Prepare for CRAN v0.1.18 release

lance-waller-lab · Jan 23, 2024 · 08a2fd7 · 08a2fd7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: envi
 Type: Package
 Title: Environmental Interpolation using Spatial Kernel Density Estimation
-Version: 0.1.17
-Date: 2023-02-01
+Version: 0.1.18
+Date: 2024-01-22
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # envi (development version)
 
+## envi v0.1.18
+* Fixed bug in calculation of False Discovery Rate in internal `pval_correct()` function
+* Fixed test for `plot_perturb()` function that was presenting a warning by specifying `cref0`
+* Argument `plot_cols` correctly renamed `cols` in `div_plot()` and `seq_plot()` functions
+
 ## envi v0.1.17
 * Fixed broken link in CITATION
 

diff --git a/R/div_plot.R b/R/div_plot.R
@@ -3,7 +3,7 @@
 #' Internal function to convert 'im' object or 'SpatRaster' object to values readable by \code{\link[fields]{image.plot}} function within the \code{\link{plot_obs}}, \code{\link{plot_predict}}, and \code{\link{plot_perturb}} functions. 
 #' 
 #' @param input An object of class 'im' or 'SpatRaster' from the \code{\link{lrren}} function.
-#' @param plot_cols Character string of length three (3) specifying the colors for plotting: 1) presence, 2) neither, and 3) absence from the \code{\link{plot_obs}} function. 
+#' @param cols Character string of length three (3) specifying the colors for plotting: 1) presence, 2) neither, and 3) absence from the \code{\link{plot_obs}} function. 
 #' @param midpoint Numeric. The value to center the diverging color palette. 
 #' @param thresh_up Numeric. The upper value to concatenate the color key. The default (NULL) uses the maximum value from \code{input}.
 #' @param thresh_low Numeric. The lower value to concatenate the color key. The default (NULL) uses the minimum value from \code{input}.

diff --git a/R/pval_correct.R b/R/pval_correct.R
@@ -24,27 +24,15 @@ pval_correct <- function(input,
                          type = c("FDR", "Sidak", "Bonferroni"),
                          alpha = 0.05,
                          nbc = NULL) {
-
-# False Discovery Rate
-  if (type == "FDR") {
-  sort_pvals <- sort(input, decreasing = TRUE)
-
-  fdr <- function(pvals, alpha) {
-    m <- length(pvals)
-    for (i in 1:length(pvals)) {
-      if (pvals[i] <= (i/m) * alpha) { 
-        pcrit <- pvals[i]
-        return(pcrit)
-      }
-    }
-    max(pcrit, min(pvals, na.rm = TRUE))
-  }
 
-  out_alpha <- fdr(sort_pvals, alpha)
-  return(out_alpha)
+  # False Discovery Rate (Benjamini & Hochberg)
+  if (type == "FDR") {
+    sort_pvals <- sort(input)
+    out_alpha <- fdr(sort_pvals, alpha)
+    return(out_alpha)
   }
 
-  # Bonferroni correction
+  # Sidak correction
   if (type == "Sidak") {
     out_alpha <- 1 - (1 - alpha) ^ (1 / length(input) )
     return(out_alpha)

diff --git a/R/seq_plot.R b/R/seq_plot.R
@@ -3,7 +3,7 @@
 #' Internal function to convert 'im' object or 'SpatRaster' object to values readable by \code{\link[fields]{image.plot}} function within the \code{\link{plot_perturb}} function. 
 #' 
 #' @param input An object of class 'im' or 'SpatRaster' from the \code{\link{perlrren}} function.
-#' @param plot_cols Character string of length three (3) specifying the colors for plotting: 1) presence, 2) neither, and 3) absence from the \code{\link{plot_obs}} function. 
+#' @param cols Character string of length three (3) specifying the colors for plotting: 1) presence, 2) neither, and 3) absence from the \code{\link{plot_obs}} function. 
 #' @param thresh_up Numeric. The upper value to concatenate the color key. The default (NULL) uses the maximum value from \code{input}.
 #' @param digits Integer. The number of significant digits for the labels using the \code{\link[base]{round}} function (default is 1).
 #'

diff --git a/R/utils.R b/R/utils.R
@@ -81,3 +81,15 @@ as.im.SpatRaster <- function (from, factor.col.name = NULL) {
   im <- spatstat.geom::im(val, xcol = xx, yrow = yy)
   return(im)
 }
+
+# False Discovery Rate (Benjamini & Hochberg)
+fdr <- function(pvals, alpha) {
+  pcrit <- NULL
+  m <- length(pvals)
+  for (i in 1:m) {
+    if (pvals[i] <= (i/m) * alpha) { 
+      pcrit <- pvals[i]
+    }
+  }
+  return(max(pcrit, pvals[1]))
+}
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ envi: Environmental Interpolation using Spatial Kernel Density Estimation <img s
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5347826.svg)](https://doi.org/10.5281/zenodo.5347826)
 <!-- badges: end -->
 
-**Date repository last updated**: February 01, 2023
+**Date repository last updated**: January 22, 2024
 
 <h2 id="overview">
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,7 +1,13 @@
-## This is the seventeenth resubmission
+## This is the eighteenth resubmission
 
 * Updates since previous submission:
-  * Fixed broken link in CITATION based on v0.1.16 auto-check
+  * Fixed bug in calculation of False Discovery Rate in internal `pval_correct()` function
+  * Fixed test for `plot_perturb()` function that was presenting a warning by specifying `cref0`
+  * Argument `plot_cols` correctly renamed `cols` in `div_plot()` and `seq_plot()` functions
+
+* CRAN Package Check Results 2024-01-22 for 'envi' v0.1.17 in r-patched-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64:
+  * NOTE: Package suggested but not available for checking: 'RStoolbox'
+  * SOLUTION: 'RStoolbox' recently updated 2024-01-17 so will remain as SUGGESTS for 'envi' v0.1.18
 
 * Documentation for "envi-package.Rd", "pval_correct.Rd", DESCRIPTION, and vignette references the following DOIs, which throws a NOTE but are valid URLs:
   * <https://doi.org/10.1002/sim.4780090616>

diff --git a/inst/CITATION b/inst/CITATION
@@ -2,16 +2,16 @@ bibentry(bibtype = "manual",
   title          = "envi: Environmental Interpolation using Spatial Kernel Density Estimation",
   author         = as.person("Ian D. Buller"),
   publisher      = "The Comprehensive R Archive Network",
-  year           = "2023",
-  number         = "0.1.16",
+  year           = "2024",
+  number         = "0.1.18",
   doi            = "10.5281/zenodo.5347826",
   url            = "https://cran.r-project.org/package=envi",
 
   textVersion    = 
-  paste("Ian D. Buller (2023).",
+  paste("Ian D. Buller (2024).",
         "envi: Environmental Interpolation using Spatial Kernel Density Estimation.",
         "The Comprehensive R Archive Network.",
-        "v0.1.16.",
+        "v0.1.18.",
         "DOI:10.5281/zenodo.5347826",
         "Accessed by: https://cran.r-project.org/package=envi"),
 

diff --git a/man/div_plot.Rd b/man/div_plot.Rd
diff --git a/man/seq_plot.Rd b/man/seq_plot.Rd
diff --git a/tests/testthat/test-plot_perturb.R b/tests/testthat/test-plot_perturb.R
@@ -81,7 +81,8 @@ test_that("plot_perturb throws error with invalid arguments", {
 test_that("plot_obs works", {
   skip_on_cran()
   expect_silent(
-    plot_perturb(input = test_perlrren)
+    plot_perturb(input = test_perlrren,
+                 cref0 = "EPSG:5472")
   )
 
   # cref0 = NULL