Merge pull request #108 from NIEHS/mm-cran-0723

1.0.0

.github/workflows/check-standard.yaml

@@ -19,8 +19,8 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-          #- {os: macos-13-xlarge,   r: 'release'}
-          #- {os: windows-latest, r: 'release'}
+          - {os: macos-13-xlarge,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: amadeus
-Title: AMADEUS: A Machine for Data, Environments, and User Setup for common environmental and climate health datasets 
+Title: A Machine for Data, Environments, and User Setup for Common Environmental and Climate Health Datasets
 Version: 0.3.0
 Authors@R: c(
     person("Mitchell", "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")),
     person("Insang", "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),
     person("Eva", "Marques", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-9817-6546")),
     person("Mariana", "Alifa Kassien", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-2295-406X")),
-    person("Kyle", "Messier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9508-9623"))
+    person("Kyle", "Messier", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0001-9508-9623"))
     )
-Description: A Mechanism/Machine for Data, Environments, and User Setup package for health and climate research. It is fully tested, versioned, and open source and open access.
+Maintainer: Kyle Messier <[email protected]>
+Description: amadeus is designed to faciliate access to and utiltiy with large scale, publicly available environmental data in R. The package contains funtions for downloading (download_data()) raw data files from web URLs, processing (process_covariates()) the raw data files into interpretable spatial objects, and extracting values (calc_covariates()) from the spatial data objects at point and polygon locations. These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatio-temporal resolution. amadeus functions are tested, versioned, and open source and open access.
 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, rstac, nhdplusTools, archive, collapse, Rdpack
 Suggests: covr, withr, knitr, rmarkdown, lwgeom, FNN, doRNG

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(apply_extent)
 export(as_mysftime)
 export(calc_check_time)
 export(calc_covariates)
@@ -179,6 +180,7 @@ importFrom(stars,read_stars)
 importFrom(stars,st_mosaic)
 importFrom(stars,st_warp)
 importFrom(stats,aggregate)
+importFrom(stats,na.omit)
 importFrom(stats,setNames)
 importFrom(stringi,stri_pad)
 importFrom(terra,aggregate)

R/calculate_covariates.R

@@ -18,22 +18,22 @@
 #'  function.
 #' @note `covariate` argument value is converted to lowercase.
 #' @seealso
-#' - [`calc_modis_par`]: `"modis"`, `"MODIS"`
-#' - [`calc_koppen_geiger`]: `"koppen-geiger"`, `"koeppen-geiger"`, `"koppen"`
-#' - [`calc_ecoregion`]: `"ecoregion"`, `"ecoregions"`
-#' - [`calc_temporal_dummies`]: `"dummies"`
-#' - [`calc_hms`]: `"hms"`, `"smoke"`
-#' - [`calc_gmted`]: `"gmted"`
-#' - [`calc_narr`]: `"narr"`
-#' - [`calc_geos`]: `"geos"`, `"geos_cf"`
-#' - [`calc_sedac_population`]: `"population"`, `"sedac_population"`
-#' - [`calc_sedac_groads`]: `"roads"`, `"groads"`, `"sedac_groads"`
-#' - [`calc_nlcd`]: `"nlcd"`
-#' - [`calc_tri`]: `"tri"`
-#' - [`calc_nei`]: `"nei"`
-#' - [`calc_merra2`]: `"merra"`, `"MERRA"`, `"merra2"`, `"MERRA2"`
-#' - [`calc_gridmet`]: `"gridMET"`, `"gridmet"`
-#' - [`calc_terraclimate`]: `"terraclimate"`, `"TerraClimate"`
+#' * \code{\link{calc_modis_par}}: "modis", "MODIS"
+#' * \code{\link{calc_koppen_geiger}}: "koppen-geiger", "koeppen-geiger", "koppen"
+#' * \code{\link{calc_ecoregion}}: "ecoregion", "ecoregions"
+#' * \code{\link{calc_temporal_dummies}}: "dummies", "Dummies"
+#' * \code{\link{calc_hms}}: "hms", "smoke", "HMS"
+#' * \code{\link{calc_gmted}}: "gmted", "GMTED"
+#' * \code{\link{calc_narr}}: "narr", "NARR"
+#' * \code{\link{calc_geos}}: "geos", "geos_cf", "GEOS"
+#' * \code{\link{calc_sedac_population}}: "population", "sedac_population"
+#' * \code{\link{calc_sedac_groads}}: "roads", "groads", "sedac_groads"
+#' * \code{\link{calc_nlcd}}: "nlcd", "NLCD"
+#' * \code{\link{calc_tri}}: "tri", "TRI"
+#' * \code{\link{calc_nei}}: "nei", "NEI"
+#' * \code{\link{calc_merra2}}: "merra", "MERRA", "merra2", "MERRA2"
+#' * \code{\link{calc_gridmet}}: "gridMET", "gridmet"
+#' * \code{\link{calc_terraclimate}}: "terraclimate", "TerraClimate"
 #' @return Calculated covariates as a data.frame or SpatVector object
 #' @author Insang Song
 #' @examples
@@ -1128,15 +1128,15 @@ calc_temporal_dummies <-
 #'    - `attr(result, "sedc_threshold")``: the threshold distance
 #'  at which emission source points are excluded beyond that
 #' @note The function is originally from
-#' [chopin](https://github.com/kyle-messier/chopin)
+#' [chopin](https://github.com/NIEHS/chopin)
 #' Distance calculation is done with terra functions internally.
 #'  Thus, the function internally converts sf objects in
 #'  \code{point_*} arguments to terra.
 #'  The threshold should be carefully chosen by users.
 #' @author Insang Song
 #' @references
-#' * [Messier KP, Akita Y, & Serre ML. (2012). Integrating Address Geocoding, Land Use Regression, and Spatiotemporal Geostatistical Estimation for Groundwater Tetrachloroethylene. _Environmental Science & Technology_ 46(5), 2772-2780.](https://dx.doi.org/10.1021/es203152a)
-#' * Wiesner C. (n.d.). [Euclidean Sum of Exponentially Decaying Contributions Tutorial](https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html)
+#' \insertRef{messier2012integrating}{amadeus}
+#' \insertRef{web_sedctutorial}{amadeus}
 #' @examples
 #' library(terra)
 #' library(sf)

R/calculate_covariates_auxiliary.R

@@ -20,6 +20,7 @@
 #' coordinate location.
 #' @keywords internal
 #' @importFrom stringi stri_pad
+#' @return a data.frame or SpatVector object (depending on `from`)
 #' @export
 calc_setcolumns <- function(
     from,
@@ -507,6 +508,7 @@ calc_worker <- function(
 #' @importFrom terra vect
 #' @keywords auxiliary
 #' @author Mitchell Manware
+#' @return a data.frame or SpatVector object (depending on `geom` paramter)
 #' @export
 # nolint start
 calc_return_locs <- function(

R/download.R

@@ -34,7 +34,7 @@
 #' * \code{\link{download_nei}}: `"nei"`, `"NEI"`
 #' * \code{\link{download_gridmet}}: `"gridMET"`, `"gridmet"`
 #' * \code{\link{download_terraclimate}}: `"TerraClimate"`, `"terraclimate"`
-#' @returns NULL
+#' @return NULL
 #' @examples
 #' \dontrun{
 #' download_data(
@@ -145,7 +145,7 @@ download_data <-
 #' @param remove_zip logical(1). Remove zip file from directory_to_download.
 #' Default \code{FALSE}.
 #' @author Mariana Kassien, Insang Song, Mitchell Manware
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -318,7 +318,7 @@ download_aqs <-
 #' @param remove_zip logical(1). Remove zip file from
 #' \code{directory_to_download}. Default \code{FALSE}.
 #' @author Insang Song
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' \code{directory_to_save}.
 #' @importFrom utils download.file
 #' @importFrom Rdpack reprompt
@@ -447,7 +447,7 @@ download_ecoregion <- function(
 #' Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; netCDF (.nc4) files will be stored in a
+#' @return NULL; netCDF (.nc4) files will be stored in a
 #' collection-specific folder within \code{directory_to_save}.
 #' @importFrom utils download.file
 #' @importFrom Rdpack reprompt
@@ -625,7 +625,7 @@ download_geos <- function(
 #' Default is \code{FALSE}.
 #' @author Mitchell Manware, Insang Song
 # nolint end
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -777,7 +777,7 @@ download_gmted <- function(
 #' Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; netCDF (.nc4) files will be stored in a
+#' @return NULL; netCDF (.nc4) files will be stored in a
 #' collection-specific folder within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -1188,7 +1188,7 @@ download_merra2 <- function(
 #' Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; netCDF (.nc) files will be stored in
+#' @return NULL; netCDF (.nc) files will be stored in
 #' \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -1340,7 +1340,7 @@ download_narr <- function(
 #' @param remove_zip logical(1). Remove zip files from directory_to_download.
 #' Default is \code{FALSE}.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' respective sub-directories within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -1499,7 +1499,7 @@ download_nlcd <- function(
 #' @param remove_zip logical(1). Remove zip files from directory_to_download.
 #' Default is \code{FALSE}.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' respective sub-directories within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -1657,7 +1657,7 @@ download_sedac_groads <- function(
 #' Default is \code{FALSE}.
 #' @author Mitchell Manware, Insang Song
 # nolint end
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' respective sub-directories within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -1824,7 +1824,7 @@ download_sedac_population <- function(
 #' Download wildfire smoke data
 #' @description
 #' The \code{download_hms()} function accesses and downloads
-#' wildfire smoke plume coverage data from [NOAA's Hazard Mapping System Fire and Smoke Product](https://www.ospo.noaa.gov/Products/land/hms.html#0).
+#' wildfire smoke plume coverage data from [NOAA's Hazard Mapping System Fire and Smoke Product](https://www.ospo.noaa.gov/products/land/hms.html#0).
 #' @param data_format character(1). "Shapefile" or "KML".
 #' @param date character(2). length of 10 each. Start/end date for downloading data.
 # nolint end
@@ -1851,7 +1851,7 @@ download_sedac_population <- function(
 #' @importFrom utils head
 #' @importFrom utils tail
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' respective sub-directories within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -2040,7 +2040,7 @@ download_hms <- function(
 #' @param remove_zip logical(1). Remove zip files from directory_to_download.
 #' Default is \code{FALSE}.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' respective sub-directories within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -2192,7 +2192,7 @@ download_koppen_geiger <- function(
 #' the text file containing download commands.
 #' @author Mitchell Manware, Insang Song
 #' @import rvest
-#' @returns NULL; HDF (.hdf) files will be stored in
+#' @return NULL; HDF (.hdf) files will be stored in
 #' \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -2565,7 +2565,7 @@ download_modis <- function(
 # nolint start
 #' Download toxic release data
 #' @description
-#' The \code{download_tri()} function accesses and downloads toxic release data from the [U.S. Environmental Protection Agency's (EPA) Toxic Release Inventory (TRI) Program](https://www.epa.gov/toxics-release-inventory-tri-program/find-understand-and-use-tri).
+#' The \code{download_tri()} function accesses and downloads toxic release data from the [U.S. Environmental Protection Agency's (EPA) Toxic Release Inventory (TRI) Program](https://www.epa.gov/toxics-release-inventory-tri-program/tri-data-action-0).
 #' @param year character(2). length of 4 each. Start/end years for downloading data.
 # nolint end
 #' @param directory_to_save character(1). Directory to download files.
@@ -2578,7 +2578,7 @@ download_modis <- function(
 #' @param remove_command logical(1). Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Mariana Kassien, Insang Song
-#' @returns NULL; Comma-separated value (CSV) files will be stored in
+#' @return NULL; Comma-separated value (CSV) files will be stored in
 #' \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -2701,7 +2701,7 @@ download_tri <- function(
 #' Currently we bundle the pre-downloaded crt and its PEM (which is accepted
 #' in wget command) file in ./inst/extdata. The instruction above is for
 #' certificate updates in the future.
-#' @returns NULL; Zip and/or data files will be downloaded and stored in
+#' @return NULL; Zip and/or data files will be downloaded and stored in
 #' respective sub-directories within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -2822,7 +2822,7 @@ download_nei <- function(
 # nolint start
 #' Download OpenLandMap data
 #' @description
-#' Accesses and downloads OpenLandMap data from the [OpenLandMap website](https://www.openlandmap.org/).
+#' Accesses and downloads OpenLandMap data from the [OpenLandMap website](https://opengeohub.org/about-openlandmap/).
 #' @param product character(1). Available collection name in OpenLandMap
 #' STAC Catalog. [list_stac_files] with `id_only = TRUE` to see available collections.
 #' * "no2_s5p.l3.trop.tmwm"
@@ -2913,7 +2913,7 @@ download_nei <- function(
 #' @note `extdata/openlandmap_assets.rds` contains the available assets in OpenLandMap.
 #' Users may want to check the available assets to download data directly.
 #' For developers: JSON files should be found at STAC catalog of OpenLandMap when updated.
-#' @returns NULL; GeoTIFF (.tif) files will be stored in
+#' @return NULL; GeoTIFF (.tif) files will be stored in
 #' \code{directory_to_save}.
 #' @seealso [list_stac_files]
 #' @importFrom Rdpack reprompt
@@ -3024,7 +3024,7 @@ download_olm <- function(
 #' the text file containing download commands.
 #' @param unzip logical(1). Unzip the downloaded compressed files.
 #' Default is \code{FALSE}. Not working for this function since HUC data is in 7z format.
-#' @returns NULL. Downloaded files will be stored in \code{directory_to_save}.
+#' @return NULL. Downloaded files will be stored in \code{directory_to_save}.
 #' @author Insang Song
 #' @importFrom Rdpack reprompt
 #' @references
@@ -3155,7 +3155,7 @@ download_huc <-
 #' Accesses and downloads United States Department of Agriculture
 #' CropScape Cropland Data Layer data from 
 #' the [USDA National Agricultural Statistics Service](https://www.nass.usda.gov/Research_and_Science/Cropland/Release/index.php) or the 
-#' [George Mason University website](https://https://nassgeodata.gmu.edu/CropScape/).
+#' [George Mason University website](https://nassgeodata.gmu.edu/CropScape/).
 #' @param year integer(1). Year of the data to download.
 #' @param source character(1). Data source, one of `c("USDA", "GMU")`.
 #' * `"USDA"` will download the national data from the USDA website (available in 2008-last year).
@@ -3174,7 +3174,7 @@ download_huc <-
 #' Default is \code{FALSE}.
 #' @author Insang Song
 #' @note JSON files should be found at STAC catalog of OpenLandMap
-#' @returns NULL; Yearly comma-separated value (CSV) files will be stored in
+#' @return NULL; Yearly comma-separated value (CSV) files will be stored in
 #' \code{directory_to_save}.
 #' @examples
 #' \dontrun{
@@ -3322,7 +3322,7 @@ download_cropscape <- function(
 #' Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Insang Song
-#' @returns NULL; .bil (normals) or single grid files depending on the format
+#' @return NULL; .bil (normals) or single grid files depending on the format
 #' choice will be stored in \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -3341,7 +3341,7 @@ download_cropscape <- function(
 #' )
 #' }
 #' @references
-#' * [PRISM Climate Group](http://www.prism.oregonstate.edu/)
+#' * [PRISM Climate Group](https://prism.oregonstate.edu/)
 #' * [PRISM Web Service Guide](https://prism.oregonstate.edu/documents/PRISM_downloads_web_service.pdf)
 #' @export
 # nolint end
@@ -3458,7 +3458,7 @@ download_prism <- function(
 #' Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Mitchell Manware
-#' @returns NULL; netCDF (.nc) files will be stored in a variable-specific
+#' @return NULL; netCDF (.nc) files will be stored in a variable-specific
 #' folder within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -3468,7 +3468,7 @@ download_prism <- function(
 #' download_gridmet(
 #'   variables = "Precipitation",
 #'   year = c(2023, 2024),
-#'   directory_to_save = "./data"
+#'   directory_to_save = "./data",
 #'   acknowledgement = TRUE,
 #'   download = TRUE,
 #'   remove_command = TRUE
@@ -3600,7 +3600,7 @@ download_gridmet <- function(
 #' Remove (\code{TRUE}) or keep (\code{FALSE})
 #' the text file containing download commands.
 #' @author Mitchell Manware, Insang Song
-#' @returns NULL; netCDF (.nc) files will be stored in a variable-specific
+#' @return NULL; netCDF (.nc) files will be stored in a variable-specific
 #' folder within \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -3610,7 +3610,7 @@ download_gridmet <- function(
 #' download_terraclimate(
 #'   variables = "Precipitation",
 #'   year = c(2023, 2024),
-#'   directory_to_save = "./data"
+#'   directory_to_save = "./data",
 #'   acknowledgement = TRUE,
 #'   download = TRUE,
 #'   remove_command = TRUE