Merge pull request #13 from Spatiotemporal-Exposures-and-Toxicology/r…

…efactor-process 0.1.0
NIEHS · Feb 16, 2024 · 1a7b08a · 1a7b08a
2 parents 6000bd0 + b88ed8b
commit 1a7b08a
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Showing 46 changed files with 3,764 additions and 1,388 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,7 +3,7 @@
 ^tools/
 ^manuscript/
 ^output/
-^\.github/workflows/
+^\.github/
 ^amadeus\.Rproj$
 ^\.Rproj\.user$
 ^\.github$

diff --git a/.gitignore b/.gitignore
@@ -50,4 +50,7 @@ rsconnect/
 
 # DS_Store
 .DS_Store
-**/.DS_Store
+**/.DS_Store
+
+# custom linter dev
+\.github/linters
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: amadeus
 Title: AMADEUS: A Mechanism/Machine for Data, Environments, and User Setup
-Version: 0.0.1
+Version: 0.1.0
 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")),
@@ -12,7 +12,7 @@ Authors@R: c(
     )
 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.
 Depends: R (>= 4.1.0)
-Imports: dplyr, sf, sftime, stats, terra, methods, data.table, httr, rvest, exactextractr, utils, stringr, testthat (>= 3.0.0), doParallel, parallelly, stars, foreach, future
+Imports: dplyr, sf, sftime, stats, terra, methods, data.table, httr, rvest, exactextractr, utils, stringr, testthat (>= 3.0.0), doParallel, parallelly, stars, foreach, future, tidyr, rlang
 Suggests: covr, withr, knitr, rmarkdown, lwgeom, FNN, doRNG
 Encoding: UTF-8
 VignetteBuilder: knitr, rmarkdown

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,9 +4,11 @@ export(as_mysftime)
 export(calc_covariates)
 export(calc_ecoregion)
 export(calc_koppen_geiger)
-export(calc_modis)
+export(calc_modis_daily)
+export(calc_modis_par)
 export(calc_nei)
 export(calc_nlcd_ratio)
+export(calc_sedc)
 export(calc_temporal_dummies)
 export(calc_tri)
 export(check_for_null_parameters)
@@ -47,14 +49,21 @@ export(download_unzip)
 export(dt_to_mysftime)
 export(extract_urls)
 export(generate_date_sequence)
+export(is_date_proper)
 export(is_stdt)
-export(modis_aggregate_sds)
-export(modis_get_vrt)
-export(modis_mosaic_mod06)
-export(modis_prefilter_sds)
-export(modis_preprocess_vnp46)
-export(modis_warp_stars)
-export(modis_worker)
+export(process_bluemarble)
+export(process_bluemarble_corners)
+export(process_conformity)
+export(process_ecoregion)
+export(process_flatten_sds)
+export(process_koppen_geiger)
+export(process_modis_merge)
+export(process_modis_sds)
+export(process_modis_swath)
+export(process_modis_warp)
+export(process_nei)
+export(process_nlcd)
+export(process_tri)
 export(read_commands)
 export(test_download_functions)
 import(rvest)
@@ -69,8 +78,17 @@ importFrom(data.table,month)
 importFrom(data.table,rbindlist)
 importFrom(data.table,year)
 importFrom(doParallel,registerDoParallel)
+importFrom(dplyr,across)
+importFrom(dplyr,all_of)
+importFrom(dplyr,as_tibble)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,ends_with)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
 importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,summarize)
+importFrom(dplyr,ungroup)
 importFrom(exactextractr,exact_extract)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
@@ -80,6 +98,8 @@ importFrom(httr,GET)
 importFrom(httr,HEAD)
 importFrom(methods,is)
 importFrom(parallelly,availableWorkers)
+importFrom(rlang,inject)
+importFrom(rlang,sym)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
@@ -90,17 +110,22 @@ importFrom(sf,st_union)
 importFrom(stars,read_stars)
 importFrom(stars,st_warp)
 importFrom(stats,reshape)
+importFrom(stats,setNames)
 importFrom(stringr,str_split_i)
 importFrom(terra,buffer)
 importFrom(terra,coltab)
 importFrom(terra,crop)
 importFrom(terra,crs)
 importFrom(terra,describe)
+importFrom(terra,distance)
 importFrom(terra,ext)
 importFrom(terra,extract)
 importFrom(terra,intersect)
+importFrom(terra,is.rotated)
 importFrom(terra,merge)
+importFrom(terra,metags)
 importFrom(terra,mosaic)
+importFrom(terra,nearby)
 importFrom(terra,nlyr)
 importFrom(terra,project)
 importFrom(terra,rast)
@@ -110,6 +135,7 @@ importFrom(terra,snap)
 importFrom(terra,tapp)
 importFrom(terra,vect)
 importFrom(testthat,expect_true)
+importFrom(tidyr,pivot_wider)
 importFrom(utils,download.file)
 importFrom(utils,head)
 importFrom(utils,read.csv)