saving prgress

R/get_slope_aspect.R

@@ -0,0 +1,81 @@
+#' .. content for \description{} (no empty lines) ..
+#'
+#' .. content for \details{} ..
+#'
+#' @title
+#' @param 
+#' @return
+#' @author Whitney Bagge
+#' @export
+#' 
+#' 
+#' https://www.fao.org/soils-portal/data-hub/soil-maps-and-databases/harmonized-world-soil-database-v12/en/
+library(archive)
+get_slope_aspect<- function(slope_aspect_directory_dataset, slope_aspect_directory_raw, continent_raster_template) {
+
+  slope_aspect <- c("aspect_zero", "aspect_fortyfive", "aspect_onethirtyfive", "aspect_twotwentyfive", "aspect_undef",
+                   "slope_zero", "slope_pointfive", "slope_two", "slope_five", "slope_ten", "slope_fifteen", 
+                    "slope_thirty", "slope_fortyfive")
+
+  for(asp in slope_aspect) { 
+
+    url_out<- switch(asp,  "aspect_zero" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloAspectClN_30as.rar",
+                    "aspect_fortyfive" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloAspectClE_30as.rar", 
+                    "aspect_onethirtyfive" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloAspectClS_30as.rar",
+                    "aspect_twotwentyfive" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloAspectClW_30as.rar",
+                    "aspect_undef" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloAspectClU_30as.rar",
+                    "slope_zero" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl1_30as.rar",
+                    "slope_pointfive" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl2_30as.rar",
+                    "slope_two" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl3_30as.rar",
+                    "slope_five" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl4_30as.rar",
+                    "slope_ten" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl5_30as.rar",
+                    "slope_fifteen" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl6_30as.rar",
+                    "slope_thirty" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl7_30as.rar",
+                    "slope_fortyfive" = "https://www.fao.org/fileadmin/user_upload/soils/HWSD%20Viewer/GloSlopesCl8_30as.rar")
+
+    filename <- paste("data/slope_aspect/", asp, sep="", ".rar")
+
+    #download.file(url=url_out, destfile = filename)
+
+    rar_name <- file.path(dirname(filename), system2("unrar", c("lb", filename), stdout = TRUE))
+    system2("unrar", c("e", "-o+", filename, dirname(filename), ">/dev/null"))
+
+    GloAspectClN_30as <- rast("GloAspectClN_30as.asc")
+    GloAspectClE_30as <- rast("GloAspectClE_30as.asc")
+    GloAspectClS_30as <- rast("GloAspectClS_30as.asc")
+    GloAspectClW_30as <- rast("GloAspectClW_30as.asc")
+    GloAspectClU_30as <- rast("GloAspectClU_30as.asc")
+
+    raster_stack_aspect <- c(GloAspectClN_30as, GloAspectClE_30as, GloAspectClS_30as, GloAspectClW_30as, GloAspectClU_30as)
+
+    raster_max_aspect <- max(raster_stack_aspect, na.rm = TRUE)
+
+    transformed_raster <- transform_raster(raw_raster = rast(raster_max_aspect),
+                                           template = rast(continent_raster_template)) 
+
+
+
+    #if_else((str_detect(names(transformed_raster), "Aspect", negate=FALSE))==TRUE, c(transformed_raster), 0)
+    #if_else statement for aspect and one for slope
+
+    # Convert to dataframe
+    #dat_out<- as.data.frame(transformed_raster, xy = TRUE) |> 
+    #  as_tibble() 
+
+    #dat_full <- full_join(dat_out, dat_out, by=c("x", "y"))
+
+
+  }
+
+    # Save as parquet 
+    write_parquet(dat_full,  "data/slope_aspect_dataset/slope_dataset", compression = "gzip", compression_level = 5)
+
+
+
+  return(slope_aspect_directory_dataset)
+
+  #go with highest percentage of pixels to make categorical variable for aspect 5 categories
+  #for slope - take the median 3-arc second slope; midpoint of the slope class
+
+
+}

R/preprocess_glw_data.R

@@ -10,7 +10,7 @@
 #' 
 library(raster)
 library(terra)
-preprocess_glw_data<- function(glw_directory_raw, glw_downloaded, continent_raster_template) {
+preprocess_glw_data<- function(glw_directory_dataset, glw_directory_raw, glw_downloaded, continent_raster_template) {
 
   transformed_raster_cat <- transform_raster(raw_raster = rast(paste0(glw_downloaded, "/url_cattle.tif")),
                                          template = rast(continent_raster_template))
@@ -28,9 +28,9 @@ preprocess_glw_data<- function(glw_directory_raw, glw_downloaded, continent_rast
     as_tibble() 
 
   # Save as parquet 
-  write_parquet(dat_out_cat,  "data/glw/glw_cattle", compression = "gzip", compression_level = 5)
-  write_parquet(dat_out_sh, "data/glw/glw_sheep", compression = "gzip", compression_level = 5)
-  write_parquet(dat_out_go, "data/glw/glw_goats", compression = "gzip", compression_level = 5)
+  write_parquet(dat_out_cat,  "data/glw_dataset/glw_cattle", compression = "gzip", compression_level = 5)
+  write_parquet(dat_out_sh, "data/glw_dataset/glw_sheep", compression = "gzip", compression_level = 5)
+  write_parquet(dat_out_go, "data/glw_dataset/glw_goats", compression = "gzip", compression_level = 5)
 
 
   return(glw_directory_raw)

_targets.R

@@ -48,13 +48,17 @@ static_targets <- tar_plan(
   tar_target(soil_downloaded, soil_download(soil_directory_raw),
              format = "file", 
              repository = "local"),
+  tar_target(soil_directory_dataset, 
+             create_data_directory(directory_path = "data/soil_dataset")),
   tar_target(soil_preprocessed, 
-             preprocess_soil(soil_downloaded, continent_raster_template)),
+             preprocess_soil(soil_directory_dataset, soil_directory_raw, continent_raster_template, soil_downloaded)),
 
   # SLOPE and ASPECT -------------------------------------------------
   tar_target(slope_aspect_directory_raw, 
              create_data_directory(directory_path = "data/slope_aspect")),
-  tar_target(slope_aspect_downloaded, get_slope_aspect(slope_aspect_directory_raw, continent_polygon),
+  tar_target(slope_aspect_directory_dataset, 
+             create_data_directory(directory_path = "data/slope_aspect_dataset")),
+  tar_target(slope_aspect_downloaded, get_slope_aspect(slope_aspect_directory_dataset, slope_aspect_directory_raw, continent_raster_template),
     format = "file", 
     repository = "local"),
 
@@ -64,18 +68,22 @@ static_targets <- tar_plan(
   tar_target(glw_downloaded, get_glw_data(glw_directory_raw),
              format = "file", 
              repository = "local"),
+  tar_target(glw_directory_dataset, 
+             create_data_directory(directory_path = "data/glw_dataset")),
   tar_target(glw_preprocessed, 
-             preprocess_glw_data(glw_directory_raw, glw_downloaded, continent_raster_template)),
+             preprocess_glw_data(glw_directory_dataset, glw_directory_raw, glw_downloaded, continent_raster_template)),
 
 
 # ELEVATION -----------------------------------------------------------
 tar_target(elevation_directory_raw, 
            create_data_directory(directory_path = "data/elevation")),
-tar_target(elevation_downloaded, get_elevation(elevation_directory_raw),
+tar_target(elevation_downloaded, get_elevation(elevation_directory_raw, overwrite = FALSE),
   format = "file", 
   repository = "local"),
+tar_target(elevation_directory_dataset, 
+           create_data_directory(directory_path = "data/elevation_dataset")),
 tar_target(elevation_preprocessed, 
-           process_elevation(elevation_directory_raw, elevation_downloaded, continent_raster_template)),
+           process_elevation(elevation_directory_dataset, elevation_downloaded, elevation_directory_raw, continent_raster_template)),
 
 
 )