Merge pull request #257 from rmaia/R-4.0.0

Update minimum R version to 4.0.0

.github/workflows/R-CMD-check.yaml

@@ -49,8 +49,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: 
-            any::rcmdcheck,
-            [email protected]
+            any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

DESCRIPTION

@@ -39,7 +39,7 @@ License: GPL (>= 2)
 URL: http://pavo.colrverse.com, https://github.com/rmaia/pavo/
 BugReports: https://github.com/rmaia/pavo/issues
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.0.0)
 Imports:
     cluster,
     future.apply,
@@ -49,8 +49,7 @@ Imports:
     farver,
     plot3D,
     progressr,
-    sf,
-    viridisLite
+    sf
 Suggests:
     alphashape3d,
     imager,
@@ -68,5 +67,5 @@ Config/Needs/website:
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3

NAMESPACE

@@ -3,6 +3,7 @@
 S3method(as.rimg,"magick-image")
 S3method(as.rimg,cimg)
 S3method(as.rimg,default)
+S3method(imager::as.cimg,rimg)
 S3method(merge,rspec)
 S3method(plot,colspace)
 S3method(plot,rimg)
@@ -56,7 +57,6 @@ export(procimg)
 export(procspec)
 export(projplot)
 export(projpoints)
-export(rimg2cimg)
 export(rimg2magick)
 export(segplot)
 export(segspace)
@@ -102,7 +102,6 @@ importFrom(graphics,lines)
 importFrom(graphics,locator)
 importFrom(graphics,mtext)
 importFrom(graphics,par)
-importFrom(graphics,plot)
 importFrom(graphics,plot.default)
 importFrom(graphics,plot.new)
 importFrom(graphics,plot.window)

NEWS.md

@@ -1,9 +1,17 @@
 # pavo 2.10.0
 
+## NEW FEATURES AND SIGNIFICANT CHANGES
+
+- the `rimg2cimg()` function has been removed in favour of a custom `as.cimg()` method. 
+
 ## MINOR FEATURES AND BUG FIXES
 
 - `as.rspec()` now works out of the box with `tibble`, rather than requiring users to pass a standard data.frame.
 
+## INTERNAL CHANGES
+
+- dependency on the `viridisLite` package has been removed in favour of recent base R functions
+
 # pavo 2.9.0
 
 ## NEW FEATURES AND SIGNIFICANT CHANGES

R/aggplot.R

@@ -27,7 +27,7 @@
 #'
 #' @export
 #'
-#' @importFrom graphics legend lines par plot.default polygon
+#' @importFrom graphics legend lines par polygon
 #' @importFrom grDevices adjustcolor
 #' @importFrom stats sd
 #'
@@ -137,9 +137,11 @@ aggplot <- function(rspecdata, by = NULL, FUN.center = mean, FUN.error = sd,
     lcol <- rep(lcol, ncol(cntplotspecs))
   }
 
-  col_list <- c(
-    "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3",
-    "#FF7F00", "#FFFF33", "#A65628", "#F781BF"
+  col_list <- grDevices::palette.colors(
+    ncol(cntplotspecs),
+    palette = "Okabe-Ito",
+    alpha = 1,
+    recycle = TRUE
   )
 
   col_list <- rep_len(col_list, dim(cntplotspecs)[2])

R/as.rimg.R

@@ -213,15 +213,15 @@ NULL
 
 #' @rdname img_conversion
 #'
-#' @export
-rimg2cimg <- function(image) {
+#' @exportS3Method imager::as.cimg
+as.cimg.rimg <- function(image) {
   ## Check for imager
   if (!requireNamespace("imager", quietly = TRUE)) {
     stop("Package \"imager\" needed for conversion to cimg. Please install it.",
          call. = FALSE
     )
   }
-  suppressWarnings(imager::as.cimg(image, cc = 3))
+  NextMethod("as.cimg", image, cc = 3)
 }
 #' @rdname img_conversion
 #'

R/explorespec.R

@@ -102,7 +102,7 @@ explorespec <- function(rspecdata, by = NULL,
   arg$x <- wl
 
   if (is.null(arg$col)) {
-    col_list <- viridisLite::viridis(max(table(by)))
+    col_list <- grDevices::hcl.colors(max(table(by)))
   } else {
     col_list <- arg$col
   }

R/jndplot.R

@@ -38,7 +38,7 @@
 #'
 #' @export
 #'
-#' @importFrom graphics plot.default par plot.default points arrows
+#' @importFrom graphics par points arrows
 #' @importFrom grDevices trans3d
 #'
 #' @keywords internal

R/pavo-package.R

@@ -1,7 +1,7 @@
 #' @keywords internal
 "_PACKAGE"
 
-#' @importFrom graphics plot
+#' @importFrom graphics plot.default
 # This functions has been moved to base since R 4.0.0
 NULL
 

R/plot.rspec.R

@@ -99,7 +99,7 @@ plot.rspec <- function(x, select = NULL, type = c("overlay", "stack", "heatmap")
     }
 
     if (is.null(arg$col)) {
-      arg$col <- viridisLite::cividis(n)
+      arg$col <- grDevices::hcl.colors(n, palette = "cividis")
     } else {
       jc <- colorRampPalette(arg$col)
       arg$col <- jc(n)

R/plotsmooth.R

@@ -81,11 +81,12 @@ plotsmooth <- function(rspecdata, minsmooth = 0.05, maxsmooth = 0.20,
 
   par(mar = c(2, 2, 2, 2), oma = c(3, 3, 0, 0))
 
-  col_list <- c(
-    "#000000", "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3",
-    "#FF7F00", "#ffdd33", "#A65628", "#F781BF"
+  cols <- grDevices::palette.colors(
+    n = length(curves),
+    palette = "Okabe-Ito",
+    alpha = 1,
+    recycle = TRUE
   )
-  cols <- col_list[seq_len(curves)]
 
   # Creates the smooth data matrix
   for (i in seq_len(nplots)) {

R/procimg.R

@@ -225,7 +225,7 @@ procimg <- function(image, resize = NULL, rotate = NULL, scaledist = NULL,
 }
 
 # Internal function for calibrating image scale
-#' @importFrom graphics plot rasterImage locator
+#' @importFrom graphics rasterImage locator
 #' @importFrom stats dist
 scaler <- function(image_i, scaledist_i, col, ...) {
   # Plot

pkgdown/_pkgdown.yml

@@ -1,4 +1,4 @@
-url: http://pavo.colrverse.com
+url: https://pavo.colrverse.com
 
 home:
   title: Perceptual Analysis, Visualization and Organization of Spectral Colour Data in R
@@ -18,27 +18,24 @@ reference:
   - '`merge.rspec`'
   - '`procimg`'
   - '`procspec`'
-  - '`rimg2cimg`'
   - '`spec2rgb`'
   - '`subset.rspec`'
   - '`simulate_spec`'
+  - img_conversion
 
 - title: Visualisation
   desc: "Functions for visualising spectral data, including the results of visual modelling"
   contents:
+  - starts_with("plot.")
   - '`aggplot`'
   - '`axistetra`'
   - '`explorespec`'
   - '`legendtetra`'
-  - '`plot.colspace`'
-  - '`plot.rimg`'
-  - '`plot.rspec`'
   - '`plotsmooth`'
   - '`points.colspace`'
   - '`projplot`'
   - '`sensdata`'
   - '`tcsplot`'
-  - '`plot.sensmod`'
 
 - title: Analysis
   desc: "Functions for analysing spectral data"