some bugs in prepare_climate and climate vignette (+script) added

R/preparing.R

@@ -785,16 +785,12 @@ prepare_climate <- function(meteo_lst, write_path, period_starts = NA, period_en
     warning(paste("'time.sim' file was not found in", write_path, "and was not updated. 
                 Please make sure 'yrc_start' is", year(period_starts), "and 'yrc_end' is", year(period_ends), "."))
   } else {
-    if(!file.exists(f_write)){
-      file.create(f_write)
-    } else {
-      unlink(f_write)
-      invisible(file.create(f_write))
-    }
+    f_write <- paste(f_dir, fname, sep = "/")
+    file.create(f_write)
     time_sim <- read.delim(paste(write_path, fname, sep = "/"))
     write.table(paste0(fname, hd_txt), f_write, append = FALSE, sep = "\t", dec = ".", row.names = FALSE, col.names = FALSE, quote = FALSE)
     st_hd <- c(rep('%10s', 5))
-    write.table(paste(sprintf(st_hd, unlist(strsplit(time_sim[1,1], "\\s+"))[-1]), collapse = ' '), f_write, append = TRUE, sep = "\t", dec = ".", row.names = FALSE, col.names = FALSE, quote = FALSE)
+    write.table(paste(sprintf(st_hd, unlist(strsplit(time_sim[1,1], "\\s+"))), collapse = ' '), f_write, append = TRUE, sep = "\t", dec = ".", row.names = FALSE, col.names = FALSE, quote = FALSE)
     time_sim_v <- as.numeric(unlist(strsplit(time_sim[2,1], "\\s+"))[-1])
     time_sim_v[c(2, 4)] <- c(year(period_starts), year(period_ends))
     write.table(paste(sprintf(st_hd, time_sim_v), collapse = ' '), f_write, append = TRUE, sep = "\t", dec = ".", row.names = FALSE, col.names = FALSE, quote = FALSE)
@@ -945,7 +941,6 @@ get_usersoil_table <- function(csv_path, hsg = FALSE, keep_values = FALSE, nb_ly
                         df_hsg[i,c(paste0("SOL_Z", 1:df_hsg$NLAYERS[i]),paste0("SOL_K", 1:df_hsg$NLAYERS[i]))]))
     }
     soilp$HYDGRP <- c
-    soilp <- soilp[,!(names(soilp) %in% c("Impervious", "Depth", "Drained"))]
     print("Soil hydrological groups were calculated.")
   }
 

vignettes/climate.Rmd

@@ -0,0 +1,48 @@
+---
+title: "Climate data"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Introduction
+
+Text
+
+```{r fig-cloud, echo=FALSE, out.width='100%', fig.align = 'center'}
+knitr::include_graphics('cloud.png')
+```
+
+Text
+
+```{r ext_cli, message = FALSE, warning = FALSE}
+library(svatools)
+basin_path <- system.file("extdata", "GIS/basin.shp", package = "svatools")
+climate_lst <- load_climate_lst("../output/climate/CORDEX-BC", basin_path)
+```
+Text
+
+```{r plot_cli, message = FALSE, warning = FALSE}
+plot_weather(climate_lst[["rcp85"]][["1"]],"TMP_MAX", "year", "max")
+```
+
+Text
+
+```{r get_cli, message = FALSE, warning = FALSE}
+f_dir <- "../output/overwrite/tmp"
+files_to_copy <- paste(f_dir, c("aquifer.con", "chandeg.con", "hru.con", "reservoir.con", "rout_unit.con", "time.sim"), sep="/")
+for (rcp in c("rcp26", "rcp45", "rcp85")){
+  for (rcm in as.character(c(1:6))){
+    for(p in list(c("H", "1988-01-01", "2020-12-31"), c("N", "2032-01-01", "2065-12-31"), c("E", "2067-01-01", "2099-12-31"))){
+      cli_dir <- paste("../output/cli", rcp, paste0("rcm", rcm), p[1], sep = "/")
+      dir.create(cli_dir, recursive = TRUE)
+      file.copy(files_to_copy, paste(cli_dir, c("aquifer.con", "chandeg.con", "hru.con", "reservoir.con", "rout_unit.con", "time.sim"), sep = "/"), overwrite = TRUE)
+      prepare_climate(climate_lst[[rcp]][[rcm]], cli_dir, p[2], p[3])
+      print(paste(rcp, "rcm", rcm, p[1], p[2], "-", p[3], "set prepared."))
+    }
+  }
+}
+
+```