Merge pull request #2 from kylesnap/dev

Author: kylesnap

.Rbuildignore

@@ -7,3 +7,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+.lintr
+^doc$
+^Meta$

.gitignore

@@ -7,3 +7,6 @@ ernest.Rproj
 /.vscode
 inst/doc
 docs
+.lintr
+/doc/
+/Meta/

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: ernest
-Title: The Nested Sampling Toolkit
+Title: The R Nested Sampling Toolkit
 Version: 0.0.0.9000
 Authors@R: 
     person("Kyle", "Dewsnap", , "kyle.dewsnap@ubc.ca", role = c("aut", "cre"),
@@ -15,25 +15,31 @@ Imports:
     ggplot2,
     glue,
     lifecycle,
+    matrixStats,
     posterior,
-    prettyunits,
     R6,
-    Rcpp,
     rlang (>= 1.1.0),
     tibble,
+    tidyselect,
     utils,
     vctrs
 Suggests: 
+    ggdist,
     knitr,
-    mvtnorm,
+    LaplacesDemon,
     rmarkdown,
     testthat (>= 3.0.0),
-    vdiffr
+    vdiffr,
+    xml2
 LinkingTo:
-    Rcpp
+    cpp11,
+    testthat
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Depends: 
+    R (>= 2.10)
+LazyData: true

NAMESPACE

@@ -1,74 +1,75 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("variables<-",ernest_sampler)
-S3method(as_draws,ernest_sampler)
-S3method(as_draws_list,ernest_sampler)
-S3method(as_draws_matrix,ernest_sampler)
-S3method(autoplot,ernest_sampler)
-S3method(calculate,ernest_sampler)
+S3method(as_draws,ernest_run)
+S3method(as_draws_matrix,ernest_run)
+S3method(as_draws_rvars,ernest_run)
+S3method(autoplot,ernest_estimates)
+S3method(autoplot,ernest_run)
+S3method(calculate,ernest_run)
 S3method(compile,ernest_sampler)
-S3method(format,ernest_lrps)
-S3method(format,summary.ernest_sampler)
+S3method(create_likelihood,"function")
+S3method(create_likelihood,ernest_likelihood)
+S3method(format,ernest_likelihood)
+S3method(format,ernest_prior)
+S3method(format,ernest_run)
+S3method(format,summary.ernest_run)
 S3method(generate,ernest_sampler)
-S3method(make_ptype,character)
-S3method(make_ptype,data.frame)
-S3method(make_ptype,numeric)
-S3method(nested_sampling,"function")
-S3method(nested_sampling,default)
-S3method(nvariables,ernest_sampler)
-S3method(plot,ernest_sampler)
-S3method(print,ernest_lrps)
-S3method(print,summary.ernest_sampler)
-S3method(propose_live,ernest_lrps)
-S3method(propose_live,rw_cube)
-S3method(propose_uniform,ernest_lrps)
-S3method(refresh_lrps,rw_cube)
-S3method(refresh_lrps,uniform_cube)
-S3method(set_variables,ernest_sampler)
-S3method(summary,ernest_sampler)
-S3method(update_sampler,ernest_lrps)
-S3method(update_sampler,rw_cube)
-S3method(variables,ernest_sampler)
+S3method(plot,ernest_estimates)
+S3method(plot,ernest_run)
+S3method(print,ernest_likelihood)
+S3method(print,ernest_prior)
+S3method(print,ernest_run)
+S3method(print,summary.ernest_run)
+S3method(summary,ernest_run)
+S3method(visualize,ernest_run)
+export(as_draws)
+export(as_draws_matrix)
+export(as_draws_rvars)
 export(calculate)
 export(compile)
+export(create_cauchy_prior)
+export(create_likelihood)
+export(create_normal_prior)
+export(create_prior)
+export(create_t_prior)
+export(create_uniform_prior)
 export(generate)
-export(glance)
 export(nested_sampling)
 export(rwmh_cube)
 export(unif_cube)
+export(visualize)
 import(rlang)
 importFrom(R6,R6Class)
-importFrom(Rcpp,sourceCpp)
+importFrom(cli,cli_progress_bar)
+importFrom(cli,cli_progress_done)
+importFrom(cli,cli_progress_update)
 importFrom(generics,calculate)
 importFrom(generics,compile)
 importFrom(generics,generate)
-importFrom(generics,glance)
+importFrom(generics,visualize)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,autoplot)
 importFrom(ggplot2,facet_grid)
-importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_ribbon)
-importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
+importFrom(ggplot2,scale_fill_viridis_d)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,vars)
 importFrom(glue,glue)
-importFrom(graphics,plot)
 importFrom(lifecycle,deprecated)
-importFrom(posterior,"variables<-")
 importFrom(posterior,as_draws)
-importFrom(posterior,as_draws_list)
 importFrom(posterior,as_draws_matrix)
-importFrom(posterior,nvariables)
-importFrom(posterior,set_variables)
-importFrom(posterior,variables)
+importFrom(posterior,as_draws_rvars)
 importFrom(rlang,"%@%")
 importFrom(rlang,"%@%<-")
 importFrom(rlang,"%|%")
 importFrom(rlang,"%||%")
 importFrom(tibble,tibble)
 importFrom(utils,head)
 importFrom(utils,tail)
+importFrom(vctrs,vec_c)
+importFrom(vctrs,vec_size)
 useDynLib(ernest, .registration = TRUE)

R/RcppExports.R

@@ -0,0 +1,90 @@
+#' Transform nested sampling runs to `draws` objects
+#'
+#' Try to transform an [ernest_run-class] to a format supported by the
+#' [posterior][posterior::posterior-package] package.
+#'
+#' @param x An `ernest_run` object.
+#' @inheritParams rlang::args_dots_empty
+#' @param units Which units to express the sampled points. If `"original"`,
+#' points are expressed on the scale of the prior space. If `"unit_cube"`,
+#' points are expressed on the scale of the (0-1)-unit hypercube.
+#' @param radial Whether to return an additional column `.radial`, containing
+#' the radial coordinate (i.e., the squared sum of squares) for each sampled
+#' point.
+#'
+#' @returns
+#' A [draws][posterior::as_draws()] object, containing the posterior samples
+#' from the nested sampling run. Each samples are also bound to their importance
+#' weight (in log. units).
+#'
+#' The exact type of the returned object depends on the function used:
+#' * For `as_draws` and `as_draws_matrix`, a [posterior::draws_matrix()]
+#' object, which has classes `c("draws_matrix", "draws", "matrix")`.
+#' * For `as_draws_rvars`, a [posterior::draws_rvars()] object, which has
+#' classes `c("draws_rvars", "draws", "list")`.
+#'
+#' @examples
+#' # Load example run
+#' library(posterior)
+#' data(ernest_run_example)
+#'
+#' # View importance weights
+#' dm <- as_draws(ernest_run_example)
+#' weights(dm) |> head()
+#'
+#' # Summarize points after resampling
+#' dm |>
+#'  resample_draws() |>
+#'  summarize_draws()
+#'
+#' # View the radial coordinate in the unit-space over the run
+#' dm_rad <- as_draws_rvars(ernest_run_example, units = "unit_cube", radial = TRUE)
+#' plot(
+#'   x = ernest_run_example$log_volume,
+#'   y = draws_of(dm_rad$.radial),
+#'   xlab = "Log volume",
+#'   ylab = "Radial coordinate"
+#' )
+#' @rdname as_draws.ernest
+#' @method as_draws ernest_run
+#' @export
+as_draws.ernest_run <- function(x, ..., units = c("original", "unit_cube"), radial = FALSE) {
+  as_draws_matrix.ernest_run(x, ..., units = units, radial = radial)
+}
+
+#' @rdname as_draws.ernest
+#' @method as_draws_matrix ernest_run
+#' @export
+as_draws_matrix.ernest_run <- function(x, ..., units = c("original", "unit_cube"), radial = FALSE) {
+  as_draws_matrix_(x, ..., units = units, radial = radial)
+}
+
+#' @rdname as_draws.ernest
+#' @method as_draws_rvars ernest_run
+#' @export
+as_draws_rvars.ernest_run <- function(x, ..., units = c("original", "unit_cube"), radial = FALSE) {
+  posterior::as_draws_rvars(
+    as_draws_matrix(x, ..., units = units, radial = radial)
+  )
+}
+
+#' Internal function for `as_draws_matrix` conversion
+#' @noRd
+as_draws_matrix_ <- function(x, ..., units, radial, error_call = caller_env()) {
+  check_dots_empty(call = error_call)
+  units <- arg_match0(units, values = c("original", "unit_cube"), error_call)
+  check_bool(radial, error_call = error_call)
+
+  points <- if (units == "original") x$samples else x$samples_unit
+  if (radial) {
+    radial_col <- sqrt(rowSums(points^2))
+    points <- cbind(points, ".radial" = radial_col)
+  }
+  weights <- x$log_weight - max(x$log_evidence)
+
+  posterior::weight_draws(
+    posterior::as_draws_matrix(points),
+    weights,
+    log = TRUE
+  )
+}