Merge remote-tracking branch 'origin/main' into isong-calc-covars

DESCRIPTION

@@ -2,7 +2,7 @@ Package: NRTAPmodel
 Title: The SET group near real time air pollution model
 Version: 0.1.1
 Authors@R: c(
-    person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("aut", "cre")),
+    person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9508-9623")),
     person("Insang", "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),
     person("Eva", "Marques", role = c("aut", "ctb")),
     person("Mitchell", "Manware", role = c("aut", "ctb")),
@@ -19,6 +19,8 @@ Encoding: UTF-8
 VignetteBuilder: knitr, rmarkdown
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+Config/Needs/website: tidyverse/tidytemplate
 Config/testhat/edition: 3
 License: MIT + file LICENSE
-URL: https://spatiotemporal-exposures-and-toxicology.github.io/NRTAPmodel/
+URL: https://github.com/Spatiotemporal-Exposures-and-Toxicology/NRTAPmodel, 
+https://spatiotemporal-exposures-and-toxicology.github.io/NRTAPmodel/

_pkgdown.yml

@@ -0,0 +1,60 @@
+url: https://spatiotemporal-exposures-and-toxicology.github.io/NRTAPmodel/
+
+
+template:
+  bootstrap: 5
+  bootswatch: minty
+
+navbar:
+  structure:
+    left:  [reference, articles]
+    right: [search, github]
+
+
+development:
+  mode: auto
+
+reference:
+  - title: download data
+    desc: Download environmental data and process functions 
+    contents:
+      - starts_with("download")
+      - starts_with("build")
+
+  - title: check functions
+    desc: Download environmental data and process functions 
+    contents:
+      - matches("check")
+
+  - title: spacetime data and cross-validation
+    desc: future stdt package materials 
+    contents:
+      - matches("stdt")
+      - matches("dt")
+      - starts_with("generate")
+      - starts_with("extract")
+      - matches("cv")
+
+  - title: geographic covariate
+    desc: functions to calculate geographic covariates
+    contents:
+      - starts_with("calc")
+
+
+  - title: base learning
+    desc: fitting base learner models
+    contents:
+      - matches("base_learner")
+
+  - title: meta learning
+    desc: fitting the meta learner model
+    contents:
+      - matches("meta")
+
+  - title: other functions
+    desc: other helper functions
+    contents:
+      - read_commands
+      - startup_nrtap
+      - test_download_functions
+

tests/testthat/test-download_functions.R

@@ -633,6 +633,7 @@ testthat::test_that("MODIS-MOD09GA download URLs have HTTP status 200.", {
     urls <- extract_urls(commands = commands, position = 4)
     # check HTTP URL status
     url_status <- check_urls(urls = urls, size = 10L, method = "HEAD")
+    Sys.sleep(10)
     # implement unit tests
     test_download_functions(directory_to_save = directory_to_save,
                             commands_path = commands_path,