JOSS Review: Add small POC about Performance claims about wdpar HOT 7 CLOSED

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> # System command to execute:
> # R CMD BATCH --no-restore --no-save global-example-script.R
> 
> # Initialization
> ## define countries for processing data
> country_names <- "global"
> 
> ## define file path to save data
> path <- paste0(
+   "~/wdpa-data/global-", format(Sys.time(), "%Y-%m-%d"), ".gpkg"
+ )
> 
> ## load packages
> library(sf)
Linking to GEOS 3.10.2, GDAL 3.4.3, PROJ 8.2.0; sf_use_s2() is TRUE
> library(wdpar)
> 
> # Preliminary processing
> ## prepare folder if needed
> export_dir <- suppressWarnings(normalizePath(dirname(path)))
> if (!file.exists(export_dir)) {
+   dir.create(export_dir, showWarnings = FALSE, recursive = TRUE)
+ }
> 
> ## preapre user data directory
> data_dir <- rappdirs::user_data_dir("wdpar")
> if (!file.exists(data_dir)) {
+   dir.create(data_dir, showWarnings = FALSE, recursive = TRUE)
+ }
> 
> # Main processing
> ## download data
> raw_data <- wdpa_fetch(
+   country_names, wait = TRUE, download_dir = data_dir, verbose = TRUE
+ )
 [100%] Downloaded 194 bytes...
 [100%] Downloaded 1537392988 bytes...


Warning message:
In CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  :
  GDAL Message 1: organizePolygons() received a polygon with more than 100 parts. The processing may be really slow.  You can skip the processing by setting METHOD=SKIP, or only make it analyze counter-clock wise parts by setting METHOD=ONLY_CCW if you can assume that the outline of holes is counter-clock wise defined
> 
> ## clean data
> result_data <- wdpa_clean(raw_data, erase_overlaps = FALSE, verbose = TRUE)
ℹ initializing
✔ initializing [36ms]

ℹ retaining only areas with specified statuses
✔ retaining only areas with specified statuses [17.9s]

ℹ removing UNESCO Biosphere Reserves
✔ removing UNESCO Biosphere Reserves [18.8s]

ℹ removing points with no reported area
✔ removing points with no reported area [18.1s]

ℹ wrapping dateline
✔ wrapping dateline [4m 48.2s]

ℹ repairing geometry
✔ repairing geometry [31m 16.9s]

ℹ reprojecting data
✔ reprojecting data [29.2s]

ℹ repairing geometry
✔ repairing geometry [10m 21s]

ℹ further geometry fixes (i.e. buffering by zero)
✔ further geometry fixes (i.e. buffering by zero) [6m 19.2s]

ℹ buffering points to reported area
✔ buffering points to reported area [48.8s]

ℹ repairing geometry
✔ repairing geometry [8m 8.8s]

ℹ snapping geometry to tolerance
✔ snapping geometry to tolerance [15s]

ℹ repairing geometry
✔ repairing geometry [11m 57s]

ℹ formatting attribute data
✔ formatting attribute data [50ms]

ℹ removing slivers
✔ removing slivers [13.1s]

ℹ calculating spatial statistics
✔ calculating spatial statistics [6.6s]

> 
> # Exports
> ## save result
> sf::write_sf(result_data, path, overwrite = TRUE)
> 
> proc.time()
    user   system  elapsed 
4583.412  201.009 4876.970 

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] wdpar_1.3.3 sf_1.0-8   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9         magrittr_2.0.3     units_0.8-0        tidyselect_1.1.1  
 [5] R6_2.5.1           rlang_0.4.12       fansi_0.5.0        dplyr_1.0.7       
 [9] tools_4.1.2        grid_4.1.2         KernSmooth_2.23-20 utf8_1.2.2        
[13] e1071_1.7-11       DBI_1.1.3          ellipsis_0.3.2     class_7.3-19      
[17] assertthat_0.2.1   tibble_3.1.6       lifecycle_1.0.1    crayon_1.4.2      
[21] purrr_0.3.4        vctrs_0.3.8        glue_1.5.1         proxy_0.4-27      
[25] compiler_4.1.2     pillar_1.6.4       generics_0.1.1     classInt_0.4-7    
[29] pkgconfig_2.0.3