9 @@
 #'
 #' @description
 #' Custom [print()] function for `seroincidence.by` objects
-#' (from [estimate_scr_by()])
+#' (from [est_seroincidence_by()])
 #'
-#' @param x A list containing output of function [estimate_scr_by()].
+#' @param x A list containing output of function [est_seroincidence_by()].
 #' @param ... Additional arguments affecting the summary produced.
 #' @inherit print.seroincidence return
 #' @examples
@@ -22,7 +22,7 @@
 #'   example_noise_params_pk
 #'
 #' # estimate seroincidence
-#' est2 <- estimate_scr_by(
+#' est2 <- est_seroincidence_by(
 #'   strata = c("catchment"),
 #'   pop_data = xs_data,
 #'   curve_params = curve,
@@ -51,7 +51,7 @@ print.seroincidence.by <- function(x, ...) {
   cat("`antigen_isos` -",
       "Character vector of antigen isotypes used in analysis.\n")
   cat("`Strata`       -",
-      "Input parameter strata of function `estimate_scr_by()`\n")
+      "Input parameter strata of function `est_seroincidence_by()`\n")
   cat("\n")
   cat("Call the `summary()` function to obtain output results.\n")
   invisible(x)

R/print.summary.seroincidence.by.R

@@ -23,7 +23,7 @@
 #'   example_noise_params_pk
 #'
 #' # estimate seroincidence
-#' est2 <- estimate_scr_by(
+#' est2 <- est_seroincidence_by(
 #'   strata = c("catchment"),
 #'   pop_data = xs_data,
 #'   curve_params = curve,

R/strat_ests_barplot.R

@@ -1,7 +1,7 @@
 #' Barplot method for `summary.seroincidence.by` objects
 #'
 #' @param object a `summary.seroincidence.by` object (generated by applying the
-#' `summary()` method to the output of [estimate_scr_by()]).
+#' `summary()` method to the output of [est_seroincidence_by()]).
 #' @param yvar the name of a stratifying variable in `object`.
 #' @param color_var
 #' [character] the name of the fill color variable (e.g., "Country").