Address CRAN review

DESCRIPTION

@@ -13,7 +13,8 @@ Description: A collection of utilities and 'ggplot2' extensions to assist with
   visualisations in genomic epidemiology. This includes the 'phylepic' chart,
   a visual combination of a phylogenetic tree and a matched epidemic curve.
   The included 'ggplot2' extensions such as date axes binned by week are
-  relevant for other applications in epidemiology and beyond.
+  relevant for other applications in epidemiology and beyond. The approach is
+  described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/helpers_ggplot.R

@@ -11,6 +11,8 @@
 #'   limit of the desired output range respectively.
 #'
 #' @rdname oob
+#' @return A numerical vector of the same length as `x` where out of bound
+#'   values have been replaced by `Inf` or `-Inf` accordingly.
 #' @export
 oob_infinite <- function(x, range = c(0, 1)) {
   force(range)

R/plot.phylepic.R

@@ -1,6 +1,6 @@
 #' Plot "phylepic" objects
 #'
-#' The `autoplot` and `plot` methods for "phylepic" objects assemble various
+#' The `autoplot()` and `plot()` methods for "phylepic" objects assemble various
 #' panels into the final plot. To facilitate customisations, the plots from
 #' each panel can be overwritten. Some effort is made to ensure that the
 #' specified plots will look reasonable when assembled.
@@ -30,6 +30,8 @@
 #' @param height.tree Relative height of the tree panel.
 #' @param ... Ignored.
 #'
+#' @return `plot()` is usually called to display the plot, whereas `autoplot()`
+#'   returns a "ggplot" object that can later be displayed with `print()`.
 #' @family phylepic plots
 #' @export
 plot.phylepic <- function(

cran-comments.md

@@ -2,6 +2,6 @@
 
 0 errors | 0 warnings | 0 notes
 
-* Re-uploaded to quote package names in DESCRIPTION and fix HTML validation.
+* Re-uploaded to fix missing \value Rd items and add citation to description.
 * While some functions do not include examples in documentation, the vignette walks through
   examples of how to use all of the features.