dieghernan · dieghernan · Nov 20, 2023 · Nov 20, 2023
diff --git a/NEWS.md b/NEWS.md
@@ -1,17 +1,27 @@
 # tidyterra (development version)
 
+**tidyterra** has been accepted on JOSS. Please use the result of
+`citation("tidyterra")` or the following string:
+
+> Hernangómez, D. (2023). "Using the tidyverse with terra objects: the tidyterra
+> package." *Journal of Open Source Software*, *8*(91), 5751. ISSN 2475-9066,
+> <https://doi.org/10.21105/joss.05751>
+
+Other changes on this version:
+
 -   Support for SpatRasters with a color table
     -   `autoplot.SpatRaster()` can detect now SpatRasters with color tables.
     -   `geom_spatraster()` can detect now SpatRasters with color tables.
     -   New scales for plotting SpatRasters with color tables:
         `scale_fill_coltab()` and rest of family scales (`colour`).
     -   tidyverse verbs keeps the associated `coltab` of a SpatRaster.
--   By default all the discrete scales of tidyterra now have the following
+-   By default all the discrete scales of **tidyterra** now have the following
     setup: `na.translate = FALSE`.
+-   By default, all the non-discrete (e.g. continuous or breaks) scales of
+    **tidyterra** have now `na.value = "transparent"` (#120).
 -   Enhanced `glimpse.Spat()` with meta-information on type of geometry, crs,
     etc.
 -   New messaging interface thanks to [**cli**](https://cli.r-lib.org/) package.
--   Update citation.  
 
 # tidyterra 0.4.1
 

diff --git a/R/scales_coltab.R b/R/scales_coltab.R
@@ -61,7 +61,7 @@
 #' }
 scale_fill_coltab <- function(data, ..., alpha = 1,
                               na.translate = FALSE,
-                              na.value = NA,
+                              na.value = "transparent",
                               drop = TRUE) {
   getcols <- get_coltab_pal(data)
   if (is.null(getcols)) {
@@ -88,7 +88,7 @@ scale_fill_coltab <- function(data, ..., alpha = 1,
 #' @rdname scale_coltab
 #' @export
 scale_colour_coltab <- function(data, ..., alpha = 1, na.translate = FALSE,
-                                na.value = NA, drop = TRUE) {
+                                na.value = "transparent", drop = TRUE) {
   getcols <- get_coltab_pal(data)
   if (is.null(getcols)) {
     return(ggplot2::geom_blank())

diff --git a/R/scales_cross_blended.R b/R/scales_cross_blended.R
@@ -37,10 +37,14 @@
 #' @name scale_cross_blended
 #'
 #' @inheritDotParams ggplot2::discrete_scale breaks:drop
-#' @inheritDotParams ggplot2::continuous_scale breaks:labels na.value
+#' @inheritDotParams ggplot2::continuous_scale breaks:labels
 #' @inheritDotParams ggplot2::binned_scale breaks:limits nice.breaks
 #' @param na.translate Should `NA` values be removed from the legend? Default
 #'   is `TRUE`.
+#' @param na.value Missing values will be replaced with this value. By default,
+#'   \CRANpkg{tidyterra} uses `na.value = "transparent"` so cells with `NA` are
+#'   not filled. See also
+#'   [#120](https://github.com/dieghernan/tidyterra/issues/120).
 #' @param drop Should unused factor levels be omitted from the scale? The
 #'   default (`TRUE`) removes unused factors.
 #' @inheritParams ggplot2::scale_fill_viridis_b
@@ -233,7 +237,7 @@ scale_colour_cross_blended_d <- function(palette = "cold_humid", ...,
 #' @rdname scale_cross_blended
 scale_fill_cross_blended_c <- function(palette = "cold_humid", ...,
                                        alpha = 1, direction = 1,
-                                       na.value = NA, guide = "colourbar") {
+                                       na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -264,7 +268,7 @@ scale_fill_cross_blended_c <- function(palette = "cold_humid", ...,
 #' @rdname scale_cross_blended
 scale_colour_cross_blended_c <- function(palette = "cold_humid", ...,
                                          alpha = 1, direction = 1,
-                                         na.value = NA, guide = "colourbar") {
+                                         na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -294,7 +298,7 @@ scale_colour_cross_blended_c <- function(palette = "cold_humid", ...,
 #' @rdname scale_cross_blended
 scale_fill_cross_blended_b <- function(palette = "cold_humid", ...,
                                        alpha = 1, direction = 1,
-                                       na.value = NA, guide = "coloursteps") {
+                                       na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -323,7 +327,7 @@ scale_fill_cross_blended_b <- function(palette = "cold_humid", ...,
 #' @rdname scale_cross_blended
 scale_colour_cross_blended_b <- function(palette = "cold_humid", ...,
                                          alpha = 1, direction = 1,
-                                         na.value = NA, guide = "coloursteps") {
+                                         na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -476,7 +480,7 @@ scale_fill_cross_blended_tint_c <- function(palette = "cold_humid", ...,
                                             alpha = 1, direction = 1,
                                             values = NULL,
                                             limits = NULL,
-                                            na.value = NA,
+                                            na.value = "transparent",
                                             guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
@@ -521,7 +525,7 @@ scale_colour_cross_blended_tint_c <- function(palette = "cold_humid", ...,
                                               alpha = 1, direction = 1,
                                               values = NULL,
                                               limits = NULL,
-                                              na.value = NA,
+                                              na.value = "transparent",
                                               guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
@@ -566,7 +570,7 @@ scale_fill_cross_blended_tint_b <- function(palette = "cold_humid", ...,
                                             alpha = 1, direction = 1,
                                             values = NULL,
                                             limits = NULL,
-                                            na.value = NA,
+                                            na.value = "transparent",
                                             guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
@@ -612,7 +616,7 @@ scale_colour_cross_blended_tint_b <- function(palette = "cold_humid", ...,
                                               alpha = 1, direction = 1,
                                               values = NULL,
                                               limits = NULL,
-                                              na.value = NA,
+                                              na.value = "transparent",
                                               guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")

diff --git a/R/scales_hypso.R b/R/scales_hypso.R
@@ -40,7 +40,7 @@
 #' @name scale_hypso
 #'
 #' @inheritDotParams ggplot2::discrete_scale breaks:drop
-#' @inheritDotParams ggplot2::continuous_scale breaks:labels na.value
+#' @inheritDotParams ggplot2::continuous_scale breaks:labels
 #' @inheritDotParams ggplot2::binned_scale breaks:limits nice.breaks
 #' @inheritParams scale_cross_blended
 #' @param palette A valid palette name. The name is matched to the list of
@@ -224,7 +224,7 @@ scale_colour_hypso_d <- function(palette = "etopo1_hypso", ...,
 #' @rdname scale_hypso
 scale_fill_hypso_c <- function(palette = "etopo1_hypso", ...,
                                alpha = 1, direction = 1,
-                               na.value = NA, guide = "colourbar") {
+                               na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -254,7 +254,7 @@ scale_fill_hypso_c <- function(palette = "etopo1_hypso", ...,
 #' @rdname scale_hypso
 scale_colour_hypso_c <- function(palette = "etopo1_hypso", ...,
                                  alpha = 1, direction = 1,
-                                 na.value = NA, guide = "colourbar") {
+                                 na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -284,7 +284,7 @@ scale_colour_hypso_c <- function(palette = "etopo1_hypso", ...,
 #' @rdname scale_hypso
 scale_fill_hypso_b <- function(palette = "etopo1_hypso", ...,
                                alpha = 1, direction = 1,
-                               na.value = NA, guide = "coloursteps") {
+                               na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -313,7 +313,7 @@ scale_fill_hypso_b <- function(palette = "etopo1_hypso", ...,
 #' @rdname scale_hypso
 scale_colour_hypso_b <- function(palette = "etopo1_hypso", ...,
                                  alpha = 1, direction = 1,
-                                 na.value = NA, guide = "coloursteps") {
+                                 na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -463,7 +463,7 @@ scale_fill_hypso_tint_c <- function(palette = "etopo1_hypso", ...,
                                     alpha = 1, direction = 1,
                                     values = NULL,
                                     limits = NULL,
-                                    na.value = NA,
+                                    na.value = "transparent",
                                     guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
@@ -507,7 +507,7 @@ scale_colour_hypso_tint_c <- function(palette = "etopo1_hypso", ...,
                                       alpha = 1, direction = 1,
                                       values = NULL,
                                       limits = NULL,
-                                      na.value = NA,
+                                      na.value = "transparent",
                                       guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
@@ -552,7 +552,7 @@ scale_fill_hypso_tint_b <- function(palette = "etopo1_hypso", ...,
                                     alpha = 1, direction = 1,
                                     values = NULL,
                                     limits = NULL,
-                                    na.value = NA, guide = "coloursteps") {
+                                    na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -596,7 +596,7 @@ scale_colour_hypso_tint_b <- function(palette = "etopo1_hypso", ...,
                                       alpha = 1, direction = 1,
                                       values = NULL,
                                       limits = NULL,
-                                      na.value = NA, guide = "coloursteps") {
+                                      na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }

diff --git a/R/scales_terrain.R b/R/scales_terrain.R
@@ -23,7 +23,7 @@
 #' @name scale_terrain
 #'
 #' @inheritDotParams ggplot2::discrete_scale breaks:drop
-#' @inheritDotParams ggplot2::continuous_scale breaks:labels na.value
+#' @inheritDotParams ggplot2::continuous_scale breaks:labels
 #' @inheritDotParams ggplot2::binned_scale breaks:limits nice.breaks
 #' @inheritParams scale_cross_blended
 #'
@@ -127,7 +127,7 @@ scale_colour_terrain_d <- function(..., alpha = 1, direction = 1,
 #' @export
 #' @rdname scale_terrain
 scale_fill_terrain_c <- function(..., alpha = 1, direction = 1,
-                                 na.value = NA, guide = "colourbar") {
+                                 na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -152,7 +152,7 @@ scale_fill_terrain_c <- function(..., alpha = 1, direction = 1,
 #' @export
 #' @rdname scale_terrain
 scale_colour_terrain_c <- function(..., alpha = 1, direction = 1,
-                                   na.value = NA, guide = "colourbar") {
+                                   na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -178,7 +178,7 @@ scale_colour_terrain_c <- function(..., alpha = 1, direction = 1,
 #' @export
 #' @rdname scale_terrain
 scale_fill_terrain_b <- function(..., alpha = 1, direction = 1,
-                                 na.value = NA, guide = "coloursteps") {
+                                 na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -203,7 +203,7 @@ scale_fill_terrain_b <- function(..., alpha = 1, direction = 1,
 #' @export
 #' @rdname scale_terrain
 scale_colour_terrain_b <- function(..., alpha = 1, direction = 1,
-                                   na.value = NA, guide = "coloursteps") {
+                                   na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }

diff --git a/R/scales_whitebox.R b/R/scales_whitebox.R
@@ -27,7 +27,7 @@
 #' @name scale_whitebox
 #'
 #' @inheritDotParams ggplot2::discrete_scale breaks:drop
-#' @inheritDotParams ggplot2::continuous_scale breaks:labels na.value
+#' @inheritDotParams ggplot2::continuous_scale breaks:labels
 #' @inheritDotParams ggplot2::binned_scale breaks:limits nice.breaks
 #' @inheritParams scale_cross_blended
 #' @param palette A valid palette name. The name is matched to the list of
@@ -153,7 +153,7 @@ scale_colour_whitebox_d <- function(palette = "high_relief", ...,
 #' @rdname scale_whitebox
 scale_fill_whitebox_c <- function(palette = "high_relief", ...,
                                   alpha = 1, direction = 1,
-                                  na.value = NA, guide = "colourbar") {
+                                  na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -182,7 +182,7 @@ scale_fill_whitebox_c <- function(palette = "high_relief", ...,
 #' @rdname scale_whitebox
 scale_colour_whitebox_c <- function(palette = "high_relief", ...,
                                     alpha = 1, direction = 1,
-                                    na.value = NA, guide = "colourbar") {
+                                    na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -212,7 +212,7 @@ scale_colour_whitebox_c <- function(palette = "high_relief", ...,
 #' @rdname scale_whitebox
 scale_fill_whitebox_b <- function(palette = "high_relief", ...,
                                   alpha = 1, direction = 1,
-                                  na.value = NA, guide = "coloursteps") {
+                                  na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -242,7 +242,7 @@ scale_fill_whitebox_b <- function(palette = "high_relief", ...,
 #' @rdname scale_whitebox
 scale_colour_whitebox_b <- function(palette = "high_relief", ...,
                                     alpha = 1, direction = 1,
-                                    na.value = NA, guide = "coloursteps") {
+                                    na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }

diff --git a/R/scales_wiki.R b/R/scales_wiki.R
@@ -27,12 +27,12 @@
 #'
 #' @name scale_wiki
 #'
+#' @inheritParams scale_cross_blended
 #' @inheritDotParams ggplot2::discrete_scale breaks:drop
-#' @inheritDotParams ggplot2::continuous_scale breaks:labels na.value
+#' @inheritDotParams ggplot2::continuous_scale breaks:labels
 #' @inheritDotParams ggplot2::binned_scale breaks:limits nice.breaks
 #' @inheritParams ggplot2::scale_fill_viridis_b
 #' @inheritParams ggplot2::continuous_scale
-#' @inheritParams scale_cross_blended
 #' @seealso [terra::plot()], [ggplot2::scale_fill_viridis_c()]
 #'
 #' See also \pkg{ggplot2} docs on additional `...` parameters:
@@ -140,7 +140,7 @@ scale_color_wiki_d <- scale_colour_wiki_d
 #' @export
 #' @rdname scale_wiki
 scale_fill_wiki_c <- function(..., alpha = 1, direction = 1,
-                              na.value = NA, guide = "colourbar") {
+                              na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -167,7 +167,7 @@ scale_fill_wiki_c <- function(..., alpha = 1, direction = 1,
 #' @export
 #' @rdname scale_wiki
 scale_colour_wiki_c <- function(..., alpha = 1, direction = 1,
-                                na.value = NA, guide = "colourbar") {
+                                na.value = "transparent", guide = "colourbar") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -199,7 +199,7 @@ scale_color_wiki_c <- scale_colour_wiki_c
 #' @export
 #' @rdname scale_wiki
 scale_fill_wiki_b <- function(..., alpha = 1, direction = 1,
-                              na.value = NA, guide = "coloursteps") {
+                              na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }
@@ -226,7 +226,7 @@ scale_fill_wiki_b <- function(..., alpha = 1, direction = 1,
 #' @export
 #' @rdname scale_wiki
 scale_colour_wiki_b <- function(..., alpha = 1, direction = 1,
-                                na.value = NA, guide = "coloursteps") {
+                                na.value = "transparent", guide = "coloursteps") {
   if (alpha < 0 || alpha > 1) {
     cli::cli_abort("{.arg alpha} {.field {alpha}} not in {.field [0,1]}")
   }

diff --git a/R/stat_spatraster.R b/R/stat_spatraster.R
@@ -47,7 +47,7 @@
 #'     aes(color = after_stat(value)),
 #'     geom = "point", maxcell = 250
 #'   ) +
-#'   scale_colour_viridis_c(na.value = NA) +
+#'   scale_colour_viridis_c(na.value = "transparent") +
 #'   facet_wrap(~lyr)
 #'
 #' # Using points and labels
@@ -68,7 +68,7 @@
 #'     alpha = 0.85,
 #'     maxcell = 20
 #'   ) +
-#'   scale_colour_viridis_c(na.value = NA)
+#'   scale_colour_viridis_c(na.value = "transparent")
 #' }
 stat_spatraster <- function(mapping = aes(),
                             data,