Merge pull request #18 from birdflow-science/update-preprocess

preprocess_species updated for latest version of ebirdst. Fixes #17  …

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BirdFlowR
 Title: Forecast and Visualize Bird Movement
-Version: 0.0.0.9003
+Version: 0.0.0.9017
 Authors@R: 
     c(person("Ethan", "Plunkett",  email = "plunkett@umass.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4405-2251")),
@@ -9,11 +9,11 @@ Description: BirdFlowR forecasts bird movement and distribution from previously
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Suggests: 
     auk,
     BirdFlowModels,
-    ebirdst,
+    ebirdst (>= 2.2021.0),
     knitr,
     rmarkdown,
     rnaturalearthdata,

NEWS.md

@@ -1,26 +1,32 @@
-# BirdFlowR 0.0.0.9003  2023-02-27
-
-* Updated installation instructions.  Closing [#11](https://github.com/birdflow-science/BirdFlowR/issues/11).
-
-* Added docker file. [Usage instructions.](https://github.com/birdflow-science/BirdFlowR/pull/15#issuecomment-1445152787) 
-
-# BirdFlowR 0.0.0.9002  2023-02-23
-
-* Added "biocViews:" before "Imports:" in DESCRIPTION so that devtools can find
-and install rhdf5 (from Bioconductor) while installing the packages BirdFlowR 
-needs. [#13](https://github.com/birdflow-science/BirdFlowR/issues/13) 
-
-* Vignette now attempts to load rnaturalearthdata with utils::install.packages() 
-instead of devtools::install_cran() in attempt to fix [#11](https://github.com/birdflow-science/BirdFlowR/issues/11) 
-
-* Updated get_naturalearth() so that it handles some cases in which it previously
-failed.  In particular extents that span more than 180 deg of longitude, and 
-extents that cross the 180 deg. meridian that defines the edge of the WGS84 
-projection both now work. The function still doesn't handle polar projections or
-global extents in most projections. Fixes [#14](https://github.com/birdflow-science/BirdFlowR/issues/14) 
-
-# BirdFlowR 0.0.0.9001   2023-02-21
-* Switched order of package installation in readme and added installation of
-rnaturalearthdata to vignette [#11](https://github.com/birdflow-science/BirdFlowR/issues/11) 
-
-* Added a `NEWS.md` file to track changes to the package.
+
+# BirdflowR 0.0.0.9017
+
+* Fix bug introduced by ebirdst 2.2021.0 (switch from raster to terra)
+[#17](https://github.com/birdflow-science/BirdFlowR/issues/17).
+
+# BirdFlowR 0.0.0.9003  2023-02-27
+
+* Updated installation instructions.  Closing [#11](https://github.com/birdflow-science/BirdFlowR/issues/11).
+
+* Added docker file. [Usage instructions.](https://github.com/birdflow-science/BirdFlowR/pull/15#issuecomment-1445152787) 
+
+# BirdFlowR 0.0.0.9002  2023-02-23
+
+* Added "biocViews:" before "Imports:" in DESCRIPTION so that devtools can find
+and install rhdf5 (from Bioconductor) while installing the packages BirdFlowR 
+needs. [#13](https://github.com/birdflow-science/BirdFlowR/issues/13) 
+
+* Vignette now attempts to load rnaturalearthdata with utils::install.packages() 
+instead of devtools::install_cran() in attempt to fix [#11](https://github.com/birdflow-science/BirdFlowR/issues/11) 
+
+* Updated get_naturalearth() so that it handles some cases in which it previously
+failed.  In particular extents that span more than 180 deg of longitude, and 
+extents that cross the 180 deg. meridian that defines the edge of the WGS84 
+projection both now work. The function still doesn't handle polar projections or
+global extents in most projections. Fixes [#14](https://github.com/birdflow-science/BirdFlowR/issues/14) 
+
+# BirdFlowR 0.0.0.9001   2023-02-21
+* Switched order of package installation in readme and added installation of
+rnaturalearthdata to vignette [#11](https://github.com/birdflow-science/BirdFlowR/issues/11) 
+
+* Added a `NEWS.md` file to track changes to the package.

R/preprocess_species.R

@@ -102,9 +102,18 @@ preprocess_species <- function(species,
 
 ){
 
+  # ebirdst is listed under suggests so may not be installed.
+  # I anticipate a group of users who work with fit models provided by the
+  # BirdFlow team but don't fit their own models, and my initial installation
+  # of ebirdst was tricky so I didn't want all users to need to import it.
+  a <- requireNamespace("ebirdst", versionCheck = list(op =">=", version = "2.2021.0"))
+  if(!a){
+    stop("Install ebirdst >= 2.2021.0 to use preprocess_species()")
+  }
+
   # Validate inputs
   if(length(species) != 1)
-    stop("Can only preprpocess one species at a time")
+    stop("Can only preprocess one species at a time")
   stopifnot( is.logical( tiff ),
              is.logical( hdf5 ),
              length( tiff ) == 1,
@@ -249,9 +258,7 @@ preprocess_species <- function(species,
       cat("Calculating resolution\n")
     # Load low res abundance data and calculate total areas birds occupy at any
     # time (active_sq_m)
-    abunds <- terra::rast(ebirdst::load_raster("abundance",
-                                               path = sp_path,
-                                               resolution="lr"))
+    abunds <- ebirdst::load_raster("abundance",path = sp_path, resolution="lr")
 
 
     mask <- make_mask(x = abunds)
@@ -422,11 +429,6 @@ preprocess_species <- function(species,
   abunds_uci <- ebirdst::load_raster("abundance", metric = "upper",
                                      path = sp_path, resolution=load_res)
 
-  # Convert to terra::rast
-  abunds <- terra::rast(abunds)
-  abunds_lci <- terra::rast(abunds_lci)
-  abunds_uci <- terra::rast(abunds_uci)
-
   if(verbose)
     cat("Creating mask in target resolution and projection\n")
 

tests/testthat/test-preprocess_species.R

@@ -1,8 +1,5 @@
 test_that("preprocess_species runs on test dataset", {
 
-
-  skip_on_ci()
-  skip_on_covr()
   skip_on_cran()
 
   # Run on example data setting resolution based on gb (and then overiding for example_data)
@@ -13,8 +10,6 @@ test_that("preprocess_species runs on test dataset", {
 
 test_that("preprocess_species runs with pre-set resolution and matches prior results", {
 
-  skip_on_ci()
-  skip_on_covr()
   skip_on_cran()
 
   # Using snapshot on 50 m version because it results in a small object.