clean up for CRAN

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: tidysdm
-Title: Species Distribution Models with tidymodels
+Title: Species Distribution Models with Tidymodels
 Version: 0.9.1.9001
 Authors@R: c(
     person("Michela", "Leonardi", role = "aut"),
@@ -52,10 +52,12 @@ Suggests:
     ranger,
     readr,
     rmarkdown,
+    spelling,
     stacks,
     testthat (>= 3.0.0),
     tidyterra,
-    xgboost
+    xgboost,
+    V8
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LazyData: true

NEWS.md

@@ -1,3 +1,7 @@
+# `tidysdm` 0.9.2
+
+* Clean up for CRAN
+
 # `tidysdm` 0.9.1
 
 * Add a `spatial_recipe` class. This is a BREAKING change that makes previously

R/sample_pseudoabs.R

@@ -4,20 +4,18 @@
 #' of semantics) points from a raster given a set of presences.
 #' The locations returned as the center points of the sampled cells, which can
 #' not overlap with the presences. The following methods are implemented:
-#' {/itemize:
-#' /item: 'random': pseudo-absences/background randomly sampled from the region covered by the
+#' * 'random': pseudo-absences/background randomly sampled from the region covered by the
 #' raster (i.e. not NAs).
-#' /item: 'dist_min': pseudo-absences/background randomly sampled from the region excluding a buffer
+#' * 'dist_min': pseudo-absences/background randomly sampled from the region excluding a buffer
 #' of 'dist_min' from presences (distances in 'm' for lonlat rasters, and in map
 #' units for projected rasters).
-#' /item: 'dist_max': pseudo-absences/background randomly sampled from the unioned buffers
+#' * 'dist_max': pseudo-absences/background randomly sampled from the unioned buffers
 #' of 'dist_max' from presences (distances in 'm' for lonlat rasters, and in map
 #' units for projected rasters). Using the union of buffers means that areas that
 #' are in multiple buffers are not oversampled. This is also referred to as "thickening".
-#' /item: 'dist_disc': pseudo-absences/background randomly sampled from the unioned discs around presences
+#' * 'dist_disc': pseudo-absences/background randomly sampled from the unioned discs around presences
 #' with the two values of 'dist_disc' defining the minimum and maximum distance from
 #' presences.
-#' }
 #' @param data An [`sf::sf`] data frame, or a data frame with coordinate variables.
 #' These can be defined in `coords`, unless they have standard names
 #' (see details below).

README.md

@@ -2,7 +2,7 @@
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/EvolEcolGroup/tidysdm/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EvolEcolGroup/tidysdm/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/EvolEcolGroup/tidysdm/branch/main/graph/badge.svg?token=KLOzxJoLBO)](https://codecov.io/gh/EvolEcolGroup/tidysdm)
+[![codecov](https://codecov.io/gh/EvolEcolGroup/tidysdm/branch/main/graph/badge.svg?token=KLOzxJoLBO)](https://app.codecov.io/gh/EvolEcolGroup/tidysdm)
 <!-- badges: end -->
 
 The goal of `tidysdm` is to implement Species Distribution Models using the

data-raw/helper_functions/submitting_to_cran.R

@@ -0,0 +1,27 @@
+# to this in the dev branch to make sure that all the fundamental issues have been resolved
+# run the spell checking
+usethis::use_spell_check(lang = "en-GB")
+
+# check the links
+urlchecker::url_check()
+
+# enhanced local checks
+devtools::check(remote = TRUE, manual = TRUE)
+
+source("./data-raw/helper_functions/check_returns_in_documentation.R")
+
+# now create a cran_submission branch for the final remote tests
+
+# TO DO MANUALLY: update cran-comments.md accordingly
+# update version number
+# update news
+
+# first check with rhub
+tidysdm_checks <- rhub::check_for_cran()
+
+# check on macos and windows via devtools
+devtools::check_mac_release()
+devtools::check_win_devel()
+
+# TO DO MANUALLY: if everything passes, edit the cran-comments.md to explain any notes
+devtools::release()

inst/WORDLIST

@@ -1,5 +1,6 @@
 BCI
 CMD
+DALEX
 Ecol
 GAMs
 GBIF
@@ -13,6 +14,7 @@ Lacerta
 MaxEnt
 Maxent
 Maxnet
+POSIXlt
 Prepping
 Randin
 SDM
@@ -32,10 +34,10 @@ cellsize
 center
 codecov
 color
+colorized
 colors
 com
 coords
-crossvalidating
 crossvalidation
 crs
 cutoff
@@ -47,21 +49,21 @@ fn
 fp
 gam
 gams
-gbm
 ggplot
 ggplots
 glm
 glmnet
 iter
 jan
 jlx
+kap
+lacerta
 lh
 lonlat
 lqpht
 lubridate
 magrittr
 manpage
-mars
 maxent
 maxnet
 mtry
@@ -72,7 +74,6 @@ palaeo
 palaeoclimate
 palaeoclimatic
 palaeodata
-pastclim
 pred
 prepping
 prob
@@ -85,8 +86,10 @@ rsplit
 schreiberi
 sdm
 spatialsample
+stackexchange
 stackoverflow
 stat
+svm
 thres
 tibble
 tibbles

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)