1.0.7

.Rbuildignore

@@ -23,4 +23,5 @@ vignettes/download_functions.Rmd
 vignettes/epa_download.Rmd
 vignettes/protected_datasets.Rmd
 inst/extdata/air.2m
+inst/extdata/nasa/token.txt
 LICENSE.md

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: amadeus
-Title: Accessing and Analyzing Large-Scale Environmental Data in R
-Version: 1.0.3
+Title: Accessing and Analyzing Large-Scale Environmental Data
+Version: 1.0.6
 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")),
@@ -13,7 +13,18 @@ Maintainer: Kyle Messier <[email protected]>
 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
+Suggests: 
+    covr,
+    withr,
+    knitr,
+    rmarkdown,
+    lwgeom,
+    FNN,
+    doRNG,
+    devtools,
+    stringr,
+    tigris,
+    spelling
 RdMacros: Rdpack
 Encoding: UTF-8
 VignetteBuilder: knitr, rmarkdown
@@ -22,5 +33,6 @@ RoxygenNote: 7.3.2
 Config/Needs/website: tidyverse/tidytemplate
 Config/testhat/edition: 3
 License: MIT + file LICENSE
-URL: https://github.com/NIEHS/amadeus
+URL: https://niehs.github.io/amadeus/
 BugReports: https://github.com/NIEHS/amadeus/issues
+Language: en-US

R/calculate_covariates.R

@@ -37,6 +37,8 @@
 #' @return Calculated covariates as a data.frame or SpatVector object
 #' @author Insang Song
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_covariates(
@@ -106,12 +108,14 @@ calc_covariates <-
           ...
         )
       }, error = function(e) {
-        print(e)
-        print(args(what_to_run))
         stop(
           paste0(
-            "Please refer to the argument list and the error message above ",
-            "to rectify the error.\n"
+            e,
+            "\n",
+            paste0(deparse(args(what_to_run)), collapse = "\n"),
+            "\n",
+            "Please refer to the argument list and ",
+            "the error message above to rectify the error.\n"
           )
         )
       })
@@ -150,6 +154,8 @@ calc_covariates <-
 #' @importFrom terra merge
 #' @importFrom methods is
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_koppen_geiger(
@@ -307,6 +313,8 @@ calc_koppen_geiger <-
 #' @importFrom future.apply future_Map
 #' @importFrom collapse rowbind
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_nlcd(
@@ -471,6 +479,8 @@ calc_nlcd <- function(from,
 #' @importFrom terra extract
 #' @importFrom data.table year
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_ecoregion(
@@ -598,10 +608,12 @@ calc_ecoregion <-
 #' @importFrom sf st_as_sf
 #' @importFrom sf st_drop_geometry
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' locs <- data.frame(lon = -78.8277, lat = 35.95013, id = "001")
 #' calc_modis_daily(
-#'   from = mod06l2_warp,
+#'   from = mod06l2_warp, # dervied from process_modis() example
 #'   locs = locs,
 #'   locs_id = "id",
 #'   radius = 0,
@@ -812,6 +824,8 @@ calc_modis_daily <- function(
 #' @importFrom future.apply future_lapply
 #' @importFrom parallelly availableWorkers
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' locs <- data.frame(lon = -78.8277, lat = 35.95013, id = "001")
 #' locs <- terra::vect(locs, geom = c("lon", "lat"), crs = "EPSG:4326")
@@ -1026,6 +1040,8 @@ process_modis_swath, or process_blackmarble.")
 #' @importFrom data.table month
 #' @importFrom data.table as.data.table
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_temporal_dummies(
@@ -1308,6 +1324,8 @@ The result may not be accurate.\n",
 #' @importFrom dplyr ungroup
 #' @importFrom dplyr summarize
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_tri(
@@ -1397,10 +1415,12 @@ calc_tri <- function(
 #' @importFrom terra project
 #' @importFrom terra intersect
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_nei(
-#'   from = nei, # derived from process_nei example,
+#'   from = nei, # derived from process_nei example
 #'   locs = loc,
 #'   locs_id = "id"
 #' )
@@ -1459,6 +1479,8 @@ calc_nei <- function(
 #' @importFrom dplyr all_of
 #' @importFrom stats setNames
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_hms(
@@ -1692,6 +1714,8 @@ calc_hms <- function(
 #' @importFrom terra nlyr
 #' @importFrom terra crs
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_gmted(
@@ -1813,6 +1837,8 @@ calc_gmted <- function(
 #' @importFrom terra nlyr
 #' @importFrom terra crs
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_narr(
@@ -1906,6 +1932,8 @@ calc_narr <- function(
 #' @importFrom terra nlyr
 #' @importFrom terra crs
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_geos(
@@ -1983,6 +2011,8 @@ calc_geos <- function(
 #' @return a data.frame or SpatVector object
 #' @importFrom methods is
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_sedac_population(
@@ -2098,6 +2128,8 @@ calc_sedac_population <- function(
 #' @importFrom terra linearUnits
 #' @importFrom methods is
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_sedac_groads(
@@ -2212,6 +2244,8 @@ calc_sedac_groads <- function(
 #' @importFrom terra nlyr
 #' @importFrom terra crs
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_merra2(
@@ -2301,6 +2335,8 @@ calc_merra2 <- function(
 #' @importFrom terra nlyr
 #' @importFrom terra crs
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_gridmet(
@@ -2386,6 +2422,8 @@ calc_gridmet <- function(
 #' @importFrom terra nlyr
 #' @importFrom terra crs
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' calc_terraclimate(
@@ -2469,6 +2507,8 @@ calc_terraclimate <- function(
 #' @importFrom dplyr lag
 #' @importFrom dplyr select
 #' @examples
+#' ## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
+#' ##       amount of data which is not included in the package.
 #' \dontrun{
 #' loc <- data.frame(id = "001", lon = -78.90, lat = 35.97)
 #' terracliamte_covar <- calc_terraclimate(

R/download.R

@@ -109,10 +109,16 @@ download_data <-
         )
       },
       error = function(e) {
-        print(e)
-        print(args(what_to_run))
-        stop(paste0("Please refer to the argument list and ",
-                    "the error message above to rectify the error.\n"))
+        stop(
+          paste0(
+            e,
+            "\n",
+            paste0(deparse(args(what_to_run)), collapse = "\n"),
+            "\n",
+            "Please refer to the argument list and ",
+            "the error message above to rectify the error.\n"
+          )
+        )
       }
     )
   }
@@ -1016,7 +1022,7 @@ download_merra2 <- function(
   identifiers_df <- as.data.frame(identifiers)
   colnames(identifiers_df) <- c("collection_id", "estd_name", "DOI")
   if (!all(collection %in% identifiers_df$collection_id)) {
-    print(identifiers_df)
+    message(identifiers_df)
     stop(paste0("Requested collection is not recognized.\n
     Please refer to the table above to find a proper collection.\n"))
   }
@@ -2181,15 +2187,17 @@ download_koppen_geiger <- function(
 #' 
 #' \insertRef{article_roman2018vnp46}{amadeus}
 #' @examples
+#' \dontrun{
+#' ## NOTE: Examples are wrapped in `/dontrun{}` to avoid sharing sensitive
+#' ##       NASA EarthData tokden information.
 #' # example with MOD09GA product
 #' download_modis(
 #'   product = "MOD09GA",
 #'   version = "61",
 #'   horizontal_tiles = c(8, 8),
 #'   vertical_tiles = c(4, 4),
 #'   date = c("2024-01-01", "2024-01-01"),
-#'   nasa_earth_data_token =
-#'     system.file("extdata", "nasa", "token.txt", package = "amadeus"),
+#'   nasa_earth_data_token = "./pathtotoken/token.txt",
 #'   directory_to_save = tempdir(),
 #'   acknowledgement = TRUE,
 #'   download = FALSE, # NOTE: download skipped for examples,
@@ -2207,8 +2215,7 @@ download_koppen_geiger <- function(
 #'       "extdata", "nasa", "LAADS_query.2024-08-02T12_49.csv",
 #'       package = "amadeus"
 #'     ),
-#'   nasa_earth_data_token =
-#'     system.file("extdata", "nasa", "token.txt", package = "amadeus"),
+#'   nasa_earth_data_token = "./pathtotoken/token.txt",
 #'   directory_to_save = tempdir(),
 #'   acknowledgement = TRUE,
 #'   download = FALSE, # NOTE: download skipped for examples,
@@ -2221,13 +2228,13 @@ download_koppen_geiger <- function(
 #'   horizontal_tiles = c(8, 8),
 #'   vertical_tiles = c(4, 4),
 #'   date = c("2024-01-01", "2024-01-01"),
-#'   nasa_earth_data_token =
-#'     system.file("extdata", "nasa", "token.txt", package = "amadeus"),
+#'   nasa_earth_data_token = "./pathtotoken/token.txt",
 #'   directory_to_save = tempdir(),
 #'   acknowledgement = TRUE,
 #'   download = FALSE, # NOTE: download skipped for examples,
 #'   remove_command = TRUE
 #' )
+#' }
 # nolint end
 #' @export
 download_modis <- function(