Merge branch 'develop' into develop

CHANGELOG.md

@@ -47,6 +47,8 @@ see if you need to change any of these:
 - Added the new feature of the block-based SDA workflow, which supports the parallel computation.
 - Added new SDA workflow for the 342 North America anchor sites.
 - Added new feature of preparing initial conditions for MODIS LAI, AGB, ISCN SOC, and soil moisture across NA anchor sites.
+- Added GEDI AGB preparation workflow.
+- Added new feature of downloading datasets from the NASA DAAC ORNL database.
 
 ### Fixed
 

docker/depends/pecan_deps_from_github.txt

@@ -7,3 +7,4 @@ ropensci/geonames
 ropensci/nneo
 SticsRPacks/SticsOnR
 SticsRPacks/SticsRFiles
+VangiElia/GEDI4R

docker/depends/pecan_package_dependencies.csv

@@ -75,9 +75,11 @@
 "future","*","modules/data.atmosphere","Suggests",FALSE
 "future","*","modules/data.land","Imports",FALSE
 "future","*","modules/data.remote","Imports",FALSE
+"GEDI4R","*","modules/data.remote","Suggests",FALSE
 "geonames","> 0.998","modules/data.atmosphere","Imports",FALSE
 "getPass","*","base/remote","Suggests",FALSE
 "getPass","*","modules/data.land","Suggests",FALSE
+"getPass","*","modules/data.remote","Suggests",FALSE
 "ggmcmc","*","modules/meta.analysis","Suggests",FALSE
 "ggplot2","*","base/utils","Suggests",FALSE
 "ggplot2","*","base/visualization","Imports",FALSE
@@ -103,6 +105,7 @@
 "grDevices","*","modules/allometry","Imports",FALSE
 "grDevices","*","modules/assim.batch","Imports",FALSE
 "grDevices","*","modules/benchmark","Imports",FALSE
+"grDevices","*","modules/data.remote","Suggests",FALSE
 "grid","*","base/visualization","Suggests",FALSE
 "gridExtra","*","modules/assim.sequential","Suggests",FALSE
 "gridExtra","*","modules/benchmark","Imports",FALSE
@@ -112,10 +115,12 @@
 "httr","*","base/remote","Imports",FALSE
 "httr","*","modules/data.atmosphere","Imports",FALSE
 "httr","*","modules/data.land","Imports",FALSE
+"httr","*","modules/data.remote","Suggests",FALSE
 "IDPmisc","*","modules/assim.batch","Imports",FALSE
 "jsonlite","*","base/remote","Imports",FALSE
 "jsonlite","*","models/stics","Imports",FALSE
 "jsonlite","*","modules/data.atmosphere","Imports",FALSE
+"jsonlite","*","modules/data.remote","Suggests",FALSE
 "knitr",">= 1.42","base/db","Suggests",FALSE
 "knitr",">= 1.42","base/qaqc","Suggests",FALSE
 "knitr",">= 1.42","modules/allometry","Suggests",FALSE
@@ -471,6 +476,7 @@
 "rlang","*","modules/assim.sequential","Imports",FALSE
 "rlang","*","modules/benchmark","Imports",FALSE
 "rlang","*","modules/data.land","Imports",FALSE
+"rlang","*","modules/data.remote","Imports",FALSE
 "rlang","*","modules/uncertainty","Imports",FALSE
 "rlang",">= 0.2.0","modules/data.atmosphere","Imports",FALSE
 "rlist","*","modules/assim.sequential","Suggests",FALSE
@@ -531,6 +537,7 @@
 "sf","*","modules/assim.sequential","Suggests",FALSE
 "sf","*","modules/data.atmosphere","Imports",FALSE
 "sf","*","modules/data.land","Imports",FALSE
+"sf","*","modules/data.remote","Suggests",FALSE
 "SimilarityMeasures","*","modules/benchmark","Imports",FALSE
 "sirt","*","modules/data.land","Imports",FALSE
 "sp","*","base/visualization","Suggests",FALSE
@@ -631,6 +638,7 @@
 "utils","*","modules/assim.batch","Imports",FALSE
 "utils","*","modules/assim.sequential","Suggests",FALSE
 "utils","*","modules/benchmark","Imports",FALSE
+"utils","*","modules/data.remote","Suggests",FALSE
 "utils","*","modules/photosynthesis","Imports",FALSE
 "vdiffr",">= 1.0.2","base/qaqc","Suggests",FALSE
 "withr","*","base/db","Suggests",FALSE

modules/assim.sequential/R/sda_plotting.R

@@ -918,8 +918,8 @@ post.analysis.multisite.ggplot <- function(settings, t, obs.times, obs.mean, obs
 ##' @param CI range of confidence interval.
 ##' @param unit list of unit used for y axis label.
 ##' @param style color option.
-##' @param PDF_w width of exported PDF file.
-##' @param PDF_h height of exported PDF file.
+##' @param PDF_w width of exported PDF file, passed on to `base::pdf()`.
+##' @param PDF_h height of exported PDF file, passed on to `base::pdf()`.
 ##' @param t.inds index of period that will be plotted.
 ##' @export
 ##' @author Dongchen Zhang

modules/data.land/R/download.SM_CDS.R

@@ -1,16 +1,4 @@
 #' Download CDS soil moisture data for the SDA workflow.
-#'
-#' @param outfolder physical paths to where the unziped soil moisture files are downloaded.
-#' @param time.points A vector contains each time point within the start and end date.
-#' @param overwrite flag determine if we want to overwrite existing files when downloading.
-#' @param auto.create.key flag determine if we want to automatically create the credential file.
-#'
-#' @return A vector containing file paths to the downloaded files.
-#' @export
-#' 
-#' @examples
-#' @author Dongchen Zhang
-#' @importFrom dplyr %>%
 #' @details 
 #' Introduction on how to play with the CDS python API
 #' to correctly build the python environment with the cdsapi installed, you need to follow those steps.
@@ -42,6 +30,18 @@
 #' run this function.
 #' go to `https://cds.climate.copernicus.eu/api-how-to#install-the-cds-api-key` website.
 #' copy and paste url and key to the prompt window.
+#'
+#' @param outfolder physical paths to where the unziped soil moisture files are downloaded.
+#' @param time.points A vector contains each time point within the start and end date.
+#' @param overwrite flag determine if we want to overwrite existing files when downloading.
+#' @param auto.create.key flag determine if we want to automatically create the credential file.
+#'
+#' @return A vector containing file paths to the downloaded files.
+#' @export
+#' 
+#' @examples
+#' @author Dongchen Zhang
+#' @importFrom dplyr %>%
 download.SM_CDS <- function(outfolder, time.points, overwrite = FALSE, auto.create.key = FALSE) {
   #load cdsapi from python environment.
   tryCatch({

modules/data.remote/DESCRIPTION

@@ -28,19 +28,29 @@ Imports:
     PEcAn.logger,
     magrittr,
     PEcAn.remote,
+    rlang,
     terra,
     doParallel,
     parallel,
     foreach
 Suggests:
     data.table,
     dplyr,
+    getPass,
+    GEDI4R,
     ggplot2,
+    grDevices,
+    httr,
+    jsonlite,
     lubridate,
     raster,
     reshape,
+    sf,
     testthat (>= 1.0.2),
-    tibble
+    tibble,
+    utils
+Remotes:
+    github::VangiElia/GEDI4R
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyLoad: yes

modules/data.remote/NAMESPACE

@@ -1,8 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+export(GEDI_AGB_plot)
 export(Landtrendr_AGB_prep)
 export(MODIS_LAI_prep)
 export(MODIS_LC_prep)
+export(NASA_DAAC_download)
 export(Prep_AGB_IC_from_2010_global)
 export(SMAP_SMP_prep)
 export(call_MODIS)
@@ -16,3 +18,4 @@ importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(magrittr,"%>%")
 importFrom(purrr,"%>%")
+importFrom(rlang,.data)