Merge pull request #61 from Spatiotemporal-Exposures-and-Toxicology/r…

…eflow-path

0.5.0

.Rbuildignore

@@ -1,14 +1,14 @@
-tools
 tests
-.github
-.html$
-.rmd$
-.gitignore
-^LICENSE\.md$
+tools
 figure
-docs
-slurm_test
 containers
-^codemeta\.json$
-^README\.Rmd$
-manuscript
+input
+.github
+\/*_litr.rmd
+README.Rmd
+codemeta.json
+_pkgdown.yml
+\*.yml
+\*.html
+^LICENSE\.md$
+^CODE_OF_CONDUCT\.md$

.gitignore

@@ -13,3 +13,6 @@
 
 # litr knitted html
 **/*.html
+
+# input
+input

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: chopin
 Title: CHOPIN: Computation for Climate and Health research On Parallelized INfrastructure
-Version: 0.4.0.20240222
+Version: 0.5.0.20240311
 Authors@R: c(
     person("Insang", "Song", , "geoissong@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8732-3256")),
@@ -31,6 +31,7 @@ Imports:
     exactextractr (>= 0.8.2),
     future,
     future.apply,
+    igraph,
     methods,
     rlang (>= 0.4.9),
     sf (>= 1.0-10),
@@ -40,7 +41,6 @@ Suggests:
     covr,
     doParallel,
     future.batchtools,
-    igraph,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
@@ -49,4 +49,4 @@ Suggests:
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 LitrVersionUsed: 0.9.0
-LitrId: 65b64b88def74fbb9156429f0cf0d121
+LitrId: ba8fdef0630a85538766d09ecaacae6a

NAMESPACE

@@ -17,6 +17,8 @@ export(get_clip_ext)
 export(is_bbox_within_reference)
 export(is_within_ref)
 export(kernelfunction)
+export(par_cut_coords)
+export(par_def_q)
 export(par_fallback)
 export(par_grid)
 export(par_hierarchy)
@@ -44,19 +46,25 @@ importFrom(dplyr,ungroup)
 importFrom(dplyr,where)
 importFrom(exactextractr,exact_extract)
 importFrom(future.apply,future_lapply)
+importFrom(igraph,components)
+importFrom(igraph,graph_from_edgelist)
+importFrom(igraph,mst)
 importFrom(methods,is)
 importFrom(rlang,"!!!")
 importFrom(rlang,inject)
 importFrom(rlang,sym)
 importFrom(sf,sf_use_s2)
+importFrom(sf,st_area)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_as_sfc)
 importFrom(sf,st_bbox)
 importFrom(sf,st_cast)
+importFrom(sf,st_coordinates)
 importFrom(sf,st_covered_by)
 importFrom(sf,st_crs)
 importFrom(sf,st_interpolate_aw)
 importFrom(sf,st_intersection)
+importFrom(sf,st_intersects)
 importFrom(sf,st_length)
 importFrom(sf,st_make_grid)
 importFrom(sf,st_make_valid)
@@ -65,9 +73,12 @@ importFrom(sf,st_set_crs)
 importFrom(sf,st_transform)
 importFrom(sf,st_within)
 importFrom(stars,st_as_stars)
+importFrom(stats,quantile)
+importFrom(stats,setNames)
 importFrom(stats,weighted.mean)
 importFrom(terra,as.polygons)
 importFrom(terra,buffer)
+importFrom(terra,crds)
 importFrom(terra,crop)
 importFrom(terra,crs)
 importFrom(terra,distance)
@@ -80,3 +91,4 @@ importFrom(terra,project)
 importFrom(terra,rast)
 importFrom(terra,set.crs)
 importFrom(terra,vect)
+importFrom(utils,combn)

NEWS.md

@@ -1,6 +1,18 @@
-# 0.3.0.20240202
-- README.md is replaced by README.Rmd
+# 0.5.0
+- `par_grid` unifies the classes of grid inputs
+- `par_cut_coords`: a supplementary function effectively operating with `par_def_q` for `mode = "grid_quantile"` in `par_make_gridset`. X- and Y-coordinates (of centroids for polygon inputs) are split into quantile groups to balance the number of features in each grid; does not account for geometric complexity (i.e., number of vertices)
+- Padded grid generation in `par_make_gridset` is done only by `terra::buffer`
+- `extract_at*` functions get `max_cells`, which is passed to `exactextractr::exact_extract` for speedup in expense of memory pressure
+- Added a new vignette on the demonstration of climate/weather data extraction
+
+# 0.4.0
+- `surf` argument in `extract_at*()` accepts file paths
+- Raster cropping is now optional
 
-# 0.3.0.20240131
-- Made NEWS.md
+# 0.3.1
+- Dropped `rast_short`
+- Added examples
+
+# 0.3.0
+- README.md is replaced by README.Rmd
 - Documentation is clarified about the second argument in `...` in `par_*` functions

R/check.R

@@ -99,14 +99,6 @@ reproject_std <-
     input,
     crs_standard = "EPSG:4326"
   ) {
-    if (
-      !grepl("[[:alpha:]]+{3,4}\\:([[:alpha:]]{2,4}[0-9]{2,2}|[0-9]{4,7})",
-             crs_standard)
-    ) {
-      stop("crs_standard seems to be in invalid format.
-        It should be '[authority]:[code]' format.
-        Please refer to https://epsg.io, ?sf::st_crs or ?terra::crs.\n")
-    }
 
     bound_package <- dep_check(input)
     input_crs <- switch(