Merge pull request #11 from ropensci/colors

adds cpr_make_pal()

DESCRIPTION

@@ -60,7 +60,9 @@ Suggests:
     withr,
     fs,
     readr,
-    usethis
+    usethis,
+    scales,
+    colorBlindness
 Config/testthat/edition: 3
 Depends: 
     R (>= 4.1.0)

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(cpr_classify_endem)
 export(cpr_classify_signif)
+export(cpr_make_pal)
 export(cpr_iter_test)
 export(cpr_rand_comm)
 export(cpr_rand_test)

R/cpr_make_pal.R

@@ -0,0 +1,70 @@
+#' Make a palette of colors for plotting CANAPE results
+#'
+#' Palettes can also be loaded by name directly (see "Other colors" below).
+#'
+#' Palettes with the name 'mishler2014' correspond to colors used in Mishler et
+#' al. 2014. This color scheme has been widely used to show CANAPE
+#' results, but some colors may not be distinguishable to people with color
+#' vision deficiency (CVD).
+#'
+#' Palettes with the name 'canaper1' or 'canaper2' are based on the Okabe-Ito
+#' palette (endemism; Okabe & Ito 2002) or RColorBrewer (significance) and
+#' should be CVD-friendly.
+#'
+#' Names of colors correspond to either endemism type or
+#' *p*-rank output by [cpr_classify_endem()] or [cpr_classify_signif()],
+#' respectively.
+#'
+#' @param name Character vector of length 1; name of palette to select. Must be
+#'   one of 'mishler2014', 'canaper1', or 'canaper2'
+#' @param type Character vector of length 1; type of palette to select. Must be
+#'  one of 'endem' (endemism) or 'signif' (*p*-rank significance)
+#' @references Mishler, B., Knerr, N., González-Orozco, C. et al.  (2014)
+#'   Phylogenetic measures of biodiversity and
+#'   neo- and paleo-endemism in Australian Acacia. Nat Commun, 5: 4473.
+#'   \doi{10.1038/ncomms5473}
+#' @references Okabe, M., & Ito, K. (2002) Color
+#'   Universal Design (CUD) - How to make figures and presentations that are
+#'   friendly to Colorblind people. J*FLY Data
+#'   Depository for Drosophila Researchers. <https://jfly.uni-koeln.de/color>
+#' @return Named character vector; color hex codes
+#' @family colors
+#' @export
+#' @examples
+#' cpr_make_pal("mishler2014", "endem")
+#' cpr_make_pal("canaper1", "endem")
+#' scales::show_col(cpr_make_pal("mishler2014", "endem"))
+cpr_make_pal <- function(name, type) {
+  # Check input: name
+  assertthat::assert_that(assertthat::is.string(name))
+  assertthat::assert_that(assertthat::noNA(name))
+  assertthat::assert_that(
+    name %in% c("mishler2014", "canaper1", "canaper2"),
+    msg = "'name' may only include 'mishler2014', 'canaper1', or 'canaper2'"
+  )
+  # Check input: type
+  assertthat::assert_that(assertthat::is.string(type))
+  assertthat::assert_that(assertthat::noNA(type))
+  assertthat::assert_that(
+    type %in% c("endem", "signif"),
+    msg = "'type' may only include 'endem' or 'signif'"
+  )
+  if (type == "endem" && name == "mishler2014") {
+    return(mishler_endem_cols)
+  }
+  if (type == "endem" && name == "canaper1") {
+    return(cpr_endem_cols)
+  }
+  if (type == "endem" && name == "canaper2") {
+    return(cpr_endem_cols_2)
+  }
+  if (type == "signif" && name == "mishler2014") {
+    return(mishler_signif_cols)
+  }
+  if (type == "signif" && name == "canaper1") {
+    return(cpr_signif_cols)
+  }
+  if (type == "signif" && name == "canaper2") {
+    return(cpr_signif_cols_2)
+  }
+}

R/data.R

@@ -124,58 +124,101 @@
 #' biod_results
 "biod_results"
 
-#' Color palette for plotting results of randomization test
+#' Original color palette for plotting results of CANAPE
+#'
+#' Character vector with names corresponding to endemism types
+#' and values corresponding to color codes. Original palette used by
+#' Mishler et al. (2014). May not be distinguishable to people with
+#' color-vision deficiency (CVD).
+#'
+#' @srrstats {G1.4} uses roxygen
+#'
+#' @family colors
+#'
+#' @references Mishler, B., Knerr, N., González-Orozco, C. et al.  (2014)
+#'   Phylogenetic measures of biodiversity and neo- and paleo-endemism in
+#'   Australian Acacia. Nat Commun, 5: 4473. \doi{10.1038/ncomms5473}
+#'
+#' @examples
+#' mishler_signif_cols
+#' scales::show_col(mishler_signif_cols)
+"mishler_signif_cols"
+
+#' CVD-friendly color palette for plotting results of randomization test
 #'
 #' Character vector with names corresponding to significance levels
 #' and values corresponding to color codes.
 #'
 #' @srrstats {G1.4} uses roxygen
 #'
+#' @family colors
+#'
 #' @examples
 #' cpr_signif_cols
-#' \dontrun{
 #' scales::show_col(cpr_signif_cols)
-#' }
 "cpr_signif_cols"
 
-#' Color palette for plotting results of randomization test, version 2
+#' CVD-friendly color palette for plotting results of randomization test,
+#' version 2
 #'
 #' Character vector with names corresponding to significance levels and values
 #' corresponding to color codes, with "not significant" colored grey.
 #'
 #' @srrstats {G1.4} uses roxygen
 #'
+#' @family colors
+#'
 #' @examples
 #' cpr_signif_cols_2
-#' \dontrun{
 #' scales::show_col(cpr_signif_cols_2)
-#' }
 "cpr_signif_cols_2"
 
-#' Color palette for plotting results of CANAPE
+#' Original color palette for plotting results of CANAPE
 #'
 #' Character vector with names corresponding to endemism types
-#' and values corresponding to color codes.
+#' and values corresponding to color codes. Original palette used by
+#' Mishler et al. (2014). May not be distinguishable to people with
+#' color-vision deficiency (CVD).
 #'
 #' @srrstats {G1.4} uses roxygen
 #'
+#' @family colors
+#'
+#' @references Mishler, B., Knerr, N., González-Orozco, C. et al.  (2014)
+#'   Phylogenetic measures of biodiversity and neo- and paleo-endemism in
+#'   Australian Acacia. Nat Commun, 5: 4473. \doi{10.1038/ncomms5473}
+#'
+#' @examples
+#' mishler_endem_cols
+#' scales::show_col(mishler_endem_cols)
+"mishler_endem_cols"
+
+#' CVD-friendly color palette for plotting results of CANAPE
+#'
+#' Character vector with names corresponding to endemism types
+#' and values corresponding to color codes. Should be distinguishable to
+#' people with color-vision deficiency (CVD).
+#'
+#' @srrstats {G1.4} uses roxygen
+#'
+#' @family colors
+#'
 #' @examples
 #' cpr_endem_cols
-#' \dontrun{
 #' scales::show_col(cpr_endem_cols)
-#' }
 "cpr_endem_cols"
 
-#' Color palette for plotting results of CANAPE, version 2
+#' CVD-friendly color palette for plotting results of CANAPE, version 2
 #'
 #' Character vector with names corresponding to endemism types and values
-#' corresponding to color codes, with "not significant" colored grey.
+#' corresponding to color codes, with "not significant" colored grey. Should
+#' be distinguishable to people with color-vision deficiency (CVD).
 #'
 #' @srrstats {G1.4} uses roxygen
 #'
+#' @family colors
+#'
 #' @examples
 #' cpr_endem_cols_2
-#' \dontrun{
 #' scales::show_col(cpr_endem_cols_2)
-#' }
 "cpr_endem_cols_2"

_pkgdown.yml

@@ -21,13 +21,20 @@ reference:
 - title: Classification
   desc: Functions to classify the results of the randomization test
 - contents: starts_with("cpr_classify")
-- title: Data
+- title: Datasets
   desc: Datasets included in this package
 - contents:
   - acacia
   - biod_example
   - phylocom
   - biod_results
 - title: Color palettes
-  desc: Palettes for plotting classification results
-- contents: matches("_cols")
+  desc: Colors for plotting classification results
+- contents:
+  - cpr_make_pal
+  - mishler_endem_cols
+  - cpr_endem_cols
+  - cpr_endem_cols_2
+  - mishler_signif_cols
+  - cpr_signif_cols
+  - cpr_signif_cols_2

codemeta.json

@@ -14,7 +14,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.2.0 (2022-04-22)",
+  "runtimePlatform": "R version 4.2.1 (2022-06-23)",
   "author": [
     {
       "@type": "Person",
@@ -249,6 +249,30 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=usethis"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "scales",
+      "name": "scales",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=scales"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "colorBlindness",
+      "name": "colorBlindness",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=colorBlindness"
     }
   ],
   "softwareRequirements": {
@@ -385,7 +409,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "280.144KB",
+  "fileSize": "9701.825KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -410,6 +434,13 @@
     }
   ],
   "releaseNotes": "https://github.com/ropensci/canaper/blob/master/NEWS.md",
+  "readme": "https://github.com/ropensci/canaper/blob/main/README.md",
   "contIntegration": ["https://github.com/ropensci/canaper/actions", "https://codecov.io/gh/ropensci/canaper?branch=main"],
-  "developmentStatus": "https://www.repostatus.org/#wip"
+  "developmentStatus": "https://www.repostatus.org/#active",
+  "review": {
+    "@type": "Review",
+    "url": "https://github.com/ropensci/software-review/issues/475",
+    "provider": "https://ropensci.org"
+  },
+  "keywords": ["biodiversity", "canape"]
 }

data-raw/cpr_cols.R

@@ -27,6 +27,31 @@ cpr_signif_cols_2 <-
 
 usethis::use_data(cpr_signif_cols_2, overwrite = TRUE)
 
+# - Randomization, Mishler 2014
+mishler_signif_cols <-
+  c(
+    "< 0.01" = "#7D170E", #  Dark red
+    "< 0.025" = "#E73323", # Light red
+    "not significant" = "#FAFAD6", # Beige
+    "> 0.975" = "#5577F7", # Light blue
+    "> 0.99" = "#2E4086" # Dark blue
+  )
+
+usethis::use_data(mishler_signif_cols, overwrite = TRUE)
+
+# - Mishler 2014
+# original biodiverse colors
+mishler_endem_cols <-
+  c(
+    "neo" = "#E73323",
+    "paleo" = "#5577F7",
+    "not significant" = "#FAFAD6",
+    "mixed" = "#BF84F8",
+    "super" = "#8E25F6"
+  )
+
+usethis::use_data(mishler_endem_cols, overwrite = TRUE)
+
 # - CANAPE (Okabe-Ito CVD safe)
 cpr_endem_cols <-
   c(
@@ -55,8 +80,8 @@ usethis::use_data(cpr_endem_cols_2, overwrite = TRUE)
 # - cpr_signif_cols
 tibble(
   var_a = names(cpr_signif_cols),
-  var_b = 1:length(cpr_signif_cols),
-  var_c = 1:length(cpr_signif_cols),
+  var_b = seq_along(cpr_signif_cols),
+  var_c = seq_along(cpr_signif_cols),
 ) |>
   ggplot(aes(x = var_b, y = var_c, color = var_a)) +
   geom_point(size = 3) +
@@ -68,8 +93,8 @@ colorBlindness::cvdPlot()
 # - cpr_signif_cols_2
 tibble(
   var_a = names(cpr_signif_cols_2),
-  var_b = 1:length(cpr_signif_cols_2),
-  var_c = 1:length(cpr_signif_cols_2),
+  var_b = seq_along(cpr_signif_cols_2),
+  var_c = seq_along(cpr_signif_cols_2),
 ) |>
   ggplot(aes(x = var_b, y = var_c, color = var_a)) +
   geom_point(size = 3) +
@@ -81,8 +106,8 @@ colorBlindness::cvdPlot()
 # - cpr_endem_cols
 tibble(
   var_a = names(cpr_endem_cols),
-  var_b = 1:length(cpr_endem_cols),
-  var_c = 1:length(cpr_endem_cols),
+  var_b = seq_along(cpr_endem_cols),
+  var_c = seq_along(cpr_endem_cols),
 ) |>
   ggplot(aes(x = var_b, y = var_c, color = var_a)) +
   geom_point(size = 3) +
@@ -94,8 +119,8 @@ colorBlindness::cvdPlot()
 # - cpr_endem_cols_2
 tibble(
   var_a = names(cpr_endem_cols_2),
-  var_b = 1:length(cpr_endem_cols_2),
-  var_c = 1:length(cpr_endem_cols_2),
+  var_b = seq_along(cpr_endem_cols_2),
+  var_c = seq_along(cpr_endem_cols_2),
 ) |>
   ggplot(aes(x = var_b, y = var_c, color = var_a)) +
   geom_point(size = 3) +