update from main

.Rbuildignore

@@ -6,3 +6,6 @@
 ^data-raw$
 ^\.github$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -4,9 +4,8 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
 
 permissions: read-all
 
@@ -40,7 +39,8 @@ jobs:
 
       - uses: codecov/codecov-action@v4
         with:
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
           file: ./cobertura.xml
           plugin: noop
           disable_search: true

.gitignore

@@ -5,3 +5,4 @@
 *.DS_Store
 /data-raw/geodata/
 *.tif
+docs

DESCRIPTION

@@ -9,7 +9,7 @@ Authors@R: c(
   )
 Description: What the package does (one paragraph).
 License: MIT + file LICENSE
-URL: https://github.com/idem-lab/sdmtools
+URL: https://github.com/idem-lab/sdmtools, https://idem-lab.github.io/sdmtools/
 BugReports: https://github.com/idem-lab/sdmtools/issues
 Depends: 
     R (>= 4.1.0)
@@ -30,7 +30,7 @@ Imports:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     testthat (>= 3.0.0)
 Remotes: 

NAMESPACE

@@ -12,6 +12,7 @@ export(inside_mask)
 export(make_africa_mask)
 export(make_mpp_list)
 export(mask_all)
+export(mask_from_all)
 export(maskpointsdf)
 export(match_ref)
 export(nearest_land)

R/assign_nearest_land.R

@@ -2,7 +2,7 @@
 #' @title Assign to nearest raster cell on mask
 #' @description
 #' Adapted from seegSDM.
-#' Reposition observations to a location within mask if within a specified distance.
+#' Reposition point observations to a location within mask if within a specified distance.
 #' Useful for when coastal observations drop off jagged mask and similar
 #'
 #' @param dat_object data.frame
@@ -19,15 +19,21 @@ assign_nearest_land <- function(dat_object,
                                 max_distance,
                                 verbose=TRUE) {
 
-  stopifnot(sum(colnames(dat_object) %in% c("longitude", "latitude"))==2)
-  message("dat_object object must contain columns 'longitude' and 'latitude'.")
+  if(!sum(colnames(dat_object) %in% c("longitude", "latitude"))==2) {
 
-  # ensure that data object is spatial data frame
-  spat_dat <- sf::st_as_sf(dat_object)
+    stop("Error: dat_object object must contain columns 'longitude' and 'latitude'.")
+
+    }
+
+  # ensure that data object is a simple features spatial data frame
+  spat_dat <- sf::st_as_sf(dat_object, coords = c("longitude", "latitude"))
 
   # assert that mask is SpatRaster
-  stopifnot(inherits(mask_object, 'SpatRaster'))
-  message("mask must be a SpatRaster")
+  if(!inherits(mask_object, 'SpatRaster')) {
+
+    stop("Error: mask must be a SpatRaster")
+
+  }
 
   # isolate coord info from spatial data frame
   data_coords <- sf::st_coordinates(spat_dat)

R/inside_mask.R

@@ -2,9 +2,10 @@
 #' @title title
 #' @description  Checks whether longitude and latitude coincide with
 #' non-missing pixels of a raster. The function takes two arguments:
-#' points, a dataframe containing columns named
-#' longitude' and 'latitude', and mask is a raster. Returns a dataframe
-#' of longitude and latitude only those rows with points falling on
+#' points, a dataframe containing at a minimum columns named
+#' longitude' and 'latitude' (but could include other attributes),
+#' and mask is a raster. Returns a dataframe of the same dimensions as the
+#' input object, containing only those rows with points falling on
 #' non-missing pixels. If all points fall on missing pixels,
 #' the function throws an error.
 #'

R/mask_from_all.R

@@ -0,0 +1,58 @@
+#' @title Create mask from raster layers
+#' @description
+#' Creates a mask where a cell in any layer of `r` that is `NA` will be returned
+#' as `NA`.
+#'
+#' @details
+#' Similar in intention to `mask_all`, but (a) will work on larger rasters
+#' because it only holds the values of a single layer in memory at a time, and
+#' (b) returns a mask layer, rather than masking each layer in `r`.
+#' **Can be very slow**
+#'
+#'
+#' @param r `SpatRaster` with >1 layer.
+#'
+#' @return `SpatRaster` with values `NA` or 1.
+#' @export
+#'
+#' @examples
+#' r <- example_raster(seed = 10)
+#' s <- example_raster(seed = 11)
+#'
+#' r[10:20] <- NA
+#'
+#' s[5:15] <- NA
+#'
+#' q <- mask_from_all(c(r,s))
+#'
+#' library("terra")
+#' plot(c(r,s,q))
+#'
+mask_from_all <- function(r){
+
+  j <- terra::nlyr(r)
+
+  if(j == 1){stop("Must have >1 layer")}
+
+  k <- which(is.na(terra::values(r[[1]])))
+
+  for(i in 2:j){
+
+    a <- which(is.na(terra::values(r[[i]])))
+
+    b <- c(k, a)
+
+    d <- duplicated(b)
+
+    k <- b[!d]
+
+  }
+
+  z <- r[[1]]
+
+  z[] <- 1
+  z[k] <- NA
+
+  z
+
+}

R/split_rast.R

@@ -82,7 +82,7 @@ split_rast <- function(
     ) |>
     dplyr::mutate(
       r = purrr::pmap(
-        .l = list(xmin, xmax, ymin, ymax, x, write_temp),
+        .l = list(xmin, xmax, ymin, ymax),
         .f = function(xmin, xmax, ymin, ymax, x, write_temp){
 
           xt <- terra::ext(c(xmin, xmax, ymin, ymax))
@@ -97,7 +97,9 @@ split_rast <- function(
 
           z
 
-        }
+        },
+        x,
+        write_temp
       )
     ) |>
     dplyr::pull(r)

R/standardise_rast.R

@@ -3,9 +3,7 @@
 #'
 #' **Defunct**.
 #'
-#' DO NOT USE THIS FUNCTION
-#'
-#' Instead use `terra::scale`
+#' DO NOT USE THIS FUNCTION; use `terra::scale` instead
 #'
 #' @param x A `SpatRaster` object.
 #'

R/std_rast.R

@@ -3,6 +3,7 @@
 #' by dividing by the maximum value in each layer. *Only operates by layer*
 #'
 #' @param x `SpatRaster` to standardise
+#' @param reverse `logical` if `TRUE` will subtract standardised values from 1
 #' @param filename Optional `character` path and filename to write output
 #' @param overwrite `logical` if `TRUE` will overwrite `filename`
 #'
@@ -14,9 +15,9 @@
 #'
 #'
 #' @examples
-#' example_raster() |>
-#'   std_rast()
-std_rast <- function(x, filename = NULL, overwrite = TRUE){
+#' example_raster(seed = 3010) |>
+#'   std_rast(reverse = TRUE)
+std_rast <- function(x, reverse = FALSE, filename = NULL, overwrite = TRUE){
   vals <- terra::values(x)
 
   nvs <- apply(
@@ -29,6 +30,10 @@ std_rast <- function(x, filename = NULL, overwrite = TRUE){
 
   r <- x
 
+  if(reverse){
+    nvs <- 1 - nvs
+  }
+
   r[] <- nvs
 
 

R/writereadrast.R

@@ -6,7 +6,9 @@
 #'
 #' @param x A `terra::SpatRaster`
 #' @param filename A `character` file path and name to save `x` to disc.
-#' @param overwrite `logical`; overwrite existing raster.
+#' @param overwrite `logical`; overwrite existing raster. **NB:** by default,
+#' `overwrite = TRUE`, this is the opposite of the default behaviour of
+#' `terra::writeRaster`
 #' @param layernames `character` of length `nlyr(x)`
 #'
 #' @return A `terra::SpatRaster` object reading from disc at `filename`.
@@ -16,6 +18,12 @@
 #' \dontrun{
 #' # create raster then assign
 #' r <- sdmtools::example_raster()
+#'
+#' # usual workflow in two slow tedious boring steps
+#' terra::writeRaster(r, "LowerSpringvale.tif")
+#' s <- terra::rast("LowerSpringvale.tif")
+#'
+#' Better workflow in one fast enjoyable lithesome step with `sdmtools`
 #' r <- writereadrast(r, "tootgarook.tif")
 #'
 #' # or roll into single step with pipe

README.Rmd

@@ -25,6 +25,7 @@ knitr::opts_chunk$set(
 ![GitHub last commit](https://img.shields.io/github/last-commit/idem-lab/sdmtools)
 ![GitHub R package version](https://img.shields.io/github/r-package/v/idem-lab/sdmtools)
 ![GitHub commits since latest release](https://img.shields.io/github/commits-since/idem-lab/sdmtools/latest)
+[![Codecov test coverage](https://codecov.io/gh/idem-lab/sdmtools/graph/badge.svg)](https://app.codecov.io/gh/idem-lab/sdmtools)
 <!-- badges: end -->
 
 A set of helper functions to facilitate species distribution modelling.

README.md

@@ -21,6 +21,8 @@ commit](https://img.shields.io/github/last-commit/idem-lab/sdmtools)
 version](https://img.shields.io/github/r-package/v/idem-lab/sdmtools)
 ![GitHub commits since latest
 release](https://img.shields.io/github/commits-since/idem-lab/sdmtools/latest)
+[![Codecov test
+coverage](https://codecov.io/gh/idem-lab/sdmtools/graph/badge.svg)](https://app.codecov.io/gh/idem-lab/sdmtools)
 <!-- badges: end -->
 
 A set of helper functions to facilitate species distribution modelling.
@@ -258,10 +260,7 @@ functions, rather than storing it.
 
 ``` r
 library(terra)
-#> terra 1.7.79
-```
-
-``` r
+#> terra 1.8.5
 r <- example_raster()
 r
 #> class       : SpatRaster 
@@ -273,9 +272,6 @@ r
 #> name        :   example 
 #> min value   : 0.0627102 
 #> max value   : 7.3352526
-```
-
-``` r
 plot(r)
 ```
 
@@ -292,9 +288,6 @@ v
 #>  dimensions  : 10, 0  (geometries, attributes)
 #>  extent      : 0.2293562, 8.00672, 1.375653, 8.951683  (xmin, xmax, ymin, ymax)
 #>  coord. ref. :
-```
-
-``` r
 plot(v)
 ```
 
@@ -310,13 +303,12 @@ africa_mask <- make_africa_mask(type = "vector")
 #> Loading ISO 19139 XML schemas...
 #> Loading ISO 19115 codelists...
 #> Please Note: Because you did not provide a version, by default the version being used is 202403 (This is the most recent version of admin unit shape data. To see other version options use function listShpVersions)
+#> Start tag expected, '<' not found
+#> Start tag expected, '<' not found
 #> although coordinates are longitude/latitude, st_union assumes that they are
 #> planar
 #> Warning: [crs<-] not all geometries were transferred, use svc for a geometry
 #> collection
-```
-
-``` r
 plot(africa_mask)
 ```
 

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://idem-lab.github.io/sdmtools/
+template:
+  bootstrap: 5
+