housekeeping. ecmwf transform and anomalies still in progress.

R/calculate_weather_anomalies.R

@@ -11,7 +11,7 @@
 calculate_weather_anomalies <- 
   function( # tranformed files
     nasa_weather_transformed,
-    nasa_weather_directory_transformed, # TODO rename this to nasa_weather_transformed_directory
+    nasa_weather_transformed_directory, # TODO rename this to nasa_weather_transformed_directory
     # historical means
     weather_historical_means,
     # directory for saving anomalies 
@@ -35,7 +35,7 @@ calculate_weather_anomalies <-
     }
 
     # Open dataset to transformed data
-    weather_transformed_dataset <- open_dataset(nasa_weather_directory_transformed)
+    weather_transformed_dataset <- open_dataset(nasa_weather_transformed_directory)
 
     # Get historical means for DOY
     doy <- model_dates |> filter(date == date_selected) |> pull(day_of_year)

R/calculate_weather_historical_means.R

@@ -4,13 +4,13 @@
 #'
 #' @title
 #' @param nasa_weather_transformed
-#' @param nasa_weather_directory_transformed
+#' @param nasa_weather_transformed_directory
 #' @param weather_historical_means_directory
 #' @return
 #' @author Emma Mendelsohn
 #' @export
 calculate_weather_historical_means <- function(nasa_weather_transformed,
-                                               nasa_weather_directory_transformed,
+                                               nasa_weather_transformed_directory,
                                                weather_historical_means_directory,
                                                days_of_year,
                                                overwrite = FALSE) {
@@ -28,7 +28,7 @@ calculate_weather_historical_means <- function(nasa_weather_transformed,
     return(file.path(weather_historical_means_directory, save_filename))
   }
   # Open dataset to transformed data
-  weather_transformed_dataset <- open_dataset(nasa_weather_directory_transformed)
+  weather_transformed_dataset <- open_dataset(nasa_weather_transformed_directory)
 
   # Filter for day of year and calculate historical means and standard deviations
   historical_means <- weather_transformed_dataset |> 

R/download_modis_ndvi_delete.R

@@ -11,7 +11,7 @@
 #' @author Emma Mendelsohn
 #' @export
 download_modis_ndvi_delete <- function(modis_ndvi_token, modis_ndvi_bundle_request,
-                                download_directory = modis_ndvi_directory_raw,
+                                download_directory = modis_ndvi_raw_directory,
                                 overwrite = FALSE) {
 
   return(modis_ndvi_token)

R/preprocess_nasa_weather.R

@@ -4,16 +4,16 @@
 #'
 #' @title
 #' @param nasa_weather_downloaded
-#' @param nasa_weather_directory_pre_transformed
+#' @param nasa_weather_pre_transformed_directory
 #' @return
 #' @author Emma Mendelsohn
 #' @export
 preprocess_nasa_weather <- function(nasa_weather_downloaded,
-                                    nasa_weather_directory_pre_transformed) {
+                                    nasa_weather_pre_transformed_directory) {
 
-  nasa_weather_directory_raw <- unique(dirname(nasa_weather_downloaded))
+  nasa_weather_raw_directory <- unique(dirname(nasa_weather_downloaded))
 
-  open_dataset(nasa_weather_directory_raw) |> 
+  open_dataset(nasa_weather_raw_directory) |> 
     distinct() |> 
     rename_all(tolower) |> 
     rename(relative_humidity = rh2m, temperature = t2m, precipitation= prectotcorr,
@@ -22,8 +22,8 @@ preprocess_nasa_weather <- function(nasa_weather_downloaded,
     mutate(date = lubridate::make_date(year, month, day)) |> 
     select(x, y, everything(), -yyyymmdd) |>  # terra::rast - the first with x (or longitude) and the second with y (or latitude) coordinates 
     group_by(year) |> 
-    write_dataset(nasa_weather_directory_pre_transformed)
+    write_dataset(nasa_weather_pre_transformed_directory)
 
-  return(list.files(nasa_weather_directory_pre_transformed, full.names = TRUE, recursive = TRUE))
+  return(list.files(nasa_weather_pre_transformed_directory, full.names = TRUE, recursive = TRUE))
 
 }

R/transform_ecmwf_forecasts.R

@@ -4,14 +4,14 @@
 #'
 #' @title
 #' @param ecmwf_forecasts_downloaded
-#' @param necmwf_forecasts_directory_transformed
+#' @param necmwf_forecasts_transformed_directory
 #' @param continent_raster_template
 #' @param overwrite
 #' @return
 #' @author Emma Mendelsohn
 #' @export
 transform_ecmwf_forecasts <- function(ecmwf_forecasts_downloaded,
-                                      ecmwf_forecasts_directory_transformed,
+                                      ecmwf_forecasts_transformed_directory,
                                       continent_raster_template, 
                                       n_workers = 1,
                                       overwrite = FALSE) {
@@ -21,11 +21,11 @@ transform_ecmwf_forecasts <- function(ecmwf_forecasts_downloaded,
   save_filename <- glue::glue("{filename}.gz.parquet")
 
   # Check if file already exists
-  existing_files <- list.files(ecmwf_forecasts_directory_transformed)
+  existing_files <- list.files(ecmwf_forecasts_transformed_directory)
   message(paste0("Transforming ", save_filename))
   if(save_filename %in% existing_files & !overwrite){
     message("file already exists, skipping transform")
-    return(file.path(ecmwf_forecasts_directory_transformed, save_filename))
+    return(file.path(ecmwf_forecasts_transformed_directory, save_filename))
   }
 
   # Read in with terra
@@ -70,9 +70,9 @@ transform_ecmwf_forecasts <- function(ecmwf_forecasts_downloaded,
     select(x,y, mean, std, data_date, step_range, data_type, short_name)
 
   # Save as parquet 
-  write_parquet(dat_out, here::here(ecmwf_forecasts_directory_transformed, save_filename), compression = "gzip", compression_level = 5)
+  write_parquet(dat_out, here::here(ecmwf_forecasts_transformed_directory, save_filename), compression = "gzip", compression_level = 5)
 
-  return(file.path(ecmwf_forecasts_directory_transformed, save_filename))
+  return(file.path(ecmwf_forecasts_transformed_directory, save_filename))
 
 
 }

R/transform_modis_ndvi.R

@@ -5,14 +5,14 @@
 #' @title
 #' @param modis_ndvi_downloaded_subset
 #' @param continent_raster_template
-#' @param modis_ndvi_directory_transformed
+#' @param modis_ndvi_transformed_directory
 #' @param overwrite
 #' @return
 #' @author Emma Mendelsohn
 #' @export
 transform_modis_ndvi <- function(modis_ndvi_downloaded_subset,
                                  continent_raster_template,
-                                 modis_ndvi_directory_transformed, 
+                                 modis_ndvi_transformed_directory, 
                                  overwrite = FALSE) {
 
   # Extract start and end dates from the raw downloaded file name
@@ -26,10 +26,10 @@ transform_modis_ndvi <- function(modis_ndvi_downloaded_subset,
   message(paste0("Transforming ", save_filename))
 
   # Check if file already exists
-  existing_files <- list.files(modis_ndvi_directory_transformed)
+  existing_files <- list.files(modis_ndvi_transformed_directory)
   if(save_filename %in% existing_files & !overwrite){
     message("file already exists, skipping transform")
-    return(file.path(modis_ndvi_directory_transformed, save_filename))
+    return(file.path(modis_ndvi_transformed_directory, save_filename))
   }
 
   # Transform with template raster
@@ -44,9 +44,9 @@ transform_modis_ndvi <- function(modis_ndvi_downloaded_subset,
            end_date = end_date)
 
   # Save as parquet 
-  write_parquet(dat_out, here::here(modis_ndvi_directory_transformed, save_filename), compression = "gzip", compression_level = 5)
+  write_parquet(dat_out, here::here(modis_ndvi_transformed_directory, save_filename), compression = "gzip", compression_level = 5)
 
-  return(file.path(modis_ndvi_directory_transformed, save_filename))
+  return(file.path(modis_ndvi_transformed_directory, save_filename))
 
 
 }

R/transform_nasa_weather.R

@@ -5,12 +5,12 @@
 #' @title
 #' @param nasa_weather_downloaded
 #' @param continent_raster_template
-#' @param nasa_weather_directory_transformed
+#' @param nasa_weather_transformed_directory
 #' @return
 #' @author Emma Mendelsohn
 #' @export
 transform_nasa_weather <- function(nasa_weather_pre_transformed,
-                                   nasa_weather_directory_transformed, 
+                                   nasa_weather_transformed_directory, 
                                    continent_raster_template,
                                    overwrite = FALSE) {
 
@@ -20,10 +20,10 @@ transform_nasa_weather <- function(nasa_weather_pre_transformed,
   message(paste0("Transforming ", save_filename))
 
   # Check if file already exists
-  existing_files <- list.files(nasa_weather_directory_transformed)
+  existing_files <- list.files(nasa_weather_transformed_directory)
   if(dirname(save_filename) %in% existing_files & !overwrite){
     message("files already exist, skipping transform")
-    return(file.path(nasa_weather_directory_transformed, save_filename))
+    return(file.path(nasa_weather_transformed_directory, save_filename))
   }
 
   # Read in continent template raster
@@ -63,12 +63,12 @@ transform_nasa_weather <- function(nasa_weather_pre_transformed,
   # This crashes r
   # dat_out |> 
   #   group_by(year, month) |> 
-  #   write_dataset(nasa_weather_directory_transformed)
+  #   write_dataset(nasa_weather_transformed_directory)
 
   # Save as parquet 
-  suppressWarnings(dir.create(here::here(nasa_weather_directory_transformed, dirname(save_filename)))) # unnecessary but matching structure of pretransformed dataset
-  write_parquet(dat_out, here::here(nasa_weather_directory_transformed, save_filename), compression = "gzip", compression_level = 5)
+  suppressWarnings(dir.create(here::here(nasa_weather_transformed_directory, dirname(save_filename)))) # unnecessary but matching structure of pretransformed dataset
+  write_parquet(dat_out, here::here(nasa_weather_transformed_directory, save_filename), compression = "gzip", compression_level = 5)
 
-  return(file.path(nasa_weather_directory_transformed, save_filename))
+  return(file.path(nasa_weather_transformed_directory, save_filename))
 
 }

R/transform_sentinel_ndvi.R

@@ -5,13 +5,13 @@
 #' @title
 #' @param raster_file
 #' @param template
-#' @param sentinel_ndvi_directory_transformed
+#' @param sentinel_ndvi_transformed_directory
 #' @return
 #' @author Emma Mendelsohn
 #' @export
 transform_sentinel_ndvi <- function(sentinel_ndvi_downloaded,
                                     continent_raster_template,
-                                    sentinel_ndvi_directory_transformed,
+                                    sentinel_ndvi_transformed_directory,
                                     overwrite = FALSE) {
 
   # Extract start and end dates from the raw downloaded file name
@@ -25,10 +25,10 @@ transform_sentinel_ndvi <- function(sentinel_ndvi_downloaded,
   message(paste0("Transforming ", save_filename))
 
   # Check if file already exists
-  existing_files <- list.files(sentinel_ndvi_directory_transformed)
+  existing_files <- list.files(sentinel_ndvi_transformed_directory)
   if(save_filename %in% existing_files & !overwrite){
     message("file already exists, skipping transform")
-    return(file.path(sentinel_ndvi_directory_transformed, save_filename))
+    return(file.path(sentinel_ndvi_transformed_directory, save_filename))
   }
 
   # Transform with template raster
@@ -43,8 +43,8 @@ transform_sentinel_ndvi <- function(sentinel_ndvi_downloaded,
            end_date = end_date)
 
   # Save as parquet 
-  write_parquet(dat_out, here::here(sentinel_ndvi_directory_transformed, save_filename), compression = "gzip", compression_level = 5)
+  write_parquet(dat_out, here::here(sentinel_ndvi_transformed_directory, save_filename), compression = "gzip", compression_level = 5)
 
-  return(file.path(sentinel_ndvi_directory_transformed, save_filename))
+  return(file.path(sentinel_ndvi_transformed_directory, save_filename))
 
 }