Merge pull request #28 from Spatiotemporal-Exposures-and-Toxicology/m…

…m-defaults-0226

0.1.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: amadeus
 Title: AMADEUS: A Mechanism/Machine for Data, Environments, and User Setup
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
     person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9508-9623")),
     person("Mitchell", "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")),

NAMESPACE

@@ -31,7 +31,7 @@ export(download_aqs_data)
 export(download_data)
 export(download_ecoregion_data)
 export(download_epa_certificate)
-export(download_geos_cf_data)
+export(download_geos_data)
 export(download_gmted_data)
 export(download_hms_data)
 export(download_koppen_geiger_data)

R/download.R

@@ -15,7 +15,7 @@
 #' Please refer to:
 #' * \link{download_aqs_data}: "aqs", "AQS"
 #' * \link{download_ecoregion_data}: "ecoregion"
-#' * \link{download_geos_cf_data}: "geos"
+#' * \link{download_geos_data}: "geos"
 #' * \link{download_gmted_data}: "gmted", "GMTED"
 #' * \link{download_koppen_geiger_data}: "koppen", "koppengeiger"
 #' * \link{download_merra2_data}: "merra2", "merra", "MERRA", "MERRA2"
@@ -49,7 +49,7 @@ download_data <-
     what_to_run <- switch(dataset_name,
       aqs = download_aqs_data,
       ecoregion = download_ecoregion_data,
-      geos = download_geos_cf_data,
+      geos = download_geos_data,
       gmted = download_gmted_data,
       koppen = download_koppen_geiger_data,
       koppengeiger = download_koppen_geiger_data,
@@ -144,7 +144,7 @@ download_aqs_data <-
       data_download_acknowledgement =
         data_download_acknowledgement
     )
-    #### 2. check for null parameteres
+    #### 2. check for null parameters
     check_for_null_parameters(mget(ls()))
     #### 3. directory setup
     directory_to_download <- download_sanitize_path(directory_to_download)
@@ -370,25 +370,23 @@ download_ecoregion_data <- function(
   #### 14. remove download command
   download_remove_command(commands_txt = commands_txt,
                           remove = remove_command)
-  if (download) {
-    #### 15. unzip files
-    download_unzip(
-      file_name = download_name,
-      directory_to_unzip = directory_to_save,
-      unzip = unzip
-    )
-    #### 16. remove zip files
-    download_remove_zips(
-      remove = remove_zip,
-      download_name = download_name
-    )
-  }
+  #### 15. unzip files
+  download_unzip(
+    file_name = download_name,
+    directory_to_unzip = directory_to_save,
+    unzip = unzip
+  )
+  #### 16. remove zip files
+  download_remove_zips(
+    remove = remove_zip,
+    download_name = download_name
+  )
 }
 
 # nolint start 
 #' Download atmospheric composition data from the NASA Global Earth Observing System (GEOS) model.
 #' @description
-#' The \code{download_goes_cf_data()} function accesses and downloads various
+#' The \code{download_geos_data()} function accesses and downloads various
 #' atmospheric composition collections from the [NASA Global Earth Observing System (GEOS) model](https://gmao.gsfc.nasa.gov/GEOS_systems/).
 # nolint end
 #' @param date_start character(1). length of 10. Start date for downloading
@@ -409,7 +407,7 @@ download_ecoregion_data <- function(
 #' @author Mitchell Manware, Insang Song
 #' @return NULL;
 #' @export
-download_geos_cf_data <- function(
+download_geos_data <- function(
     date_start = "2023-09-01",
     date_end = "2023-09-01",
     collection =
@@ -643,24 +641,22 @@ download_gmted_data <- function(
     download = download,
     system_command = system_command
   )
-  #### 18. Remove command file
+  #### 17. Remove command file
   download_remove_command(
     commands_txt = commands_txt,
     remove = remove_command
   )
-  if (download) {
-    #### 17. end if unzip == FALSE
-    download_unzip(
-      file_name = download_name,
-      directory_to_unzip = directory_to_save,
-      unzip = unzip
-    )
-    #### 19. remove zip files
-    download_remove_zips(
-      remove = remove_zip,
-      download_name = download_name
-    )
-  }
+  #### 18. end if unzip == FALSE
+  download_unzip(
+    file_name = download_name,
+    directory_to_unzip = directory_to_save,
+    unzip = unzip
+  )
+  #### 19. remove zip files
+  download_remove_zips(
+    remove = remove_zip,
+    download_name = download_name
+  )
 }
 
 # nolint start

R/download_test_support.R

@@ -7,7 +7,7 @@
 
 #' Check if sample of download URLs have HTTP Status 200
 #' @param url Download URL to be checked.
-#' @param method httr method to obtain URL (`"HEAD"`` or `"GET"`)
+#' @param method httr method to obtain URL (`"HEAD"` or `"GET"`)
 #' @author Insang Song; Mitchell Manware
 #' @importFrom httr HEAD
 #' @importFrom httr GET

R/process.R

@@ -13,6 +13,7 @@
 #' - [`process_nlcd`]: `"nlcd"`, `"NLCD"`
 #' - [`process_tri`]: `"tri"`, `"TRI"`
 #' - [`process_nei`]: `"nei"`, `"NEI`
+#' - [`process_geos`]: `"geos"`
 #' - [`process_gmted`]: `"gmted"`, `"GMTED"`
 #' - [`process_aqs`]: `"aqs"`, `"AQS"`
 #' - [`process_hms`]: `"hms"`, `"HMS"`, `"smoke"`
@@ -76,8 +77,12 @@ process_covariates <-
       }, error = function(e) {
         print(e)
         print(args(what_to_run))
-        stop("Please refer to the argument list and
-the error message above to rectify the error.\n")
+        stop(
+          paste0(
+            "Please refer to the argument list and the error message above to ",
+            "rectify the error.\n"
+          )
+        )
       })
 
     return(res_covariate)
@@ -618,7 +623,7 @@ process_nlcd <-
 #' @export
 process_ecoregion <-
   function(
-    path = "./input/data/ecoregions/raw/us_eco_l3_state_boundaries.shp"
+    path = NULL
   ) {
     ecoreg <- terra::vect(path)
     ecoreg <- ecoreg[, grepl("^(L2_KEY|L3_KEY)", names(ecoreg))]
@@ -655,8 +660,7 @@ process_conformity <-
       locs_epsg <- locs$crs_dt
     } else {
       if (!all(keyword %in% names(locs))) {
-        stop("locs should be stdt or 
-have 'lon', 'lat', (and 'time') fields.\n")
+        stop("locs should be stdt or have 'lon', 'lat', (and 'time') fields.\n")
       }
       if (!methods::is(locs, "SpatVector")) {
         if (methods::is(locs, "sf")) {
@@ -1318,7 +1322,7 @@ process_gmted <- function(
 process_narr <- function(
     date = c("2023-09-01", "2023-09-01"),
     variable = NULL,
-    path = "../../data/covariates/narr/") {
+    path = NULL) {
   #### directory setup
   path <- download_sanitize_path(path)
   #### check for variable
@@ -1453,7 +1457,7 @@ process_narr <- function(
 }
 
 #' Import and clean GEOS-CF data downloaded with
-#' `download_geos_cf_data` or `download_data(dataset_name = "geos")`. Function
+#' `download_geos_data` or `download_data(dataset_name = "geos")`. Function
 #' returns a SpatRast object containing the user-defined variables of interest.
 #' Layer names indicate the variable, pressure level, date (YYYYMMDD), and, if
 #' applicable, the hour (HHMMSS).
@@ -1474,7 +1478,7 @@ process_narr <- function(
 process_geos <-
   function(date = c("2018-01-01", "2018-01-01"),
            variable = NULL,
-           path = "../../data/covariates/geos_cf/") {
+           path = NULL) {
     #### directory setup
     path <- download_sanitize_path(path)
     #### check for variable

tests/testthat/test-calculate_covariates.R

@@ -81,6 +81,22 @@ testthat::test_that("calc_dummies works well", {
 
 })
 
+testthat::test_that("calc_temporal_dummies errors.", {
+  withr::local_package("terra")
+  ncp <- data.frame(lon = -78.8277, lat = 35.95013)
+  ncp$site_id <- "3799900018810101"
+  testthat::expect_error(
+    calc_temporal_dummies(
+      ncp
+    )
+  )
+  testthat::expect_error(
+    calc_temporal_dummies(
+      terra::vect(ncp)
+    )
+  )
+})
+
 testthat::test_that("calc_ecoregion works well", {
   withr::local_package("terra")
   withr::local_package("sf")