From d81df21307060bd496c9562c6cf9bb4a76a77a51 Mon Sep 17 00:00:00 2001
From: Moritz Shore <moritzshore@gmail.com>
Date: Fri, 3 Feb 2023 15:59:33 -0500
Subject: [PATCH] documentation changes
---
R/run_soft_cal.R | 88 ++++++++++++++++++++++--------------------------
1 file changed, 41 insertions(+), 47 deletions(-)
diff --git a/R/run_soft_cal.R b/R/run_soft_cal.R
index f400dc4..4cc21e7 100644
--- a/R/run_soft_cal.R
+++ b/R/run_soft_cal.R
@@ -1,11 +1,9 @@
#' Runs the SWAT+ soft-calibration routine.
#'
-#' more info here
+#' write more info here?
#'
#' @param project_path Character string, path to the SWAT+ project folder
-#' (i.e. TxtInOut).
#' @param os string of operating system
-#' to only activate nutrient plant stress.
#' @param keep_folder (optional) If \code{keep_folder = TRUE}
#' '.model_run/verification' is kept and not deleted after finishing model runs.
#' In this case '.model_run' is reused in a new model run if \code{refresh = FALSE}.
@@ -21,7 +19,6 @@ soft_calibrate <- function(project_path, os, keep_folder = FALSE) {
# create a temporary directory copy of the model setup
temp_directory = build_model_run(project_path)
-
print("downloading sft files")
# downloads any missing sft file
download_sft_files(temp_directory)
@@ -46,6 +43,9 @@ soft_calibrate <- function(project_path, os, keep_folder = FALSE) {
print("disabling the SFT routine")
# disables the soft-calibration routine
+ # I originally wrote this since i was working in the original swat directory
+ # it technically isnt needed when working with a copy, but it might be useful
+ # so i'll leave it in here for now...
toggle_sft(temp_directory, switch = "off")
print("reading results")
@@ -64,6 +64,7 @@ soft_calibrate <- function(project_path, os, keep_folder = FALSE) {
#' @importFrom dplyr %>%
#'
download_sft_files <- function(path) {
+ # "water_balance.sft" currently does not exist on bitbucket but needs to be downloaded!!
# TEMP until the water_balance.sft file is hosted
if ("water_balance.sft" %in% list.files(path) == FALSE) {
stop("water_balance.sft needs to present in your directory TEMP: for now...")
@@ -72,27 +73,27 @@ download_sft_files <- function(path) {
# add a backslash onto the path, so its compatible with build_model_run()
path = paste0(path, "/")
-
- # this could be passed as a parameter
+ # the desired files might be better passed as a parameter instead of hard coded here
required_files = c("codes.sft", "wb_parms.sft")
- # "water_balance.sft" currently does not exist on bitbucket but needs to be downloaded!!
-
+ # The download repository for the sft files:
# I hope this remains constant for all the files???
# or can we host this on our own gitlab?
- # this could be passed as a parameter
+ # this could also be passed as a parameter
source__online_directory = "https://bitbucket.org/blacklandgrasslandmodels/modular_swatplus/raw/3d2126fb115077b51be90526238c83cd79e3ef4c/database_files/"
- # find out which sft files are missing and download them.
+ # find out which .sft files are missing and download them.
for (file in required_files) {
if (file %in% list.files(path) == FALSE) {
paste(file, "not in your SWAT+ directory. downloading now...") %>% print()
+ # not sure how we want to handle error-prone code?
try(download.file(
url = paste0(source__online_directory, file),
destfile = paste0(path, file)
))
+ # check to see if the file was downloaded
if (file %in% list.files(path)) {
paste(file, "downloaded successfully") %>% print()
} else{
@@ -104,43 +105,38 @@ download_sft_files <- function(path) {
}
}
-
#' toggles the soft calibration routine either ON or OFF
#'
-#' @param path text string to (temporary) directory
+#' @param path string to (temporary) directory
#' @param switch string, either "off" or "on"
#' @keywords internal
#' @importFrom dplyr %>%
#'
toggle_sft <- function(path, switch) {
- # file.cio modifications
-
# add a backslash onto the path, so its compatible with build_model_run()
path = paste0(path, "/")
+ # file.cio modification:
# read the file.cio in
file.cio = readLines(con = paste0(path, "file.cio"))
- # grab the 22nd line
- file_cio_line_22 = file.cio[22]
- # split that line based of white space
- line22 = file_cio_line_22 %>% base::strsplit("\\s+") %>% unlist()
+ # grab the 22nd line and split that line based of white space
+ line22 = file.cio[22] %>% base::strsplit("\\s+") %>% unlist()
if (switch == "on") {
- # replace the the column values 4,5,6 with the sft file names
+ # replace the the column values 4,5,6 with the .sft file names
line22[4] = "codes.sft"
line22[5] = "wb_parms.sf"
line22[6] = "water_balance.sft"
}
if (switch == "off") {
- # replace the the column values 4,5,6 with the sft file names
+ # replace the the column values 4,5,6 with NULL to disable
line22[4] = "null"
line22[5] = "null"
line22[6] = "null"
}
-
# merge them back together
new_line22 = paste(line22, collapse = " ")
@@ -151,15 +147,16 @@ toggle_sft <- function(path, switch) {
writeLines(text = file.cio, con = paste0(path, "file.cio"))
# codes.sft modifications:
-
- # read in the codes.sft file (warnings turned off because of "incomplete final line)
+ # read in the codes.sft file (warnings turned off because of "incomplete final line")
codes.sft = readLines(con = paste0(path, "codes.sft"), warn = F)
- # split that line based of white space
- # find out what the column index is of HYD_HRU
+ # split that line based on white space
line2 = codes.sft[2] %>% base::strsplit("\\s+") %>% unlist()
+
+ # find out what the column index is of HYD_HRU
hyd_hru_col_index = which(line2 == "HYD_HRU")
+ # split line 3 based on white space
line3 = codes.sft[3] %>% base::strsplit("\\s+") %>% unlist()
if (switch == "on") {
@@ -172,11 +169,9 @@ toggle_sft <- function(path, switch) {
line3[hyd_hru_col_index] = "n"
}
- # merge line 3 back together
- line3 = paste(line3, collapse = " ")
- # and apply it to the file
- codes.sft[3] = line3
+ # merge line 3 back together and apply it to the file
+ codes.sft[3] = paste(line3, collapse = " ")
# write the modified codes.sft file
writeLines(text = codes.sft, con = paste0(path, "codes.sft"))
@@ -189,9 +184,9 @@ toggle_sft <- function(path, switch) {
}
}
-#' reads and reformats the SWAT+ soft calibration routine output
+#' reads and re-formats the SWAT+ soft calibration output
#'
-#' @param path text string to (temporary) directory
+#' @param path string to (temporary) directory
#' @keywords internal
#' @importFrom data.table fread
#' @importFrom tidyr unite
@@ -203,9 +198,10 @@ read_wb_aa <- function(path) {
# add a backslash onto the path, so its compatible with build_model_run()
path = paste0(path, "/")
-
- # read the wb_aa file from its PATH
- basin_wb_aa = fread(paste0(path, "basin_wb_aa.txt"), fill = TRUE, )
+ # read the wb_aa file from its path
+ # fill = TRUE then in case the rows have unequal length, blank fields are
+ # implicitly filled. (which is the case for this file)
+ basin_wb_aa = fread(paste0(path, "basin_wb_aa.txt"), fill = TRUE)
# change the column names to those of the second row in the text file.
colnames(basin_wb_aa) <-
@@ -226,7 +222,7 @@ read_wb_aa <- function(path) {
# Unite the last three rows into one string (as they were intended to be)
# the new column will be named description and describes what the softcal
# algorithm did in that step. (So its probably important).
- # the united columns are separated by a space (trailing space exists now)
+ # the united columns are separated by a space (trailing space exists now..)
basin_wb_aa = tidyr::unite(data = basin_wb_aa,
col = description,
no_name_columns,
@@ -239,13 +235,14 @@ read_wb_aa <- function(path) {
# and convert them to numeric
basin_wb_aa = basin_wb_aa %>% mutate_at(dbl_cols, as.numeric)
+ # return the formatted table as a tibble
return(basin_wb_aa %>% tibble())
}
#' Modify ‘water_balance.sft’ with values for fractions. Only the values WYR and
#' BFR columns need to be modified
#'
-#' @param path text string to (temporary) directory
+#' @param path string to (temporary) directory
#' @keywords internal
#' @importFrom dplyr %>%
#'
@@ -257,33 +254,30 @@ modify_wb_parms <- function(path) {
WYLD_PCP_Ratio = readline(prompt = "Enter your value for WYLD_PCP_Ratio: ") %>% as.numeric()
Subsurface_WYLD_Ratio = readline(prompt = "Enter your value for Subsurface_WYLD_Ratio: ") %>% as.numeric()
-
# read the water balance file
water_balance_sft = readLines(paste0(path, "water_balance.sft"))
- # extract the line with the column names
+ # extract the line with the column names and split based off whitespace
line5 = water_balance_sft[5] %>% base::strsplit("\\s+") %>% unlist()
# locate the desired parameters
WYLD_PCP_Ratio_INDEX = which(line5 == "WYLD_PCP_Ratio")
Subsurface_WYLD_Ratio_INDEX = which(line5 == "Subsurface_WYLD_Ratio")
- # extract the line with the parameter values
+ # extract the line with the parameter values based off whitespace
line6 = water_balance_sft[6] %>% base::strsplit("\\s+") %>% unlist()
# change the values with the user given values
line6[WYLD_PCP_Ratio_INDEX] = WYLD_PCP_Ratio
line6[Subsurface_WYLD_Ratio_INDEX] = Subsurface_WYLD_Ratio
- # merge them back together
- line6 = paste(line6, collapse = " ")
-
- # add the modified parameter line back to the text file
- water_balance_sft[6] = line6
+ # merge them back together and add the modified parameter line back to the text file
+ water_balance_sft[6] = paste(line6, collapse = " ")
# and write it
writeLines(text = water_balance_sft, con = paste0(path, "water_balance.sft"))
+ # diagnostic printout
paste(
"water balance parameters updated with values:",
WYLD_PCP_Ratio,
@@ -319,6 +313,9 @@ modify_wb_parms <- function(path) {
#
# - Rename the function to something like "run_swat_soft_calibration()?
# - and rename the script file to match?
+#
+# - Allow the user to keep or discard any changes made
+# if(!keep_folder) unlink(run_path, recursive = TRUE, force = TRUE)
# code to be executed: -----
@@ -328,10 +325,7 @@ modify_wb_parms <- function(path) {
# basin_wb_aa %>% ggplot() + geom_col(mapping = aes(x = description, y = wateryld))
-
# Next steps: ------
# Implement the crop yield soft cal routine
# Link WB and crop yield routines (iteratively)
-# Allow the user to keep or discard any changes made
-# if(!keep_folder) unlink(run_path, recursive = TRUE, force = TRUE)
# ....
--
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