Merge pull request #76 from metrumresearchgroup/release/0.3.7

Release/0.3.7

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pmplots
 Type: Package
 Title: Plots for Pharmacometrics
-Version: 0.3.6
+Version: 0.3.7
 Authors@R: c(
        person("Kyle T", "Baron", "", "kyleb@metrumrg.com", c("aut", "cre")),
        person("Metrum Research Group", role =  c("cph"))
@@ -35,7 +35,7 @@ Suggests:
   shiny, 
   rmarkdown
 Depends: ggplot2 (>= 3.4.0)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Collate: 
     'Aaaa.R'

NEWS.md

@@ -1,3 +1,11 @@
+# pmplots 0.3.7
+
+## Bugs fixed
+
+- Fix bug where density line was not being drawn by default over npde and 
+  cwres histograms; the bug came about from incomplete transition to 
+  changes introduced in `ggplot2` v3.4.0 (#74, #75).
+
 # pmplots 0.3.6
 
 - Update plotting code to work with new `ggplot2` behavior introduced 

R/hist.R

@@ -1,21 +1,21 @@
 ##' Generate a histogram plot
 ##'
-##' \code{cont_hist_list} is a vectorized version
-##' of \code{cont_hist}.  \code{pm_histogram} is a generic histogram
+##' `cont_hist_list` is a vectorized version
+##' of `cont_hist`.  `pm_histogram` is a generic histogram
 ##' function that is called by other functions in pmplots.
 ##'
-##' @param df the data frame containing plotting data
-##' @param x the x column for \code{geom_histogram}
+##' @param df the data frame containing plotting data.
+##' @param x the x column for [ggplot2::geom_histogram()].
 ##' @param y what to use for the y-axis on the histogram; can be
-##' \code{"count"} or \code{"density"}
-##' @param add_density if \code{TRUE}, a normal density line will
-##' be plotted over the histogram using \code{\link{add_density}}
-##' @param xs a list of information for the x axis
-##' @param fill a character value passed to \code{geom_histogram}
-##' @param col a character value passed to \code{geom_histogram}
-##' @param alpha a numeric value passed to \code{geom_histogram}
-##' @param add_layers extra layers will be added only if \code{TRUE}
-##' @param ... passed to \code{geom_histogram} and \code{add_density}
+##' `"count"` or `"density"`.
+##' @param add_density if `TRUE`, a normal density line will
+##' be plotted over the histogram using [add_density()].
+##' @param xs a list of information for the x axis.
+##' @param fill a character value passed to [ggplot2::geom_histogram()].
+##' @param col a character value passed to [ggplot2::geom_histogram()].
+##' @param alpha a numeric value passed to [ggplot2::geom_histogram()].
+##' @param add_layers extra layers will be added only if `TRUE`.
+##' @param ... passed to [ggplot2::geom_histogram()] and [add_density()].
 ##'
 ##'
 ##' @examples
@@ -25,7 +25,7 @@
 ##' cont_hist(data, x = "WT//Weight (kg)")
 ##'
 ##' @return A single plot.
-##'
+##' @md
 ##' @export
 cont_hist <- function(df, x, xs = defx(),
                       y = "count",

R/res_hist.R

@@ -1,11 +1,11 @@
 ##' Histograms of residuals or NPDE
 ##'
-##' @param df data frame to plot
-##' @param ... passed to \code{\link{cont_hist}}
-##' @param x character name for x-axis data
-##' @param xs see \code{\link{defx}}
+##' @param df data frame to plot.
+##' @param ... passed to [cont_hist()]
+##' @param x character name for x-axis data.
+##' @param xs see [defx()].
 ##' @param y what to use for the y-axis on the histogram; can be
-##' \code{"..count.."} or \code{"..density.."}
+##' "count"` or `"density"`.
 ##'
 ##' @examples
 ##' df <- pmplots_data_obs()
@@ -14,6 +14,8 @@
 ##'
 ##' @return A single plot.
 ##'
+##' @md
+##'
 ##' @export
 res_hist <- function(df, ...,
                      x = pm_axis_res(),
@@ -25,7 +27,7 @@ res_hist <- function(df, ...,
 ##' @rdname res_hist
 wres_hist <- function(df, ...,
                       x = pm_axis_wres(),
-                      y = "..density..") {
+                      y = "density") {
   res_hist(df, x = x, y = y, ...)
 }
 

inst/validation/pmplots-stories.yaml

@@ -190,6 +190,7 @@ PMP-S023:
   - PMP-TEST-040
   - PMP-TEST-041
   - PMP-TEST-074
+  - PMP-TEST-089
 PMP-S024:
   name: List plots
   description: As a user, I want to create list plots.

tests/testthat/test-pm.R

@@ -180,6 +180,22 @@ test_that("res hist [PMP-TEST-041]", {
 })
 
 
+test_that("optional density plot over histogram [PMP-TEST-089]", {
+  # issue 74
+  x <- npde_hist(df)
+  expect_is(x, "gg")
+  expect_length(x$layers, 2)
+
+  y <- npde_hist(df, add_density = FALSE)
+  expect_length(y$layers, 1)
+
+  z <- cont_hist(df, x = "NPDE", add_density = TRUE)
+  expect_length(z$layers, 2)
+
+  w <- cont_hist(df, x = "WT", add_density = FALSE)
+  expect_length(w$layers, 1)
+})
+
 test_that("eta pairs [PMP-TEST-042]", {
   p <- eta_pairs(df, c("ETA1//ETA-CL", "ETA2//ETA-V2"))
   expect_is(p,"ggmatrix")