Prepare for CRAN v0.2.8 Release

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sparrpowR
 Title: Power Analysis to Detect Spatial Relative Risk Clusters
-Version: 0.2.7
-Date: 2023-02-01
+Version: 0.2.8
+Date: 2024-01-23
 Authors@R:
     c(person(given = "Ian D.",
              family = "Buller",

NEWS.md

@@ -1,5 +1,9 @@
 # sparrpowR (development version)
 
+## sparrpowR v0.2.8
+* Fixed bug in calculation of False Discovery Rate in internal `pval_correct()` function
+* Fixed 'Moved Permanently' content by replacing the old URL with the new URL
+
 ## sparrpowR v0.2.7
 * Migrated R-spatial dependency
 * Replaced `raster` and `sp` in Imports with `terra` because of imminent package retirement

R/pval_correct.R

@@ -1,4 +1,4 @@
-#' Calculate p-value corrections
+#' Calculate p-value corrections for multiple testing
 #'
 #' Internal function to calculate various p-value corrections for use within the \code{\link{spatial_power}} and \code{\link{jitter_power}} functions.
 #'
@@ -24,22 +24,10 @@ pval_correct <- function(input,
                          type = c("FDR", "Sidak", "Bonferroni"),
                          alpha = 0.05,
                          nbc = NULL) {
-
-# False Discovery Rate
-  if (type == "FDR") {
-  sort_pvals <- sort(as.vector(input$P$v), 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))
-  }
 
+  # False Discovery Rate (Benjamini & Hochberg)
+  if (type == "FDR") {
+    sort_pvals <- sort(as.vector(input$P$v))
     out_alpha <- fdr(sort_pvals, alpha)
     return(out_alpha)
   }

R/utils.R

@@ -16,3 +16,15 @@ progBar <- function(kk, N, per = 1) {
     if (kk == N) cat("\r")
   }
 }
+
+# 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]))
+}

README.md

@@ -7,12 +7,12 @@ sparrpowR: Power analysis to detect spatial relative clusters <img src="man/figu
 [![CRAN version](https://www.r-pkg.org/badges/version-ago/sparrpowR)](https://cran.r-project.org/package=sparrpowR)
 [![CRAN RStudio mirror downloads total](https://cranlogs.r-pkg.org/badges/grand-total/sparrpowR?color=blue)](https://r-pkg.org/pkg/sparrpowR)
 [![CRAN RStudio mirror downloads monthly ](http://cranlogs.r-pkg.org/badges/sparrpowR)](https://www.r-pkg.org:443/pkg/sparrpowR)
-[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0/)
 ![GitHub last commit](https://img.shields.io/github/last-commit/machiela-lab/sparrpowR)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5347997.svg)](https://doi.org/10.5281/zenodo.5347997)
 <!-- badges: end -->
 
-**Date repository last updated**: February 01, 2023
+**Date repository last updated**: January 23, 2024
 
 <h2 id="overview">
 

cran-comments.md

@@ -1,11 +1,8 @@
-## This is the eleventh resubmission
+## This is the twelth resubmission
 
 * Actions taken since previous submission:
-  * Migrated R-spatial dependency
-  * Replaced `raster` and `sp` in Imports with `terra` because of imminent package retirement
-  * `geojsonsf`, `ggmap`, `ggplot2`, `sf`, `tidyterra` are now Suggests because they are used in the vignette
-  * Updated vignette and documentation throughout
-  * Updated citation style for CITATION file
+  * Fixed bug in calculation of False Discovery Rate in internal `pval_correct()` function
+  * Fixed 'Moved Permanently' content by replacing the old URL with the new URL
 
 * Documentation for `pval_correct()` references a doi <https://doi.org/10.2307/2283989> that throws a NOTE but is a valid URL