saving progress

R/get_elevation.R

@@ -9,9 +9,32 @@
 #' @export
 get_glw <- function() {
 
-  url_cattle <- "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/LHBICE#"
-  url_cattle_out <- GET(url_cattle)
-  unzipped_glw_cattle <- unzip(url_cattle_out)
-  Aw_layer <- if_else(str_detect(names(unzipped_glw_cattle), "Aw")==TRUE, )
-
-}
+  url_elevation <- ""
+  url_elevation_out <- GET(url_elevation)
+  unzipped_elevation <- unzip(url_elevation_out)
+
+}
+
+# Install and load required packages
+install.packages("aws.s3")
+library(aws.s3)
+install.packages("paws")
+library(paws)
+
+renv::install("ecohealthalliance/containerTemplateUtils")
+
+library(containerTemplateUtils)
+
+# Set the AWS region
+region <- "af-south-1"
+
+# Set the S3 bucket name and prefix
+bucket_name <- "deafrica-input-datasets"
+prefix <- ""  # Empty prefix to fetch all objects, or specify a specific prefix
+
+Sys.setenv("AWS_REGION"="af-south-1")
+aws_s3_download(path="data", bucket=bucket_name, key="")
+
+
+
+

R/get_glw.R

@@ -8,11 +8,19 @@
 #' @author Whitney Bagge
 #' @export
 get_glw <- function() {
+
+  taxa <- c("url_cattle","url_sheep","url_goats")
+
+  for(i in 1:length(taxa)) {                                    
+
+  url_out <- switch(taxa[i], "url_cattle" = "https://dataverse.harvard.edu/api/access/datafile/6769710", 
+                            "url_sheep" = "https://dataverse.harvard.edu/api/access/datafile/6769629",
+                            "url_goats" = "https://dataverse.harvard.edu/api/access/datafile/6769692"
+                  )
 
-  url_cattle <- "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/LHBICE#"
-  #taxa cattle sheep goat have three urls here switch function (like if_else); have the three targets 
-  url_cattle_out <- GET(url_cattle)
-  unzipped_glw_cattle <- unzip(url_cattle_out)
-  Aw_layer <- if_else(str_detect(names(unzipped_glw_cattle), "Aw")==TRUE, )
+  url_taxa_out<-download.file(url_out, destfile = paste("data/",taxa[i],sep="",".tif"))
+
+  }
+
 
-}
+}

R/preprocess_glw.R

@@ -7,10 +7,14 @@
 #' @return
 #' @author Whitney Bagge
 #' @export
-preprocess_glw <- function(glw_layer, bounding_boxes) {
+preprocess_glw <- function(bounding_boxes) {
 
-  extent_object <- extent(bounding_boxes)
-  glw_layer_out <- crop(glw_layer, extent_object)
+  taxa_tif <- c("url_cattle.tif","url_sheep.tif","url_goats.tif")
+
+  for(i in 1:length(taxa_tif)) { 
+  extent_object <- raster::extent(bounding_boxes)
+  glw_layer_out <- raster::crop(taxa_tif, extent_object)
   return(glw_layer_out)
 
+  }
 }

R/preprocess_soil.R

@@ -0,0 +1,37 @@
+#' .. content for \description{} (no empty lines) ..
+#'
+#' .. content for \details{} ..
+#'
+#' @title
+#' @param bounding_boxes
+#' @return
+#' @author Whitney Bagge
+#' @export
+
+preprocess_soil <- function(unzipped_soil, bounding_boxes) {
+
+  library(terra)
+  library(sf)
+  library(RSQLite)
+
+  hwsd <- rast("./data/soil/HWSD2.bil")
+
+  hwsd_bounded <- terra::crop(hwsd, bounding_boxes)
+
+  print(paste("UTM zone:", utm.zone <-
+                floor(((sf::st_bbox(hwsd_bounded)$xmin +
+                          sf::st_bbox(hwsd_bounded)$xmax)/2 + 180)/6)
+              + 1))
+
+  (epsg <- 32600 + utm.zone)
+
+  hwsd_bounded.utm <- project(hwsd_bounded, paste0("EPSG:", epsg), method = "near")
+
+
+ # m <- dbDriver("SQLite")
+ # con <- dbConnect(m, dbname="HWSD2.sqlite")
+ # dbListTables(con)
+ # 
+ # print(dbGetQuery(con, "select * from HWSD2_SMU_METADATA"), width=100)
+ # 
+}

R/process_elevation.R

@@ -11,7 +11,6 @@ process_elevation <- function(elevation_layer_raw, bounding_boxes) {
 
   extent_object <- extent(bounding_boxes)
   elevation_layer_raw_out <- crop(elevation_layer_raw, extent_object)
-
   return(elevation_layer_raw_out)
 
 }

R/soil_download.R

@@ -0,0 +1,35 @@
+#' .. content for \description{} (no empty lines) ..
+#'
+#' .. content for \details{} ..
+#'
+#' @title
+#' @param 
+#' @return
+#' @author Whitney Bagge
+#' @export
+soil_download <- function() {
+
+  options(timeout=200)
+
+  location <- c("soil_raster", "soil_database")
+
+  for(i in 1:length(location)) { 
+
+  url_out <- switch(location[i], "soil_raster" = "https://s3.eu-west-1.amazonaws.com/data.gaezdev.aws.fao.org/HWSD/HWSD2_RASTER.zip", 
+                                 "soil_database" = "https://www.isric.org/sites/default/files/HWSD2.sqlite")
+
+
+  file_name <- paste("data/soil/",location[i],sep="",".zip")
+
+  download.file(url=url_out, destfile = file_name)
+
+  unzipped_soil <- unzip(file_name, exdir = "data/soil/")
+
+
+
+  return("data/soil/")
+
+  }
+
+}
+

_targets.R

@@ -115,28 +115,25 @@ source_targets <- tar_plan(
   format = "file"
   ),
 
+  ## SOIL
+
+
   ## GLW
 
-  tar_target(glw_cattle, get_glw()),
-  tar_target(glw_sheep, get_glw()),
-  tar_target(glw_goats, get_glw()),
-  tar_target(glw_cattle_preprocessed, preprocess_glw(glw_cattle, bounding_boxes)),
-  #need to cache
-
+  #tar_target(glw_cattle, get_glw(url_cattle)),
+  #tar_target(glw_sheep, get_glw(url_sheep)),
+  #tar_target(glw_goats, get_glw(url_goats)),
+  #tar_target(glw_cattle_preprocessed, preprocess_glw(glw_cattle, bounding_boxes, download_directory = "data/glw")),
+  #tar_target(glw_sheep_preprocessed, preprocess_glw(glw_sheep, bounding_boxes, download_directory = "data/glw")),
+  #tar_target(glw_goats_preprocessed, preprocess_glw(glw_goats, bounding_boxes, download_directory = "data/glw")),
+
   ## ELEVATION
 
-  tar_target(elevation_layer_raw, get_elevation()),
-  tar_target(elevation_layer_processed, 
-             process_elevation(elevation_layer_processed, bounding_boxes)),
-  #need to cache
-
-  ## GRAZING CAPACITY
-
-  tar_target(grazingcap_raw, get_grazingcap()),
-  tar_target(grazingcap_processed, 
-             process_grazingcap(grazingcap_layer_processed, bounding_boxes)),
-  #need to cache
-
+  #tar_target(elevation_layer_raw, get_elevation()),
+  #tar_target(elevation_layer_processed, 
+  #          process_elevation(elevation_layer_processed, bounding_boxes)),
+
+
 )
 
 # Data Processing -----------------------------------------------------------