Merge pull request #110 from ropensci/0.9.0-cran

0.9.1-1

DESCRIPTION

@@ -25,7 +25,7 @@ Description: Geospatial data computation is parallelized by grid, hierarchy,
     simple areal interpolation (`summarize_aw`) and summation of
     exponentially decaying weights (`summarize_sedc`) are also provided.
 License: MIT + file LICENSE
-URL: https://docs.ropensci.org/chopin, https://github.com/ropensci/chopin
+URL: https://docs.ropensci.org/chopin/, https://github.com/ropensci/chopin
 BugReports: https://github.com/ropensci/chopin/issues
 Depends: 
     R (>= 4.1)

R/scale_process.R

@@ -318,6 +318,7 @@ par_grid <-
 #'   system.file("shape/nc.shp", package = "sf")
 #' )
 #' nccnty <- sf::st_transform(nccnty, "EPSG:5070")
+#' nccnty <- nccnty[seq_len(30L), ]
 #'
 #' nccntygrid <- sf::st_make_grid(nccnty, n = c(200, 100))
 #' nccntygrid <- sf::st_as_sf(nccntygrid)

R/scale_process_mirai.R

@@ -684,6 +684,7 @@ par_hierarchy_mirai <-
 #'   system.file("shape/nc.shp", package = "sf")
 #' )
 #' nccnty <- sf::st_transform(nccnty, "EPSG:5070")
+#' nccnty <- nccnty[seq_len(30L), ]
 #'
 #' nccntygrid <- sf::st_make_grid(nccnty, n = c(200, 100))
 #' nccntygrid <- sf::st_as_sf(nccntygrid)

README.md

@@ -266,7 +266,7 @@ system.time(
     )
 )
 #>    user  system elapsed 
-#>   6.021   0.109   5.733
+#>   5.979   0.058   5.786
 ```
 
 #### Generate regular grid computational regions
@@ -355,7 +355,7 @@ system.time(
 #> Input is a character. Attempt to read it with terra::rast...
 #> ℹ Task at CGRIDID: 4 is successfully dispatched.
 #>    user  system elapsed 
-#>   1.508   0.148   8.290
+#>   1.447   0.154   9.714
 
 ncpoints_srtm <-
   extract_at(
@@ -414,7 +414,7 @@ system.time(
 #> Attempt to track the data source file path...
 #> ℹ Input is not a character.
 #>    user  system elapsed 
-#>   0.964   0.119   7.923
+#>   0.847   0.132   7.721
 
 # remove mirai::daemons
 mirai::daemons(0L)
@@ -449,14 +449,14 @@ download.file(hierarchy_url, hierarchy_path, mode = "wb")
 
 nc_data <- hierarchy_path
 nc_county <- sf::st_read(nc_data, layer = "county")
-#> Reading layer `county' from data source `/tmp/RtmpqcjL3G/nc_hierarchy.gpkg' using driver `GPKG'
+#> Reading layer `county' from data source `/tmp/RtmpBBOR7A/nc_hierarchy.gpkg' using driver `GPKG'
 #> Simple feature collection with 100 features and 1 field
 #> Geometry type: POLYGON
 #> Dimension:     XY
 #> Bounding box:  xmin: 1054155 ymin: 1341756 xmax: 1838923 ymax: 1690176
 #> Projected CRS: NAD83 / Conus Albers
 nc_tracts <- sf::st_read(nc_data, layer = "tracts")
-#> Reading layer `tracts' from data source `/tmp/RtmpqcjL3G/nc_hierarchy.gpkg' using driver `GPKG'
+#> Reading layer `tracts' from data source `/tmp/RtmpBBOR7A/nc_hierarchy.gpkg' using driver `GPKG'
 #> Simple feature collection with 2672 features and 1 field
 #> Geometry type: MULTIPOLYGON
 #> Dimension:     XY
@@ -484,7 +484,7 @@ system.time(
     )
 )
 #>    user  system elapsed 
-#>   0.756   0.000   0.725
+#>   0.710   0.000   0.679
 
 # hierarchical parallelization
 system.time(
@@ -803,7 +803,7 @@ system.time(
 #> Input is a character. Attempt to read it with terra::rast...
 #> ℹ Your input function at 37047 is dispatched.
 #>    user  system elapsed 
-#>   1.600   0.166   7.868
+#>   1.449   0.178   7.734
 ```
 
 ### `par_multirasters()`: parallelize over multiple rasters
@@ -830,9 +830,9 @@ terra::writeRaster(ncelev, file.path(tdir, "test5.tif"), overwrite = TRUE)
 # check if the raster files were exported as expected
 testfiles <- list.files(tdir, pattern = "*.tif$", full.names = TRUE)
 testfiles
-#> [1] "/tmp/RtmpqcjL3G/nc_srtm15_otm.tif" "/tmp/RtmpqcjL3G/test1.tif"        
-#> [3] "/tmp/RtmpqcjL3G/test2.tif"         "/tmp/RtmpqcjL3G/test3.tif"        
-#> [5] "/tmp/RtmpqcjL3G/test4.tif"         "/tmp/RtmpqcjL3G/test5.tif"
+#> [1] "/tmp/RtmpBBOR7A/nc_srtm15_otm.tif" "/tmp/RtmpBBOR7A/test1.tif"        
+#> [3] "/tmp/RtmpBBOR7A/test2.tif"         "/tmp/RtmpBBOR7A/test3.tif"        
+#> [5] "/tmp/RtmpBBOR7A/test4.tif"         "/tmp/RtmpBBOR7A/test5.tif"
 ```
 
 ``` r
@@ -849,35 +849,35 @@ system.time(
 )
 #> ℹ Input is not a character.
 #> Input is a character. Attempt to read it with terra::rast...
-#> ℹ Your input function at /tmp/RtmpqcjL3G/nc_srtm15_otm.tif is dispatched.
+#> ℹ Your input function at /tmp/RtmpBBOR7A/nc_srtm15_otm.tif is dispatched.
 #> 
 #> Input is a character. Attempt to read it with terra::rast...
-#> ℹ Your input function at /tmp/RtmpqcjL3G/test1.tif is dispatched.
+#> ℹ Your input function at /tmp/RtmpBBOR7A/test1.tif is dispatched.
 #> 
 #> Input is a character. Attempt to read it with terra::rast...
-#> ℹ Your input function at /tmp/RtmpqcjL3G/test2.tif is dispatched.
+#> ℹ Your input function at /tmp/RtmpBBOR7A/test2.tif is dispatched.
 #> 
 #> Input is a character. Attempt to read it with terra::rast...
-#> ℹ Your input function at /tmp/RtmpqcjL3G/test3.tif is dispatched.
+#> ℹ Your input function at /tmp/RtmpBBOR7A/test3.tif is dispatched.
 #> 
 #> Input is a character. Attempt to read it with terra::rast...
-#> ℹ Your input function at /tmp/RtmpqcjL3G/test4.tif is dispatched.
+#> ℹ Your input function at /tmp/RtmpBBOR7A/test4.tif is dispatched.
 #> 
 #> Input is a character. Attempt to read it with terra::rast...
-#> ℹ Your input function at /tmp/RtmpqcjL3G/test5.tif is dispatched.
+#> ℹ Your input function at /tmp/RtmpBBOR7A/test5.tif is dispatched.
 #>    user  system elapsed 
-#>   1.471   0.206   2.572
+#>   1.418   0.107   3.952
 knitr::kable(head(res))
 ```
 
 |      mean | base_raster                       |
 |----------:|:----------------------------------|
-| 136.80203 | /tmp/RtmpqcjL3G/nc_srtm15_otm.tif |
-| 189.76170 | /tmp/RtmpqcjL3G/nc_srtm15_otm.tif |
-| 231.16968 | /tmp/RtmpqcjL3G/nc_srtm15_otm.tif |
-|  98.03845 | /tmp/RtmpqcjL3G/nc_srtm15_otm.tif |
-|  41.23463 | /tmp/RtmpqcjL3G/nc_srtm15_otm.tif |
-| 270.96933 | /tmp/RtmpqcjL3G/nc_srtm15_otm.tif |
+| 136.80203 | /tmp/RtmpBBOR7A/nc_srtm15_otm.tif |
+| 189.76170 | /tmp/RtmpBBOR7A/nc_srtm15_otm.tif |
+| 231.16968 | /tmp/RtmpBBOR7A/nc_srtm15_otm.tif |
+|  98.03845 | /tmp/RtmpBBOR7A/nc_srtm15_otm.tif |
+|  41.23463 | /tmp/RtmpBBOR7A/nc_srtm15_otm.tif |
+| 270.96933 | /tmp/RtmpBBOR7A/nc_srtm15_otm.tif |
 
 ``` r
 
@@ -920,7 +920,7 @@ pnts <- sf::st_as_sf(pnts)
 pnts$pid <- sprintf("RPID-%04d", seq(1, 5000))
 rd1 <- sf::st_read(ncrd1_path)
 #> Reading layer `ncroads_first' from data source 
-#>   `/tmp/RtmpqcjL3G/ncroads_first.gpkg' using driver `GPKG'
+#>   `/tmp/RtmpBBOR7A/ncroads_first.gpkg' using driver `GPKG'
 #> Simple feature collection with 620 features and 4 fields
 #> Geometry type: MULTILINESTRING
 #> Dimension:     XY
@@ -972,11 +972,11 @@ system.time(
   restr <- terra::nearest(x = terra::vect(pntst), y = terra::vect(rd1t))
 )
 #>    user  system elapsed 
-#>   0.459   0.003   0.415
+#>   0.471   0.000   0.449
 
 pnt_path <- file.path(tdir, "pntst.gpkg")
 sf::st_write(pntst, pnt_path)
-#> Writing layer `pntst' to data source `/tmp/RtmpqcjL3G/pntst.gpkg' using driver `GPKG'
+#> Writing layer `pntst' to data source `/tmp/RtmpBBOR7A/pntst.gpkg' using driver `GPKG'
 #> Writing 5000 features with 1 fields and geometry type Point.
 
 # we use four threads that were configured above
@@ -1022,7 +1022,7 @@ system.time(
 #> ℹ Input is a character. Trying to read with terra .
 #> ℹ Task at CGRIDID: 8 is successfully dispatched.
 #>    user  system elapsed 
-#>   0.076   0.000   0.359
+#>   0.077   0.001   0.384
 ```
 
 - We will compare the results from the single-thread and multi-thread

codemeta.json

@@ -4,7 +4,7 @@
   "identifier": "chopin",
   "description": "Geospatial data computation is parallelized by grid, hierarchy, or raster files. Based on future and mirai parallel backends, terra and sf functions as well as convenience functions in the package can be distributed over multiple threads. The simplest way of parallelizing generic geospatial computation is to start from `par_pad_*` functions to `par_grid`, `par_hierarchy`, or `par_multirasters` functions. Virtually any functions accepting classes in terra or sf packages can be used in the three parallelization functions. A common raster-vector overlay operation is provided as a function `extract_at`, which uses exactextractr, with options for kernel weights for summarizing raster values at vector geometries. Other convenience functions for vector-vector operations including simple areal interpolation (`summarize_aw`) and summation of exponentially decaying weights (`summarize_sedc`) are also provided.",
   "name": "chopin: Computation of Spatial Data by Hierarchical and Objective Partitioning of Inputs for Parallel Processing",
-  "relatedLink": "https://docs.ropensci.org/chopin",
+  "relatedLink": "https://docs.ropensci.org/chopin/",
   "codeRepository": "https://github.com/ropensci/chopin",
   "issueTracker": "https://github.com/ropensci/chopin/issues",
   "license": "https://spdx.org/licenses/MIT",
@@ -370,7 +370,7 @@
     },
     "SystemRequirements": "netcdf"
   },
-  "fileSize": "2440.244KB",
+  "fileSize": "2440.32KB",
   "releaseNotes": "https://github.com/ropensci/chopin/blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/chopin/blob/main/README.md",
   "contIntegration": "https://github.com/ropensci/chopin/actions/workflows/check-standard.yaml",