Merge pull request #119 from NIEHS/cran-0801

1.0.3

.github/workflows/check-standard.yaml

@@ -34,6 +34,12 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Install wget on Windows
+        if: matrix.config.os == 'windows-latest'
+        run: |
+          choco install wget -y
+        shell: powershell
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}

.github/workflows/test-coverage-local.yaml

@@ -27,6 +27,7 @@ jobs:
             extra-packages: |
               any::pak
               any::covr
+              any::rstac
             needs: coverage
 
       - name: Cache C++ and R dependencies

.gitignore

@@ -54,4 +54,5 @@ rsconnect/
 /doc/
 /Meta/
 inst/doc
-inst/extdata/air.2m
+inst/extdata/air.2m
+inst/extdata/nasa/token.txt

DESCRIPTION

@@ -1,15 +1,16 @@
 Package: amadeus
-Title: A Machine for Data, Environments, and User Setup for Common Environmental and Climate Health Datasets
-Version: 1.0.2
+Title: Accessing and Analyzing Large-Scale Environmental Data in R
+Version: 1.0.3
 Authors@R: c(
     person(given = "Mitchell", family = "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")),
     person(given = "Insang", family = "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),
     person(given = "Eva", family = "Marques", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-9817-6546")),
     person(given = "Mariana", family = "Alifa Kassien", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-2295-406X")),
-    person(given = "Kyle", family = "Messier", role = c("aut", "cre"), email = "kyle.messier@nih.gov", comment = c(ORCID = "0000-0001-9508-9623"))
+    person(given = "Kyle", family = "Messier", role = c("aut", "cre"), email = "kyle.messier@nih.gov", comment = c(ORCID = "0000-0001-9508-9623")),
+    person("Spatiotemporal Exposures and Toxicology Group", role = c("cph"))
     )
 Maintainer: Kyle Messier <kyle.messier@nih.gov>
-Description: Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calc_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access.
+Description: Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calc_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For calc_sedc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.
 Depends: R (>= 4.1.0)
 Imports: dplyr, sf, sftime, stats, terra, methods, data.table, httr, rvest, exactextractr, utils, stringi, testthat (>= 3.0.0), parallelly, stars, future, future.apply, tidyr, rlang, nhdplusTools, archive, collapse, Rdpack
 Suggests: covr, withr, knitr, rmarkdown, lwgeom, FNN, doRNG, devtools, stringr, tigris

R/calculate_covariates.R

@@ -1136,6 +1136,7 @@ calc_temporal_dummies <-
 #' @author Insang Song
 #' @references
 #' \insertRef{messier2012integrating}{amadeus}
+#' 
 #' \insertRef{web_sedctutorial_package}{amadeus}
 #' @examples
 #' library(terra)

R/calculate_covariates_auxiliary.R

@@ -132,7 +132,7 @@ calc_setcolumns <- function(
 #' @param time placeholder
 #' @param time_type placeholder
 #' @param level placeholder
-#' @return NULL
+#' @return NULL; provides progress messages to R console.
 #' @keywords internal
 #' @export
 calc_message <- function(
@@ -299,7 +299,7 @@ calc_time <- function(
 #' @param POSIXt logical(1). Should the time values in `covar` be of class
 #' `POSIXt`? If `FALSE`, the time values will be checked for integer class
 #' (year and year-month).
-#' @return NULL
+#' @return NULL; returns a stop error if `time` is wrong class
 #' @keywords internal
 #' @export
 # nolint start