clean up for CRAN

.Rbuildignore

@@ -20,3 +20,5 @@
 ^extras$
 ^Examples$
 
+^doc$
+^Meta$

.gitignore

@@ -5,3 +5,5 @@ inst/doc
 *~
 .DS_Store
 CRAN-RELEASE
+/doc/
+/Meta/

DESCRIPTION

@@ -2,7 +2,7 @@ Package: WVPlots
 Type: Package
 Title: Common Plots for Analysis
 Version: 1.3.3
-Date: 2021-04-10
+Date: 2023-04-14
 Authors@R: c(
     person("John", "Mount", email = "[email protected]", role = c("aut", "cre")),
     person("Nina", "Zumel", email = "[email protected]", role = c("aut")),

R/GainCurve.R

@@ -89,7 +89,7 @@ thin_frame_by_orders <- function(d, cols, groupcol, large_count) {
 #' The x-axis represents the fraction of items seen when sorted by score, and the
 #' y-axis represents the cumulative summed true outcome represented by the items seen so far.
 #' See, for example,
-#' \url{https://www.ibm.com/support/knowledgecenter/SSLVMB_24.0.0/spss/tutorials/mlp_bankloan_outputtype_02.html}.
+#' \url{https://www.ibm.com/docs/SSLVMB_24.0.0/spss/tutorials/mlp_bankloan_outputtype_02.html}.
 #'
 #' For comparison, \code{GainCurvePlot} also plots the "wizard curve": the gain curve when the
 #' data is sorted according to its true outcome.

R/PRPlot.R

@@ -109,7 +109,8 @@ PRPlot <- function(frame, xvar, truthVar, truthTarget, title,
   isoFrame$Precision <- bestF1*isoFrame$Recall/(2*isoFrame$Recall-bestF1)
   isoFrame <- isoFrame[(isoFrame$Precision<=1) & (isoFrame$Precision>0),]
   #f1check <- 2*isoFrame$Recall*isoFrame$Precision/(isoFrame$Recall+isoFrame$Precision)
-
+  Precision <- NULL  # don't look unbound in CRAN checks
+  Recall <- NULL  # don't look unbound in CRAN checks
   pString <- ''
   if(estimate_sig && requireNamespace('sigr',quietly = TRUE)) {
     sp <- sigr::permutationScoreModel(predcol,outcol,

R/ROC.R

@@ -196,6 +196,8 @@ ROCPlot <- function(frame, xvar, truthVar, truthTarget, title,
     aucString <- sprintf('%.2g',auc)
     subtitle <- paste('AUC =', aucString)
   }
+  FalsePositiveRate <- NULL  # don't look unbound in CRAN check
+  TruePositiveRate <- NULL  # don't look unbound in CRAN check
   plot <- ggplot2::ggplot() +
     ggplot2::geom_ribbon(data=rocList$lineGraph,
                          mapping=ggplot2::aes(x=FalsePositiveRate,
@@ -221,8 +223,8 @@ ROCPlot <- function(frame, xvar, truthVar, truthTarget, title,
     ggplot2::ylim(0,1) + ggplot2::xlim(0,1) +
     ggplot2::ylab('TruePositiveRate (Sensitivity)') +
     ggplot2::xlab('FalsePositiveRate (1 - Specificity)')
-  Specificity <- NULL  # don't look unbound
-  Sensitivity <- NULL  # don't look unbound
+  Specificity <- NULL  # don't look unbound in CRAN check
+  Sensitivity <- NULL  # don't look unbound in CRAN check
   if(add_beta1_ideal_curve) {
     # match the displayed curve
     a <- b <- NULL  # don't look unbound
@@ -356,6 +358,9 @@ ROCPlotPair <- function(frame, xvar1, xvar2, truthVar, truthTarget, title,
                                  title = title,
                                  funname = "WVPlots::ROCPlotPair")
   outcol <- frame[[truthVar]]==truthTarget
+  FalsePositiveRate <- NULL  # don't look unbound in CRAN check
+  TruePositiveRate <- NULL  # don't look unbound in CRAN check
+  model <- NULL  # don't look unbound in CRAN check
   if(length(unique(outcol))!=2) {
     return(NULL)
   }
@@ -491,6 +496,11 @@ ROCPlotList <- function(
     function(v) {paste0(v,', AUC=',sprintf('%.2g',rocLists[[v]]$area))}
   )
 
+  FalsePositiveRate <- NULL  # don't look unbound in CRAN check
+  TruePositiveRate <- NULL  # don't look unbound in CRAN check
+  model <- NULL  # don't look unbound in CRAN check
+  dataset <- NULL  # don't look unbound in CRAN check
+
   for(v in xvar_names) {
     rocLists[[v]]$pointGraph$model <- nmList[[v]]
     rocLists[[v]]$lineGraph$model <- nmList[[v]]
@@ -611,6 +621,12 @@ ROCPlotPair2 <- function(nm1, frame1, xvar1, truthVar1, truthTarget1,
                                   name_var_list = list(xvar2 = xvar2, truthVar2 = truthVar2),
                                   title = title,
                                   funname = "WVPlots::ROCPlotPair2")
+
+  FalsePositiveRate <- NULL  # don't look unbound in CRAN check
+  TruePositiveRate <- NULL  # don't look unbound in CRAN check
+  model <- NULL  # don't look unbound in CRAN check
+  dataset <- NULL  # don't look unbound in CRAN check
+
   test <- NULL # used as a symbol, declare not an unbound variable
   outcol1 <- frame1[[truthVar1]]==truthTarget1
   if(length(unique(outcol1))!=2) {

R/SimulateAESString.R

@@ -18,9 +18,11 @@
 #' xvar <- 'x'  # the idea is, this is passed in and not known at coding time
 #' yvar <- 'y'
 #' # what we want:
-#' #  ggplot2::ggplot(data = d, mapping = ggplot2::aes_string(x = xvar, y = yvar)) + ggplot2::geom_point()
+#' #  ggplot2::ggplot(data = d, mapping = ggplot2::aes_string(x = xvar, y = yvar)) +
+#' #     ggplot2::geom_point()
 #' # The required "tidy evaluation ideoms[sic] with `aes()`".
-#' ggplot2::ggplot(data = d, mapping = ggplot2::aes(!!!simulate_aes_string(x = xvar, y = yvar))) + ggplot2::geom_point()
+#' ggplot2::ggplot(data = d, mapping = ggplot2::aes(!!!simulate_aes_string(x = xvar, y = yvar))) +
+#'    ggplot2::geom_point()
 #'
 #' @export
 simulate_aes_string <- function(...) {

cran-comments.md

@@ -4,16 +4,12 @@
 
 ### OSX
 
-    R CMD check --as-cran WVPlots_1.3.2.tar.gz 
-    * using R version 4.0.2 (2020-06-22)
+    R CMD check --as-cran WVPlots_1.3.3.tar.gz
+    * using log directory ‘/Users/johnmount/Documents/work/WVPlots.Rcheck’
+    * using R version 4.2.2 (2022-10-31)
     * using platform: x86_64-apple-darwin17.0 (64-bit)
     * using session charset: UTF-8
-    * using option ‘--as-cran’
-    * checking for file ‘WVPlots/DESCRIPTION’ ... OK
-    * checking extension type ... Package
-    * this is package ‘WVPlots’ version ‘1.3.2’
-    * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
-    Maintainer: ‘John Mount <[email protected]>’
+    * using option ‘--as-cran
     ...
     Status: OK
 
@@ -25,30 +21,7 @@
       Timeout was reached: [win-builder.r-project.org] FTP response timeout
 
     rhub::check_for_cran()
-     854#> setting _R_CHECK_FORCE_SUGGESTS_ to false
-     855#> setting R_COMPILE_AND_INSTALL_PACKAGES to never
-     856#> setting _R_CHECK_THINGS_IN_CHECK_DIR_ to false
-     857#> setting R_REMOTES_STANDALONE to true
-     858#> setting R_REMOTES_NO_ERRORS_FROM_WARNINGS to true
-     859#> setting _R_CHECK_FORCE_SUGGESTS_ to true
-     860#> setting _R_CHECK_CRAN_INCOMING_USE_ASPELL_ to true
-     861#> * using log directory 'C:/Users/USERtuXsbaQdWo/WVPlots.Rcheck'
-     862#> * using R Under development (unstable) (2020-12-14 r79633)
-     863#> * using platform: x86_64-w64-mingw32 (64-bit)
-     864#> * using session charset: ISO8859-1
-     865#> * using option '--as-cran'
-     866#> * checking extension type ... Package
-     867#> * this is package 'WVPlots' version '1.3.2'
-     868#> * checking for file 'WVPlots/DESCRIPTION' ... OK
-     869#> * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
-     870#> Maintainer: 'John Mount '
-     871#> * checking package namespace information ... OK
-     872#> * checking package dependencies ... NOTE
-     873#> Suggests orphaned package: 'plotly'
-     ...
-     927#> Status: 1 NOTE
-     We hope plotly will move out of orphaned status soon,
-     if not we will later remove the suggestion.
+
 
 ## Downstream dependencies