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r-a-dobson · Feb 5, 2023 · 29e57b9 · 29e57b9
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -118,7 +118,7 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(error_on = "error")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual","--as-cran"), error_on = "error")
         shell: Rscript {0}
 
       - name: Show testthat output

diff --git a/NAMESPACE b/NAMESPACE
@@ -22,25 +22,4 @@ export(spatiotemp_pseudoabs)
 export(spatiotemp_resolution)
 export(spatiotemp_thin)
 export(spatiotemp_weights)
-importFrom(grDevices,dev.off)
-importFrom(grDevices,png)
-importFrom(grDevices,terrain.colors)
-importFrom(graphics,abline)
-importFrom(graphics,hist)
-importFrom(graphics,plot)
 importFrom(magrittr,"%>%")
-importFrom(methods,as)
-importFrom(stats,aggregate)
-importFrom(stats,as.formula)
-importFrom(stats,chisq.test)
-importFrom(stats,cor.test)
-importFrom(stats,dist)
-importFrom(stats,lm)
-importFrom(stats,na.omit)
-importFrom(stats,na.pass)
-importFrom(stats,predict)
-importFrom(stats,sd)
-importFrom(stats,t.test)
-importFrom(stats,var)
-importFrom(utils,read.csv)
-importFrom(utils,write.csv)
diff --git a/R/data.R b/R/data.R
@@ -37,8 +37,8 @@
 #' @docType data
 #' @references
 #' Friedl, M., Sulla-Menashe, D. (2019). MCD12Q1 MODIS/Terra+Aqua Land Cover Type Yearly L3 Global
-#' 500m SIN Grid V006. NASA EOSDIS Land Processes DAAC. Accessed 2022-11-24 from
-#' <https://doi.org/10.5067/MODIS/MCD12Q1.006>
+#' 500m SIN Grid V006. NASA EOSDIS Land Processes DAAC.
+#'
 #'
 #' Funk, Chris, Pete Peterson, Martin Landsfeld, Diego Pedreros, James Verdin, Shraddhanand Shukla,
 #' Gregory Husak, James Rowland, Laura Harrison, Andrew Hoell & Joel Michaelsen. "The climate
@@ -147,7 +147,7 @@
 #' @references
 #' Hengl T, Walsh MG, Sanderman J, Wheeler I, Harrison SP, Prentice IC. (2018) Global Mapping of
 #' Potential Natural Vegetation: An Assessment of Machine Learning Algorithms for Estimating Land
-#' Potential. PeerJ Preprints. <10.7287/peerj.preprints.26811v1>
+#' Potential. PeerJ Preprints.
 "sample_biome_data"
 
 #' @name sample_events_data
@@ -202,12 +202,12 @@
 #' @references
 #' Friedl, M., Sulla-Menashe, D. (2019). MCD12Q1 MODIS/Terra+Aqua Land Cover Type Yearly L3 Global
 #' 500m SIN Grid V006. NASA EOSDIS Land Processes DAAC. Accessed 2022-11-24 from
-#' <https://doi.org/10.5067/MODIS/MCD12Q1.006>
+#'
 #'
 #' Funk, Chris, Pete Peterson, Martin Landsfeld, Diego Pedreros, James Verdin, Shraddhanand Shukla,
 #' Gregory Husak, James Rowland, Laura Harrison, Andrew Hoell & Joel Michaelsen. "The climate
 #' hazards infrared precipitation with stations-a new environmental record for monitoring extremes".
-#' Scientific Data 2, 150066. doi:<10.1038/sdata.2015.66 2015>.
+#' Scientific Data 2, 150066.
 "sample_cov_data"
 
 #' @name sample_proj_rast

diff --git a/R/dynamicSDM-package.R b/R/dynamicSDM-package.R
diff --git a/R/extract_buffered_coords.R b/R/extract_buffered_coords.R
@@ -96,8 +96,7 @@
 #'
 #'  `extract_buffered_coords()` requires users to have installed R package `rgee` (Aybar et al.,
 #'  2020) and initialised Google Earth Engine with valid log-in credentials. Please follow
-#'  instructions on the following website
-#'  <https://cran.r-project.org/web/packages/rgee/vignettes/rgee01.html>.
+#'  instructions on the following website <https://cran.r-project.org/package=rgee>
 #'
 #'  * `datasetname` must be in the accepted Google Earth Engine catalogue layout (e.g.
 #'  “MODIS/006/MCD12Q1” or “UCSB-CHG/CHIRPS/DAILY”)

diff --git a/R/extract_buffered_raster.R b/R/extract_buffered_raster.R
@@ -85,8 +85,7 @@
 #'
 #'  `extract_buffered_raster()` requires users to have installed R package `rgee` (Aybar et al.,
 #'  2020) and initialised Google Earth Engine with valid log-in credentials. Please follow
-#'  instructions on the following website
-#'  <https://cran.r-project.org/web/packages/rgee/vignettes/rgee01.html>.
+#'  instructions on the following website <https://cran.r-project.org/package=rgee>
 #'
 #'  * `datasetname` must be in the accepted Google Earth Engine catalogue layout (e.g.
 #'  “MODIS/006/MCD12Q1” or “UCSB-CHG/CHIRPS/DAILY”)

diff --git a/R/extract_dynamic_coords.R b/R/extract_dynamic_coords.R
@@ -31,8 +31,7 @@
 #'
 #'  `extract_dynamic_coords()` requires users to have installed R package `rgee` (Aybar et al.,
 #'  2020) and initialised Google Earth Engine with valid log-in credentials. Please follow
-#'  instructions on the following website
-#'  <https://cran.r-project.org/web/packages/rgee/vignettes/rgee01.html>.
+#'  instructions on the following website <https://cran.r-project.org/package=rgee>.
 #'
 #'  * `datasetname` must be in the accepted Google Earth Engine catalogue layout (e.g.
 #'  `"MODIS/006/MCD12Q1"` "or `"UCSB-CHG/CHIRPS/DAILY"`)

diff --git a/R/extract_dynamic_raster.R b/R/extract_dynamic_raster.R
@@ -34,8 +34,7 @@
 #'
 #'  `extract_dynamic_raster()` requires users to have installed R package `rgee` (Aybar et al.,
 #'  2020) and initialised Google Earth Engine with valid log-in credentials. Please follow
-#'  instructions on the following website
-#'  <https://cran.r-project.org/web/packages/rgee/vignettes/rgee01.html>.
+#'  instructions on the following website <https://cran.r-project.org/package=rgee>.
 #'
 #'  * `datasetname` must be in the accepted Google Earth Engine catalogue layout (e.g.
 #'  “MODIS/006/MCD12Q1” or “UCSB-CHG/CHIRPS/DAILY”)

diff --git a/R/spatiotemp_check.R b/R/spatiotemp_check.R
@@ -49,7 +49,7 @@
 #'@references Zizka A, Silvestro D, Andermann T, Azevedo J, Duarte Ritter C, Edler D, Farooq H,
 #'Herdean A, Ariza M, Scharn R, Svanteson S, Wengstrom N, Zizka V, Antonelli A (2019).
 #'“CoordinateCleaner: standardized cleaning of occurrence records from biological collection
-#'databases.” Methods in Ecology and Evolution, -7. <doi:10.1111/2041-210X.13152>, R package version
+#'databases.” Methods in Ecology and Evolution, -7. \doi{10.1111/2041-210X.13152}, R package version
 #'2.0-20, <https://github.com/ropensci/CoordinateCleaner>.
 #'@return By default, returns occurrence record data frame, filtered to exclude records containing
 #'  missing, duplicate or invalid data in record co-ordinates and dates.

diff --git a/dynamicSDM.Rproj b/dynamicSDM.Rproj
@@ -19,4 +19,5 @@ LineEndingConversion: Posix
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace
diff --git a/man/dynamicSDM-package.Rd b/man/dynamicSDM-package.Rd
diff --git a/man/extract_buffered_coords.Rd b/man/extract_buffered_coords.Rd
diff --git a/man/extract_buffered_raster.Rd b/man/extract_buffered_raster.Rd
diff --git a/man/extract_dynamic_coords.Rd b/man/extract_dynamic_coords.Rd
diff --git a/man/extract_dynamic_raster.Rd b/man/extract_dynamic_raster.Rd
diff --git a/man/sample_biome_data.Rd b/man/sample_biome_data.Rd
diff --git a/man/sample_cov_data.Rd b/man/sample_cov_data.Rd
diff --git a/man/sample_explan_data.Rd b/man/sample_explan_data.Rd
diff --git a/man/spatiotemp_check.Rd b/man/spatiotemp_check.Rd