Add new features (#104)

* Add new FAQ * First stub * Fix external package * Start preparing new version * Update docs with pkgdev * Update FAQs * Improve funs * tests and checks * Update tests and functions * Update docs with pkgdev * Add tests * Documentation * Add test for keeping coltabs * Add more tests * Fix tests * Add snapshots * Update docs with pkgdev * Create wipe-cache.yaml * revdepcheck * Small typo * Rebuild docs * revdepcheck * Enhance glimpse * Complete glimpse * Update docs with pkgdev * Improve printing * Improve glimpse * Update up to autoplot * Update all but plotting funs * Continue migrating * Update template * Fix references * Add authors * Delete extra * Rebase test_cli (#100) * Update template * Fix references * Add authors * Update docs with pkgdev * End cli migration * Add auto dev * Update docs with pkgdev * revdepcheck * revdepcheck * Update docs with pkgdev * Add more references * Update docs with pkgdev * Update pkgdown , etc. * Update docs with pkgdev * Add In the wild article * Improve docs * Add more pubs * Add more references * Add j lacko * Update docs with pkgdev * Add new article * Fix citation * Add more * Start cleaning * [ImgBot] Optimize images *Total -- 5,967.86kb -> 5,739.73kb (3.82%) /vignettes/lux_ggplot-1.png -- 55.04kb -> 45.03kb (18.19%) /vignettes/contourfilled-1.png -- 76.71kb -> 63.99kb (16.59%) /vignettes/aggregate-2.png -- 50.62kb -> 42.62kb (15.8%) /vignettes/aggregate-1.png -- 38.90kb -> 33.88kb (12.9%) /img/README-spatvec-1.png -- 171.66kb -> 151.26kb (11.88%) /img/README-hypso-1.png -- 227.49kb -> 201.32kb (11.51%) /img/README-example-tile-2.png -- 1,841.75kb -> 1,780.17kb (3.34%) /img/README-example-tile-1.png -- 1,342.09kb -> 1,301.47kb (3.03%) /vignettes/spatraster-example-1.png -- 165.34kb -> 160.38kb (3%) /img/spatraster-example-1.png -- 165.34kb -> 160.38kb (3%) /img/README-example-temp-1.png -- 165.34kb -> 160.38kb (3%) /vignettes/faceted-1.png -- 45.08kb -> 43.93kb (2.56%) /vignettes/contourlines-1.png -- 206.18kb -> 201.09kb (2.47%) /img/README-hypso-2.png -- 327.35kb -> 319.85kb (2.29%) /img/README-example-temp-2.png -- 245.70kb -> 240.50kb (2.11%) /vignettes/rgb-1.png -- 287.13kb -> 282.81kb (1.51%) /vignettes/rgb-2.png -- 348.19kb -> 344.54kb (1.05%) /vignettes/hypso-1.png -- 207.95kb -> 206.11kb (0.89%) Signed-off-by: ImgBotApp <[email protected]> * Update codefactor * Update docs with pkgdev * Improve codefactor and lint * Dedupe badges * Improve docs * Update docs with pkgdev * Add examples and references * Add new reference * Update snapshots as they changed due to new version of testthat * Make get_coltab_pal robust when layers does not have a unique name * Update tests and R local version * Add JOSS data * Update docs with pkgdev * Update issn and header * Update docs with pkgdev --------- Signed-off-by: ImgBotApp <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Diego H <[email protected]> Co-authored-by: Enrico Spinielli <[email protected]> Co-authored-by: ImgBotApp <[email protected]>
dieghernan · Nov 10, 2023 · 6d868b6 · 6d868b6
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diff --git a/.github/workflows/pkgdown-gh-pages.yaml b/.github/workflows/pkgdown-gh-pages.yaml
@@ -31,6 +31,7 @@ jobs:
             local::.
             any::pkgdown
             any::metR
+            Nowosad/spDataLarge
           needs: website
 
       - name: Deploy package

diff --git a/.github/workflows/update-docs.yaml b/.github/workflows/update-docs.yaml
@@ -29,14 +29,15 @@ jobs:
             any::rcmdcheck
             any::pkgdown
             any::metR
+            Nowosad/spDataLarge
             dieghernan/pkgdev
 
           needs: website
 
       - name: Update docs
         run: |
 
-          pkgdev::precompute_vignette_all()
+          # pkgdev::precompute_vignette_all()
           pkgdev::update_docs(precompute = FALSE)
 
         shell: Rscript {0}

diff --git a/CITATION.cff b/CITATION.cff
@@ -8,8 +8,8 @@ message: 'To cite package "tidyterra" in publications use:'
 type: software
 license: MIT
 title: 'tidyterra: ''tidyverse'' Methods and ''ggplot2'' Helpers for ''terra'' Objects'
-version: 0.4.1
-doi: 10.5281/zenodo.6572471
+version: 0.4.1.9000
+doi: 10.21105/joss.05751
 abstract: Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of
   the 'terra' package. It includes also new 'geom_' functions that provide a convenient
   way of visualizing 'terra' objects with 'ggplot2'.
@@ -19,20 +19,23 @@ authors:
   email: [email protected]
   orcid: https://orcid.org/0000-0001-8457-4658
 preferred-citation:
-  type: manual
+  type: article
   title: 'Using the tidyverse with terra objects: the tidyterra package'
   authors:
   - family-names: Hernangómez
     given-names: Diego
     email: [email protected]
     orcid: https://orcid.org/0000-0001-8457-4658
-  doi: 10.5281/zenodo.6572471
+  doi: 10.21105/joss.05751
   year: '2023'
-  version: 0.4.1
-  url: https://dieghernan.github.io/tidyterra/
-  abstract: Extension of the tidyverse for SpatRaster and SpatVector objects of the
-    terra package. It includes also new geom_ functions that provide a convenient
-    way of visualizing terra objects with ggplot2.
+  url: https://doi.org/10.21105/joss.05751
+  publisher:
+    name: The Open Journal
+  volume: '8'
+  issue: '91'
+  journal: Journal of Open Source Software
+  issn: 2475-9066
+  start: '5751'
 repository: https://CRAN.R-project.org/package=tidyterra
 repository-code: https://github.com/dieghernan/tidyterra
 url: https://dieghernan.github.io/tidyterra/
@@ -42,16 +45,16 @@ contact:
   email: [email protected]
   orcid: https://orcid.org/0000-0001-8457-4658
 keywords:
-- cran
-- cran-r
-- ggplot-extension
 - r
-- r-package
+- terra
+- ggplot-extension
 - r-spatial
 - rspatial
+- cran
+- cran-r
+- r-package
 - rstats
 - rstats-package
-- terra
 references:
 - type: software
   title: 'R: A Language and Environment for Statistical Computing'
@@ -294,10 +297,10 @@ references:
   authors:
   - family-names: Henry
     given-names: Lionel
-    email: lionel@rstudio.com
+    email: lionel@posit.co
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
     orcid: https://orcid.org/0000-0003-4757-117X
   year: '2023'
 - type: software

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tidyterra
 Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
-Version: 0.4.1
+Version: 0.4.1.9000
 Authors@R: c(
     person("Diego", "Hernangómez", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-8457-4658")),
@@ -43,10 +43,12 @@ Suggests:
 VignetteBuilder: 
     knitr
 Config/Needs/coverage: covr
-Config/Needs/website: geodata, metR, dieghernan/gitdevr, ragg, styler
+Config/Needs/website: geodata, metR, dieghernan/gitdevr, ragg, styler,
+    Nowosad/spDataLarge, ggspatial
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+X-schema.org-keywords: r, terra, ggplot-extension, r-spatial, rspatial
diff --git a/NAMESPACE b/NAMESPACE
@@ -97,6 +97,7 @@ export(geom_spatraster_rgb)
 export(geom_spatvector)
 export(geom_spatvector_label)
 export(geom_spatvector_text)
+export(get_coltab_pal)
 export(glimpse)
 export(group_by)
 export(group_by_drop_default)
@@ -123,6 +124,7 @@ export(rename_with)
 export(replace_na)
 export(right_join)
 export(rowwise)
+export(scale_color_coltab)
 export(scale_color_cross_blended_b)
 export(scale_color_cross_blended_c)
 export(scale_color_cross_blended_d)
@@ -144,6 +146,7 @@ export(scale_color_whitebox_d)
 export(scale_color_wiki_b)
 export(scale_color_wiki_c)
 export(scale_color_wiki_d)
+export(scale_colour_coltab)
 export(scale_colour_cross_blended_b)
 export(scale_colour_cross_blended_c)
 export(scale_colour_cross_blended_d)
@@ -165,6 +168,7 @@ export(scale_colour_whitebox_d)
 export(scale_colour_wiki_b)
 export(scale_colour_wiki_c)
 export(scale_colour_wiki_d)
+export(scale_fill_coltab)
 export(scale_fill_cross_blended_b)
 export(scale_fill_cross_blended_c)
 export(scale_fill_cross_blended_d)
@@ -207,6 +211,7 @@ export(transmute)
 export(ungroup)
 export(whitebox.colors)
 export(wiki.colors)
+importFrom(cli,qty)
 importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)
 importFrom(dplyr,count)
@@ -252,6 +257,7 @@ importFrom(ggplot2,after_stat)
 importFrom(ggplot2,alpha)
 importFrom(ggplot2,autoplot)
 importFrom(ggplot2,fortify)
+importFrom(grDevices,col2rgb)
 importFrom(grDevices,rgb)
 importFrom(grDevices,terrain.colors)
 importFrom(magrittr,"%>%")

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,18 @@
+# tidyterra (development 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
+    setup: `na.translate = FALSE`.
+-   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
 
 -   Release for JOSS paper. No relevant changes.
@@ -47,7 +62,7 @@
     `"meyers"` and `"nordisk-familjebok"`.
 -   Added colour scales to all palettes: `scale_colour_*`.
 -   Remove use of `ggplot2::aes_string()`.
--   Adapt geom\_`spatraster_contour()` and `geom_spatraster_contour_filled()` to
+-   Adapt `geom_spatraster_contour()` and `geom_spatraster_contour_filled()` to
     the changes introduced in **ggplot2 (3.4.0)**, most notably the adoption of
     `linewidth = .2`, by default.
 

diff --git a/R/as_coordinates.R b/R/as_coordinates.R
@@ -36,7 +36,10 @@
 #'
 as_coordinates <- function(x, as.raster = FALSE) {
   if (!inherits(x, "SpatRaster")) {
-    stop("as_coordinates() needs a SpatRaster object")
+    cli::cli_abort(paste(
+      "{.fun tidyterra::as_coordinates} needs a {.cls SpatRaster} object,",
+      "not a {.cls {class(x)}} object"
+    ))
   }
 
   # Create skeleton

diff --git a/R/as_sf.R b/R/as_sf.R
@@ -53,8 +53,9 @@
 #' group_data(a_gr_sf)
 #'
 as_sf <- function(x, ...) {
-  if (!inherits(x, "SpatVector")) cli::cli_abort("x is not a SpatVector")
-
+  if (!inherits(x, "SpatVector")) {
+    cli::cli_abort("{.arg x} is a {.cls {class(x)}} not a {.cls SpatVector}")
+  }
   sfobj <- sf::st_as_sf(x, ...)
 
   if (is_grouped_spatvector(x)) {

diff --git a/R/as_spatraster.R b/R/as_spatraster.R
@@ -60,15 +60,23 @@ as_spatraster <- function(x, ..., xycols = 1:2, crs = "", digits = 6) {
   # Create from dtplyr
   if (inherits(x, "dtplyr_step")) x <- tibble::as_tibble(x)
 
-
   if (!inherits(x, "data.frame")) {
     cli::cli_abort(
-      "x should be a data.frame/tibble"
+      "{.arg x} should be a {.cls data.frame/tbl}, not {.cls {class(x)}}"
     )
   }
 
-  if (length(xycols) != 2 || !is.numeric(xycols)) {
-    stop("xycols should be two integers: `c(int, int)`")
+  if (length(xycols) != 2) {
+    cli::cli_abort(paste(
+      "{.arg xycols} should have a length of {.val {as.integer(2)}},",
+      "not {.val {length(xycols)}}"
+    ))
+  }
+
+  if (!is.numeric(xycols)) {
+    cli::cli_abort(
+      "{.arg xycols} should be a {.cls integer}, not {.cls {class(xycols)}}"
+    )
   }
 
   xycols <- as.integer(xycols)
@@ -127,7 +135,7 @@ as_spatraster <- function(x, ..., xycols = 1:2, crs = "", digits = 6) {
   xyvalind$valindex <- seq_len(nrow(xyvalind))
 
 
-  values_w_ind <- x_arrange[, -c(1:2)]
+  values_w_ind <- x_arrange[, -c(1, 2)]
   values_w_ind$valindex <- xyvalind$valindex
 
 

diff --git a/R/as_spatvector.R b/R/as_spatvector.R
@@ -74,17 +74,22 @@ as_spatvector <- function(x, ...) {
 #' @export
 as_spatvector.data.frame <- function(x, ..., geom = c("lon", "lat"), crs = "") {
   if (!length(geom) %in% c(1, 2)) {
-    stop("geom should be of lenght 1 or 2")
+    cli::cli_abort(paste(
+      "{.arg geom} should be of length {.val {as.integer(1)}} or",
+      "{.val {as.integer(2)}}, not {.val {length(geom)}}"
+    ))
   }
 
   if (!is.character(geom)) {
-    stop("geom should be of type <character>")
+    cli::cli_abort(paste(
+      "{.arg geom} should be a {.cls character}, not",
+      "{.cls {class(geom)}}"
+    ))
   }
 
   if (!all(geom %in% names(x))) {
-    stop(
-      paste0("Column(s) <", paste0(setdiff(geom, names(x)), collapse = ",")),
-      "> not found in x"
+    cli::cli_abort(
+      "Column{?s} {.var {setdiff(geom, names(x))}} not found in {.arg x}"
     )
   }
 
@@ -109,10 +114,9 @@ as_spatvector.data.frame <- function(x, ..., geom = c("lon", "lat"), crs = "") {
   tbl_end <- tidyr::drop_na(tbl, dplyr::all_of(geom))
 
   if (nrow(tbl) != nrow(tbl_end)) {
-    message(paste0(
-      "Removed ", nrow(tbl) - nrow(tbl_end),
-      " row(s) with empty geom column(s) <",
-      paste0(geom, collapse = ","), ">"
+    cli::cli_alert_warning(paste(
+      "Removed {nrow(tbl) - nrow(tbl_end)} row{?s} with empty",
+      "{.arg geom}{qty({length(geom)})} column{?s} {.val {geom}}"
     ))
   }
 

diff --git a/R/as_tibble-Spat.R b/R/as_tibble-Spat.R
@@ -151,7 +151,9 @@ as_tibble.SpatVector <- function(x, ..., geom = NULL, .name_repair = "unique") {
 
 as_tbl_internal <- function(x) {
   if (!inherits(x, c("SpatRaster", "SpatVector"))) {
-    cli::cli_abort("x is not a Spat* object")
+    cli::cli_abort(
+      "{.arg x} is not of {.cls SpatRaster} or {.cls SpatVector} object"
+    )
   }
 
   if (inherits(x, "SpatRaster")) {
@@ -255,36 +257,34 @@ make_safe_names <- function(x, geom = NULL, messages = TRUE) {
     cli::cli_alert_info(paste(
       for_message,
       "with duplicated/reserved names detected.",
-      "See `About layer/column names` section on",
-      "`?as_tibble.SpatRaster`", "\n"
-    ))
+      "See {.strong About layer/column names} section on",
+      "{.fun tidyterra::as_tibble.SpatRaster}"
+    ), wrap = TRUE)
     cli::cli_alert_warning("Renaming columns:")
   }
   if (geom == "XY") {
     names_with_coords <- c("x", "y", init_names)
     # Make new names
     newnames <- make.names(names_with_coords, unique = TRUE)
 
-    newnames <- newnames[-c(1:2)]
+    newnames <- newnames[-c(1, 2)]
   } else {
     names_with_coords <- c("geometry", init_names)
     # Make new names
     newnames <- make.names(names_with_coords, unique = TRUE)
 
-    newnames <- newnames[-c(1)]
+    newnames <- newnames[-1]
   }
   # Make new names
   if (messages) {
     names_changed <- !newnames == init_names
 
-    message(cli::col_black("New column names:"))
-    message(cli::col_black(
-      paste0("`", init_names[names_changed], "` -> `",
-        newnames[names_changed], "`",
-        collapse = "\n"
-      )
-    ))
-    message(cli::col_black("\n"))
+    msg <- paste0(
+      "`", init_names[names_changed], "` -> `",
+      newnames[names_changed], "`"
+    )
+
+    cli::cat_bullet(msg)
   }
   names(x) <- newnames
   return(x)
@@ -308,10 +308,10 @@ check_regroups <- function(x) {
 
     if (isFALSE(any_var)) {
       cli::cli_alert_warning(paste(
-        "`group_vars()` missing on data.",
-        " Have you mixed terra and tidyterra syntax?"
+        "{.fun tidyterra::group_vars.SpatVector} missing on data.",
+        " Have you mixed {.pkg terra} and {.pkg tidyterra} syntax?"
       ))
-      cli::cli_bullets(c(i = "ungrouping data"))
+      cli::cli_bullets(c(i = "Ungrouping data"))
       return(dplyr::ungroup(x))
     }
 
@@ -359,10 +359,10 @@ check_regroups <- function(x) {
 
     if (isFALSE(any_var)) {
       cli::cli_alert_warning(paste(
-        "`group_vars()` missing on data.",
-        " Have you mixed terra and tidyterra syntax?"
+        "{.fun tidyterra::group_vars.SpatVector} missing on data.",
+        " Have you mixed {.pkg terra} and {.pkg tidyterra} syntax?"
       ))
-      cli::cli_bullets(c(i = "ungrouping data"))
+      cli::cli_bullets(c(i = "Ungrouping data"))
       return(dplyr::ungroup(x))
     }