Update roxygen

michielvandijk · May 15, 2024 · 7102e12 · 7102e12
1 parent 8031e83
commit 7102e12
Show file tree

Hide file tree

Showing 2 changed files with 24 additions and 132 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,7 +23,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 SystemRequirements: GAMS
 VignetteBuilder: knitr
 Imports:

diff --git a/inst/debug.R b/inst/debug.R
@@ -31,40 +31,27 @@ options(digits=4) # limit display to four digits
 # Creates a model folder structure in c:/temp/ with the name 'mapspamc_mwi'.
 # the user can replace mwi with the country code of the case-study country or
 # choose a new name
-#model_path <- "D:/GLOBIOM_UCSB/mapspamc_2000"
-model_path <- "C:/Users/dijk158/OneDrive - Wageningen University & Research/data/mapspamc_iso3c/mapspamc_usa"
+model_path <- "c:/temp/mapspamc_aus"
 
 # Creates a database folder with the name mapspamc_db in c:/temp
-db_path <- "C:/temp"
+db_path <- "c:/temp"
 
 # Sets the location of the version of GAMS that will be used to solve the model
-#gams_path <- "C:/GAMS/win64/27.3"
+#gams_path <- "C:/GAMS/41"
 gams_path <- "C:/MyPrograms/GAMS/40"
 
 # Set mapspamc parameters for the min_entropy_5min_adm_level_2_solve_level_0 model
 param <- mapspamc_par(
   model_path = model_path,
   db_path = db_path,
   gams_path = gams_path,
-  iso3c = "USA",
+  iso3c = "AUS",
   year = 2000,
   res = "5min",
   adm_level = 2,
-  solve_level = 1,
+  solve_level = 0,
   model = "min_entropy")
 
-# Set mapspamc parameters for the max_score_30sec_adm_level_2_solve_level_0 model
-# param <- mapspamc_par(
-#   model_path = model_path,
-#   db_path = db_path,
-#   gams_path = gams_path,
-#   iso3c = "MWI",
-#   year = 2010,
-#   res = "30sec",
-#   adm_level = 2,
-#   solve_level = 0,
-#   model = "max_score")
-
 
 # Show parameters
 print(param)
@@ -74,119 +61,24 @@ create_folders(param)
 
 
 
-# SETUP ALTERNATIVE MODEL ----------------------------------------------------------------
-# Set mapspamc parameters for an alternative model that only uses adm1_level statistics
-alt_param <- mapspamc_par(
-  model_path = model_path,
-  db_path = db_path,
-  gams_path = gams_path,
-  iso3c = param$iso3c,
-  year = param$year,
-  res = param$resolution,
-  adm_level = 1,
-  solve_level = param$solve_level,
-  model = param$model)
+# PREPARE PHYSICAL AREA ------------------------------------------------------------------
+prepare_physical_area(param)
+
+# PREPARE CROPLAND -----------------------------------------------------------------------
+prepare_cropland(param)
+
+
+# PREPARE IRRIGATED AREA -----------------------------------------------------------------
+prepare_irrigated_area(param)
 
-# Show parameters
-print(alt_param)
 
 # HARMONIZE INPUT DATA -------------------------------------------------------------------
-harmonize_inputs(alt_param)
-ac
-ac <- "USCT"
-cl_slackp = 0.05
-cl_slackn = 5
-ia_slackp = 0.05
-ia_slackn = 5
-
-split_harmonized_inputs("USCT", alt_param, cl_slackp, cl_slackn, ia_slackp, ia_slackn)
-
-split_harmonized_inputs <- function(ac, alt_param, cl_slackp, cl_slackn, ia_slackp, ia_slackn) {
-  # https://stackoverflow.com/questions/7096989/how-to-save-all-console-output-to-file-in-r
-  model_folder <- create_model_folder(alt_param)
-  log_file <- file(file.path(
-    alt_param$model_path,
-    glue::glue("processed_data/intermediate_output/{model_folder}/{ac}/log_{alt_param$res}_{alt_param$year}_{ac}_{alt_param$iso3c}.log")
-  ))
-  capture.output(file = log_file, append = FALSE, split = T, {
-    cat("\n\n--------------------------------------------------------------------------------------------------------------")
-    cat("\n", ac)
-    cat("\n--------------------------------------------------------------------------------------------------------------")
-
-    ############### STEP 1: LOAD DATA ###############
-    # Load data
-    load_intermediate_data(c("cl"), ac, alt_param, local = T, mess = F)
-
-    ############### STEP 2: SET CL TO MEDIAN CROPLAND ###############
-    # Create df of cl map,  set cl to median cropland
-    # Remove few cells where gridID is missing, caused by masking grid with country borders using gdal.
-    cl_df <- cl %>%
-      dplyr::mutate(cl = cl_mean)
-
-    # Remove gridID where cl_rank is NA
-    cl_df <- cl_df %>%
-      dplyr::filter(!is.na(cl_rank))
-
-    ############### STEP 3: HARMONIZE CL   ###############
-    cl_df <- harmonize_cl(df = cl_df, ac, alt_param)
-
-
-    ############### STEP 4: HARMONIZE IA ###############
-    cl_df <- harmonize_ia(cl_df, ac, alt_param, ia_slackp = ia_slackp, ia_slackn = ia_slackn) %>%
-      dplyr::mutate(
-        ia = ifelse(is.na(ia), 0, ia),
-        ia_max = ifelse(is.na(ia_max), 0, ia_max)
-      )
-
-    ############### STEP 5: PREPARE FINAL CL MAP BY RANKING CELLS PER ADM ###############
-    cl_df <- select_grid_cells(cl_df, ac, alt_param, cl_slackp = cl_slackp, cl_slackn = cl_slackn)
-
-
-    ############### STEP 6: PREPARE FILES ###############
-    # Irrigation
-    ia_harm_df <- cl_df %>%
-      dplyr::select(gridID, ia) %>%
-      na.omit()
-
-    # Cropland: rename adm_code to alt_param$adm_level
-    adm_level_sel <- glue::glue("adm{alt_param$adm_level}_code")
-    cl_harm_df <- cl_df[c("gridID", adm_level_sel, "cl")]
-    names(cl_harm_df)[names(cl_harm_df) == adm_level_sel] <- "adm_code"
-    cl_harm_df$adm_level <- alt_param$adm_level
-
-
-    ############### STEP 6: CREATE MAPS ###############
-    # cl map
-    cl_harm_r <- gridID2raster(cl_harm_df, "cl", alt_param)
-
-    # ia map
-    ia_harm_r <- gridID2raster(ia_harm_df, "ia", alt_param)
-
-
-    ############### STEP 7: SAVE ###############
-    temp_path <- file.path(
-      alt_param$model_path,
-      glue::glue("processed_data/intermediate_output/{model_folder}/{ac}")
-    )
-    dir.create(temp_path, recursive = T, showWarnings = F)
-
-    saveRDS(cl_harm_df, file.path(
-      temp_path,
-      glue::glue("cl_harm_{alt_param$res}_{alt_param$year}_{ac}_{alt_param$iso3c}.rds")
-    ))
-    terra::writeRaster(cl_harm_r, file.path(
-      temp_path,
-      glue::glue("cl_harm_r_{alt_param$res}_{alt_param$year}_{ac}_{alt_param$iso3c}.tif")
-    ), overwrite = T)
-
-    # ia_harm
-    saveRDS(ia_harm_df, file.path(
-      temp_path,
-      glue::glue("ia_harm_{alt_param$res}_{alt_param$year}_{ac}_{alt_param$iso3c}.rds")
-    ))
-    terra::writeRaster(ia_harm_r, file.path(
-      temp_path,
-      glue::glue("ia_harm_r_{alt_param$res}_{alt_param$year}_{ac}_{alt_param$iso3c}.tif")
-    ), overwrite = T)
-  })
-}
+harmonize_inputs(param)
+
+
+# PREPARE SCORE --------------------------------------------------------------------------
+prepare_priors_and_scores(param)
+
+
+# COMBINE MODEL INPUTS -------------------------------------------------------------------
+combine_inputs(param)