Prepare for CRAN v0.2.5 Release (cont.)

* `spatstat (>=2.0-0)` is no longer Suggests
* Fixed annotation typos in the `pval_correct()` function
*  Updated packages in code rendering hexsticker

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sparrpowR
 Title: Power Analysis to Detect Spatial Relative Risk Clusters
 Version: 0.2.5
-Date: 2022-02-03
+Date: 2022-02-04
 Authors@R:
     c(person(given = "Ian D.",
              family = "Buller",
@@ -56,7 +56,6 @@ Imports:
     stats
 Suggests: 
     spatstat.data,
-    spatstat (>= 2.0-0),
     testthat,
     spelling,
     R.rsp

NAMESPACE

@@ -5,7 +5,6 @@ export(pval_correct)
 export(spatial_data)
 export(spatial_plots)
 export(spatial_power)
-import(spatstat.geom)
 importFrom(doFuture,registerDoFuture)
 importFrom(doRNG,"%dorng%")
 importFrom(fields,image.plot)

NEWS.md

@@ -1,29 +1,30 @@
 # sparrpowR (development version)
 
-# sparrpowR 0.2.5
+# sparrpowR v0.2.5
 * Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random`
   * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends.
   * `spatstat.geom` and `spatstat.random` are now Imports
-  * `spatstat.data` and `spatstat (>= 2.0-0)` are now Suggests.
+  * `spatstat.data` is now Suggests
   * [See the GitHub merge pull request](https://github.com/machiela-lab/sparrpowR/commit/4df5d85343dd222c9d4b1ae30f894ed6482bcb52).
+* Fixed annotation typos in the `pval_correct()` function
 
-# sparrpowR 0.2.4
+# sparrpowR v0.2.4
 * Addressed ERROR on R-devel CRAN environments by setting `parallelly.makeNodePSOCK.setup_strategy = sequential` for all CRAN tests as suggested by the maintainer for the `future` and `parallelly` packages who is actively working on a solution. [See the GitHub issue](https://github.com/HenrikBengtsson/parallelly/issues/65).
 
-# sparrpowR 0.2.3
+# sparrpowR v0.2.3
 * Following advice from `future` package maintainer, now `spatial_power()` and `jitter_power()` functions reset future strategy when exiting
 * Addressed ERROR in MacOS CRAN environments by setting the `parallelly.makeNodePSOCK.setup_strategy = sequential` for MacOS environments running `tcltk` until `parallelly` (>=1.26.1-9002) is on CRAN. This workaround was suggested by the `parallelly` maintainer. [See the GitHub issue](https://github.com/HenrikBengtsson/parallelly/issues/62#issuecomment-880665390).
 
-# sparrpowR 0.2.2
+# sparrpowR v0.2.2
 * Removed `LazyData: true` from 'DESCRIPTION' file because the package has no data accessed via a `data()` command and has no `data/` directory (in response to CRAN NOTE: 'LazyData' is specified without a 'data' directory)
 * Changed hyperlink for Stamen basemap in 'vignette' file with a Hypertext Transfer Protocol Secure destination
 * Added 'CITATION' file
 * Deprecation badges in 'jitter_power.Rd' and 'spatial_power.Rd' files now hyperlink to `lifecycle` r-lib.org site
 
-# sparrpowR 0.2.1
+# sparrpowR v0.2.1
 * Updated vignette with appropriate hyperlinks
 
-# sparrpowR 0.2.0
+# sparrpowR v0.2.0
 * Updates to dependencies
   * Updated `spatstat` package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). `spatstat.geom` and `spatstat.core` packages replace `spatstat` package in Depends
   * Imports `lifecycle` package to document deprecated argument `cascon` in `spatial_power()` and `jitter_power()` functions

R/package.R

@@ -49,6 +49,6 @@ NULL
 #' @importFrom sp coordinates gridded
 #' @importFrom sparr risk
 #' @importFrom stats na.omit rnorm sd
+#' @importFrom spatstat.geom as.solist disc marks plot.anylist plot.ppp ppp rsyst shift superimpose unit.square
 #' @importFrom spatstat.random rNeymanScott rpoispp runifdisc runifpoint
-#' @import spatstat.geom 
 NULL

R/pval_correct.R

@@ -3,15 +3,15 @@
 #' Internal function to calculate various p-value corrections for use within the \code{\link{spatial_power}} and \code{\link{jitter_power}} functions.
 #'
 #' @param input An object of class 'rrs' from the \code{\link{spatial_power}} or \code{\link{jitter_power}} function.
-#' @param type Character string specifying which correction for multiple comparisons. Options include a False Discovery Rate \code{p_correct = "FDR"}, an independent Sidak correction \code{p_correct = "uncorrelated Sidak"}, and an independent Bonferroni correction \code{p_correct = "uncorrelated Bonferroni"}.
+#' @param type Character string specifying which correction for multiple comparisons. Options include a False Discovery Rate \code{p_correct = "FDR"}, a Sidak correction \code{p_correct = "Sidak"}, and a Bonferroni correction \code{p_correct = "Bonferroni"}.
 #' @param alpha Numeric. The alpha level for significance threshold (default in \code{\link{spatial_power}} and \code{\link{jitter_power}} functions is 0.05).
 #' 
 #' @details This function provides functionality for multiple testing correction in five ways:
 #' 
 #' \enumerate{
 #' \item Computes a False Discovery Rate by Benjamini and Hochberg \doi{10.1111/j.2517-6161.1995.tb02031.x} (\code{p_correct = "FDR"}) by: 1) sorting the p-values (p_i) of each knot in ascending order (p_1 <= p_2 <= ... <= p_m), 2) starting from p_m find the first p_i for which p_i <= (i/m) * alpha.
-#' \item Computes an independent Sidak correction \doi{10.2307/2283989} (\code{p_correct = "uncorrelated Sidak"}) by 1 - (1 - \code{alpha}) ^ (1 / total number of gridded knots across the estimated surface). The default in the \code{\link[sparr]{risk}} function is a resolution of 128 x 128 or n = 16,384 knots and a custom resolution can be specified using the \code{resolution} argument within the \code{\link[sparr]{risk}} function.
-#' \item Computes an independent Bonferroni correction (\code{p_correct = "uncorrelated Bonferroni"}) by \code{alpha} / total number of gridded knots across the estimated surface. The default in the \code{\link[sparr]{risk}} function is a resolution of 128 x 128 or n = 16,384 knots and a custom resolution can be specified using the \code{resolution} argument within the \code{\link[sparr]{risk}} function.
+#' \item Computes a Sidak correction \doi{10.2307/2283989} (\code{p_correct = "Sidak"}) by 1 - (1 - \code{alpha}) ^ (1 / total number of gridded knots across the estimated surface). The default in the \code{\link[sparr]{risk}} function is a resolution of 128 x 128 or n = 16,384 knots and a custom resolution can be specified using the \code{resolution} argument within the \code{\link[sparr]{risk}} function.
+#' \item Computes a Bonferroni correction (\code{p_correct = "Bonferroni"}) by \code{alpha} / total number of gridded knots across the estimated surface. The default in the \code{\link[sparr]{risk}} function is a resolution of 128 x 128 or n = 16,384 knots and a custom resolution can be specified using the \code{resolution} argument within the \code{\link[sparr]{risk}} function.
 #' }
 #' 
 #' @return An object of class 'numeric' with the corrected alpha level.
@@ -44,13 +44,13 @@ pval_correct <- function(input,
     return(out_alpha)
   }
 
-  # Uncorrelated Bonferroni correction
+  # Sidak correction
   if (type == "Sidak") {
     out_alpha <- 1 - (1 - alpha) ^ (1 / prod(input$P$dim) )
     return(out_alpha)
   }
 
-  # Uncorrelated Bonferroni correction
+  # Bonferroni correction
   if (type == "Bonferroni") {
     out_alpha <- alpha / prod(input$P$dim)
     return(out_alpha)

cran-comments.md

@@ -2,15 +2,16 @@
 
 * Actions taken since previous submission:
   * Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random`
-    * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends.
+    * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends
     * `spatstat.geom` and `spatstat.random` are now Imports
-    * `spatstat.data` and `spatstat (>= 2.0-0)` are now Suggests.
-    * [See the GitHub merge pull request](https://github.com/machiela-lab/sparrpowR/commit/4df5d85343dd222c9d4b1ae30f894ed6482bcb52).
+    * `spatstat.data` is now Suggests
+    * [See the GitHub merge pull request](https://github.com/machiela-lab/sparrpowR/commit/4df5d85343dd222c9d4b1ae30f894ed6482bcb52)
+  * Fixed annotation typos in the `pval_correct()` function
 
 * Documentation for `pval_correct()` references a doi <https://doi.org/10.2307/2283989> that throws a NOTE but is a valid URL
 
 ## Test environments
-* local OS X install, R 4.1.0
+* local OS X install, R 4.1.2
 * win-builder, (devel, release, oldrelease)
 * Rhub
   * Fedora Linux, R-devel, clang, gfortran

dev/hexSticker_sparrpowR.R

@@ -4,20 +4,22 @@
 # Created by: Ian Buller, Ph.D., M.A. (GitHub: @idblr)
 # Created on: June 4, 2020
 #
-# Recently modified by:
-# Recently modified on:
+# Recently modified by: @idblr
+# Recently modified on: February 4, 2022
 #
 # Notes:
 # A) Uses the "hexSticker" pacakge
 # B) Option 1: Triforce
 # C) Various color palettes
 # D) Option 2: Orion's Sword
+# E) 2022/04/02: Updated 'spatstat' suite packages
 # ----------------------------------------------------- #
 
 # Option 1: Triforce
 
 # Packages
-library(spatstat)
+library(spatstat.geom)
+library(spatstat.random)
 library(hexSticker)
 
 # Settings
@@ -33,30 +35,31 @@ x2 <- c(1-0.33, 1.1, 1.25, 1.6, 1.5+0.33, 1-0.33)
 y2 <- c(1.5, 1, 1.433013, 1, 1.5, 1.5)
 
 # Create point patterns
-g1 <- rsyst(nx = 20, win = spatstat::owin(poly=list(x=x,y=y)))
-g2 <- rsyst(nx = 20, win = spatstat::owin(poly=list(x=rev(x),y=rev(y1))))
-g3 <- spatstat::rpoispp(lambda = 20, win = spatstat::owin(poly=list(x=x2,y=y2)))
+g1 <- rsyst(nx = 20, win = spatstat.geom::owin(poly=list(x=x,y=y)))
+g2 <- rsyst(nx = 20, win = spatstat.geom::owin(poly=list(x=rev(x),y=rev(y1))))
+g3 <- spatstat.random::rpoispp(lambda = 20, win = spatstat.geom::owin(poly=list(x=x2,y=y2)))
 
 # Set marks for point patterns (for colors)
-spatstat::marks(g1) <- 1
-spatstat::marks(g2) <- 2
-spatstat::marks(g3) <- 1
+spatstat.geom::marks(g1) <- 1
+spatstat.geom::marks(g2) <- 2
+spatstat.geom::marks(g3) <- 1
 
 # Combine point patterns and set marks to be factors
-g4 <- spatstat::superimpose(g1, g2, g3)
-spatstat::marks(g4) <- as.factor(spatstat::marks(g4))
-#spatstat::plot.ppp(g4, cols = c("moccasin", "sienna1"), show.all = F)
+g4 <- spatstat.geom::superimpose(g1, g2, g3)
+spatstat.geom::marks(g4) <- as.factor(spatstat.geom::marks(g4))
+#spatstat.geom::plot.ppp(g4, cols = c("moccasin", "sienna1"), show.all = F)
 
 # Create hexSticker
 ## the Balance Within palette https://www.color-hex.com/color-palette/14625
-s <- hexSticker::sticker(~spatstat::plot.ppp(g4, cols = c("#ee9a00", "#698b69"),
-                                             show.all = F, cex = 0.5,
-                                             pch = c(8,8)),
-                         package="sparrpowR", p_size = 5, p_color = "#ffe4b5",
-                         s_x=0.7, s_y=0.1, s_width=3.33, s_height=3.33,
+s <- hexSticker::sticker(~ spatstat.geom::plot.ppp(g4, cols = c("#ee9a00", "#698b69"),
+                                                   show.all = F, cex = 0.5,
+                                                   pch = c(8,8)),
+                         package = "sparrpowR", p_size = 5, p_color = "#ffe4b5",
+                         s_x = 0.9, s_y = 0.35, s_width = 3.33, s_height = 3.33,
                          h_fill = "#344960",
                          h_color = "#8b3a3a",
                          dpi = 1000,
                          filename = "./man/figures/sparrpowR.png",
                          white_around_sticker = T)
-# -------------------- END OF CODE -------------------- #
+
+# -------------------- END OF CODE -------------------- #