Merge pull request #57 from rnabioco/resub

update for resubmission

.Rbuildignore

@@ -9,3 +9,4 @@
 ^docs$
 ^pkgdown$
 ^cran-comments\.md$
+^CRAN-RELEASE$

DESCRIPTION

@@ -20,7 +20,7 @@ Authors@R:
              comment = c(ORCID = "0000-0002-6299-179X")),
       person(given = "RNA Bioscience Initiative",
              role = c("fnd", "cph")))
-Description: Provides ggplot2 geoms that allow groups of data points to be
+Description: Provides 'ggplot2' geoms that allow groups of data points to be
     outlined or highlighted for emphasis. This is particularly useful when
     working with dense datasets that are prone to overplotting.
 License: MIT + file LICENSE
@@ -30,7 +30,8 @@ Depends:
     R (>= 4.0.0)
 Imports: 
     ggplot2,
-    grid
+    grid,
+    rlang
 Suggests: 
     covr,
     knitr,

NAMESPACE

@@ -17,3 +17,4 @@ importFrom(grid,gpar)
 importFrom(grid,grobName)
 importFrom(grid,grobTree)
 importFrom(grid,pointsGrob)
+importFrom(rlang,on_load)

R/geom-point-trace.R

@@ -332,6 +332,7 @@ translate_shape_string <- function(shape_string) {
 
     more_problems <- if (n_bad > 5) {
       sprintf("\n* ... and %d more problem%s", n_bad - 5, ifelse(n_bad > 6, "s", ""))
+
     } else {
       ""
     }
@@ -358,6 +359,7 @@ translate_shape_string <- function(shape_string) {
 
     more_problems <- if (n_bad > 5) {
       sprintf("\n* ... and %d more problem%s", n_bad - 5, ifelse(n_bad > 6, "s", ""))
+
     } else {
       ""
     }

R/ggtrace-package.R

@@ -1,20 +1,16 @@
 #' ggtrace
 #'
-#' This package contains extra geoms for \pkg{ggplot2}.
+#' This package provides \pkg{ggplot2} geoms that allow groups of data points to be
+#' outlined or highlighted for emphasis. This is particularly useful when
+#' working with dense datasets that are prone to overplotting.
 #'
-#' Please see the help pages listed below:
-#'
-#' \itemize{
-#'   \item \code{\link{geom_point_trace}}
-#' }
-#'
-#' Also see the vignette for more usage examples:
+#' See the vignette for usage examples:
 #'
 #' \code{browseVignettes("ggtrace")}
 #'
-#' Please report issues and suggest improvements at Github:
+#' @author Ryan Sheridan \email{ryan.sheridan@@cuanschutz.edu}
 #'
-#' \url{https://github.com/rnabioco/ggtrace}
+#' @seealso Report issues and suggest improvements at \url{https://github.com/rnabioco/ggtrace/issues}
 #'
 #' @name ggtrace
 #' @docType package
@@ -24,5 +20,6 @@
 #'   pointsGrob
 #'   grobName
 #'   grobTree
+#' @importFrom rlang on_load
 #' @keywords internal
 "_PACKAGE"

R/utilities-ggplot2.R

@@ -108,13 +108,17 @@ split_with_index <- function(x, f, n = max(f)) {
 single_value <- function(x, ...) {
   UseMethod("single_value")
 }
+
 #' @export
 single_value.default <- function(x, ...) {
+
   # This is set by id() used in creating the grouping var
   identical(attr(x, "n"), 1L)
 }
+
 #' @export
 single_value.factor <- function(x, ...) {
+
   # Panels are encoded as factor numbers and can never be missing (NA)
   identical(levels(x), "1")
 }
@@ -127,6 +131,19 @@ modify_list <- function(old, new) {
   old
 }
 
+# Info needed for rbind_dfs date/time handling
+ggtrace_global <- new.env(parent = emptyenv())
+
+#' @importFrom rlang on_load
+#' @noRd
+rlang::on_load({
+  date <- Sys.Date()
+  ggtrace_global$date_origin <- date - unclass(date)
+
+  time <- Sys.time()
+  ggtrace_global$time_origin <- time - unclass(time)
+})
+
 #' Bind data frames together by common column names
 #'
 #' This function is akin to `plyr::rbind.fill`, `dplyr::bind_rows`, and
@@ -185,6 +202,7 @@ rbind_dfs <- function(dfs) {
         out[[col]] <- rep(.subset2(df, col)[1][NA], total)
       }
     }
+
     allocated[new_columns] <- TRUE
 
     if (all(allocated)) break
@@ -202,19 +220,19 @@ rbind_dfs <- function(dfs) {
       date_col <- inherits(df[[col]], "Date")
       time_col <- inherits(df[[col]], "POSIXct")
 
-      # if (is_date[[col]] && !date_col) {
-      #   out[[col]][rng] <- as.Date(
-      #     unclass(df[[col]]),
-      #     origin = ggplot_global$date_origin
-      #   )
-      #
-      # } else if (is_time[[col]] && !time_col) {
-      #   out[[col]][rng] <- as.POSIXct(
-      #     unclass(df[[col]]),
-      #     origin = ggplot_global$time_origin
-      #   )
-
-      if (date_col || time_col || inherits(df[[col]], "factor")) {
+      if (is_date[[col]] && !date_col) {
+        out[[col]][rng] <- as.Date(
+          unclass(df[[col]]),
+          origin = ggtrace_global$date_origin
+        )
+
+      } else if (is_time[[col]] && !time_col) {
+        out[[col]][rng] <- as.POSIXct(
+          unclass(df[[col]]),
+          origin = ggtrace_global$time_origin
+        )
+
+      } else if (date_col || time_col || inherits(df[[col]], "factor")) {
         out[[col]][rng] <- as.character(df[[col]])
 
       } else {
@@ -264,7 +282,6 @@ rd_aesthetics <- function(type, name) {
   )
 
   aes <- rd_aesthetics_item(obj)
-
   aes <- aes[aes != paste0("\\code{", KEEP_CLMN, "}")]
 
   res <- c(
@@ -330,7 +347,8 @@ find_global <- function(name, env, mode = "any") {
     return(get(name, envir = env, mode = mode))
   }
 
-  nsenv <- asNamespace("ggplot2")
+  nsenv <- asNamespace("ggtrace")
+
   if (exists(name, envir = nsenv, mode = mode)) {
     return(get(name, envir = nsenv, mode = mode))
   }
@@ -344,9 +362,7 @@ find_global <- function(name, env, mode = "any") {
 camelize <- function(x, first = FALSE) {
   x <- gsub("_(.)", "\\U\\1", x, perl = TRUE)
 
-  if (first) {
-    x <- firstUpper(x)
-  }
+  if (first) x <- firstUpper(x)
 
   x
 }

cran-comments.md

@@ -1,3 +1,11 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Fixed DESCRIPTION so package names are in single quotes
+* In the initial submission I was advised to check the R/utilities-ggplot2.R
+  file to verify that it does not modify the .GlobalEnv. I checked this file and
+  confirmed that it does not modify the .GlobalEnv.
+
 ## Test environments
 * Windows 10.0.20348 (on Github Actions), R 4.2.0
 * macOS 11.6.6 (on Github Actions), R 4.2.0