run_swat_verify function tested

NAMESPACE

-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(run_swat_verification)
+importFrom(data.table,fread)
+importFrom(dplyr,"%>%")
+importFrom(lubridate,int_end)
+importFrom(lubridate,int_start)
+importFrom(lubridate,interval)
+importFrom(lubridate,yday)
+importFrom(lubridate,year)
+importFrom(lubridate,ymd)
+importFrom(processx,run)
+importFrom(purrr,map)
+importFrom(purrr,set_names)
+importFrom(readr,read_lines)
+importFrom(readr,write_lines)
+importFrom(stringr,str_replace)
+importFrom(stringr,str_split)
+importFrom(stringr,str_sub)
+importFrom(stringr,str_trim)
+importFrom(tibble,as_tibble)
+importFrom(tibble,tibble)
+importFrom(vroom,vroom_lines)

R/run_swat_verify.R

@@ -12,9 +12,21 @@
 #' @param outputs Define the outputs that should be read after the simulation
 #'   run. The outputs that are defined here depend on the verification steps
 #'   that should be performed on the outputs.
+#' @param start_date (optional) Start date of the SWAT simulation. Provided as
+#'   character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+#'   in the form yyyymmdd, or in Date format.
+#' @param end_date (optional) End date of the SWAT simulation. Provided as
+#'   character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+#'   in the form yyyymmdd, or in Date format.
+#' @param years_skip (optional) Integer value to define the number of simulation
+#'   years that are skipped before writing SWAT model outputs.
+#' @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}.
+#'   \code{Default = FALSE}
 #'
 #' @return Returns the simulation results for the defined output variables as a
-#'   list tibble.
+#'   list of tibbles.
 #'
 #' @importFrom dplyr %>%
 #' @importFrom processx run
@@ -22,7 +34,9 @@
 #' @importFrom tibble tibble
 #' @export
 #'
-run_swat_verification <- function(project_path, outputs = c('wb', 'mgt', 'plt')) {
+run_swat_verification <- function(project_path, outputs = c('wb', 'mgt', 'plt'),
+                                  start_date = NULL, end_date = NULL,
+                                  years_skip = NULL, keep_folder = FALSE) {
 
   # Check settings before starting to set up '.model_run'
   ## General function input checks
@@ -30,11 +44,16 @@ run_swat_verification <- function(project_path, outputs = c('wb', 'mgt', 'plt'))
   stopifnot(all(outputs %in% c('wb', 'mgt', 'plt')))
   stopifnot(is.logical(keep_folder))
 
+  run_path <- build_model_run(project_path)
+
+  set_print_prt(project_path, run_path, outputs, years_skip)
+  set_time_sim(project_path, run_path, start_date, end_date)
+
   ## Get operating system and find SWAT executable file
   os <- get_os()
   swat_exe <- find_swat_exe(project_path, os)
 
-  msg <- run(run_os(swat_exe, os), wd = project_path,
+  msg <- run(run_os(swat_exe, os), wd = run_path,
              error_on_status = FALSE)
 
   if(msg$timeout) {
@@ -47,16 +66,19 @@ run_swat_verification <- function(project_path, outputs = c('wb', 'mgt', 'plt'))
     model_output <- list()
 
     if ('plt' %in% outputs) {
-      model_output$hru_pw_day <- read_tbl('hru_pw_day', sim_path)
+      model_output$hru_pw_day <- read_tbl('hru_pw_day', run_path)
     }
     if ('wb' %in% outputs) {
-      model_output$basin_wb_day <- read_tbl('basin_wb_day', sim_path)
+      model_output$basin_wb_day <- read_tbl('basin_wb_day', run_path)
     }
     if ('mgt' %in% outputs) {
-      model_output$mgt_out <- read_mgt(sim_path)
+      model_output$mgt_out <- read_mgt(run_path)
     }
   }
 
+  if(!keep_folder) unlink(run_path, recursive = TRUE, force = TRUE)
+
+  return(model_output)
 }
 
 #' Identify the operating system.
@@ -87,9 +109,22 @@ get_os <- function() {
   tolower(os)
 }
 
+#' Add './' to run the exe on unix systems
+#' @param exe Text string that defines the name of the executable file
+#' @param os Text string that defines the operating system
+#' @keywords internal
+#'
+run_os <- function(exe, os) {
+  if(os == 'unix') exe <- '.'%//%exe
+  return(exe)
+}
+
 #' Find the SWAT+ executable file and trigger error if 0 or more than 1
 #' file are found.
 #'
+#' @param project_path Path to the SWAT+ project folder (i.e. TxtInOut).
+#' @param os Text string that defines the operating system
+#'
 #' @keywords internal
 #'
 find_swat_exe <- function(project_path, os) {
@@ -115,6 +150,9 @@ find_swat_exe <- function(project_path, os) {
 #' Read SWAT+ output that is arranged in a tabular format (most outputs)
 #' and return the read output table in a tibble format
 #'
+#' @param out_file Name of the output file that should be read.
+#' @param run_path Path to the folder where simulations are performed
+#'
 #' @importFrom data.table fread
 #' @importFrom purrr set_names
 #' @importFrom readr read_lines
@@ -123,8 +161,8 @@ find_swat_exe <- function(project_path, os) {
 #'
 #' @keywords internal
 #'
-read_tbl <- function(out_file, sim_path) {
-  file_path <- paste0(sim_path, '/', out_file, '.txt')
+read_tbl <- function(out_file, run_path) {
+  file_path <- paste0(run_path, '/', out_file, '.txt')
 
   col_names <- read_lines(file = file_path, skip = 1, n_max = 1) %>%
     str_trim(.) %>%
@@ -133,10 +171,11 @@ read_tbl <- function(out_file, sim_path) {
 
   name_duplicate <- table(col_names) %>%
     .[. > 1]
-
-  for (i in 1:length(name_duplicate)) {
-    col_names[col_names == names(name_duplicate[i])] <-
-      paste0(names(name_duplicate[i]), 1:name_duplicate[i])
+  if(length(name_duplicate) > 0) {
+    for (i in 1:length(name_duplicate)) {
+      col_names[col_names == names(name_duplicate[i])] <-
+        paste0(names(name_duplicate[i]), 1:name_duplicate[i])
+    }
   }
 
   fread(file_path, skip = 3) %>%
@@ -146,6 +185,8 @@ read_tbl <- function(out_file, sim_path) {
 
 #' Read SWAT+ management output file and return the read output in a tibble
 #'
+#' @param run_path Path to the folder where simulations are performed
+#'
 #' @importFrom purrr map set_names
 #' @importFrom stringr str_trim str_split
 #' @importFrom tibble as_tibble
@@ -153,8 +194,8 @@ read_tbl <- function(out_file, sim_path) {
 #'
 #' @keywords internal
 #'
-read_mgt <- function(sim_path) {
-  file_path <- paste0(sim_path, '/mgt_out1.txt')
+read_mgt <- function(run_path) {
+  file_path <- paste0(run_path, '/mgt_out.txt')
 
   vroom_lines(file_path, skip = 3) %>%
     str_trim(.) %>%
@@ -169,3 +210,102 @@ read_mgt <- function(sim_path) {
                    'surf_rsd', 'soil_no3', 'soil_solp', 'op_var',
                    paste0('var', 1:7)))
 }
+
+
+#' Generate folder structure for parallel SWAT execution
+#'
+#' @param project_path Path to the SWAT project folder (i.e. TxtInOut)
+#'
+build_model_run <- function(project_path){
+  run_path <- paste0(project_path, '/.run_verify')
+  swat_files <- dir(project_path, full.names = TRUE)
+  exclude <- ".txt$|.csv$|.db$"
+  swat_files <- swat_files[!grepl(exclude,swat_files)]
+
+  dir.create(run_path, recursive = TRUE)
+  file.copy(swat_files, run_path)
+
+  return(run_path)
+}
+
+#' Read and set SWAT+ print.prt file write the updated print.prt and the original file
+#' as a backup 'print_backup.prt'
+#'
+#' @param project_path Path to the SWAT project folder (i.e. TxtInOut)
+#' @param run_path Path to the folder where simulations are performed
+#' @param outputs Define the outputs that should be read after the simulation
+#'   run. The outputs that are defined here depend on the verification steps
+#'   that should be performed on the outputs.
+#' @param years_skip (optional) Integer value to define the number of simulation
+#'   years that are skipped before writing SWAT model outputs.
+#'
+#' @importFrom readr read_lines write_lines
+#' @importFrom stringr str_replace str_sub
+#'
+#' @keywords internal
+#'
+set_print_prt <- function(project_path, run_path, outputs, years_skip) {
+  print_prt <- read_lines(paste0(project_path,'/print.prt'), lazy = FALSE)
+
+  print_prt[7] <- "n             n             n             "
+  print_prt[7] <- "n             n             n             n             "
+  print_prt[11:length(print_prt)] <-
+    paste0(str_sub(print_prt[11:length(print_prt)], 1, 29),
+           'n             n             n             n  ')
+
+  if(!is.null(years_skip)){
+    print_prt[3] <- str_replace(print_prt[3], '[:digit:]+(?=[:space:])', as.character(years_skip))
+  }
+
+  if ('wb' %in% outputs) {
+    print_prt[11] <- "basin_wb                     y             n             n             n  "
+  }
+  if ('mgt' %in% outputs) {
+    print_prt[9]  <- "n             y             n             n             "
+  }
+  if ('plt' %in% outputs) {
+    print_prt[36] <- "hru_pw                       y             n             n             n  "
+  }
+
+  write_lines(print_prt, paste0(run_path,'/print.prt'))
+}
+
+#' Read and set SWAT+ time.sim file write the updated time.sim and the original file
+#' as a backup 'time_backup.sim'
+#'
+#' @param project_path Path to the SWAT project folder (i.e. TxtInOut)
+#' @param run_path Path to the folder where simulations are performed
+#' @param start_date (optional) Start date of the SWAT simulation. Provided as
+#'   character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+#'   in the form yyyymmdd, or in Date format.
+#' @param end_date (optional) End date of the SWAT simulation. Provided as
+#'   character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+#'   in the form yyyymmdd, or in Date format.
+#' @importFrom lubridate interval int_end int_start yday year ymd
+#' @importFrom readr read_lines write_lines
+#' @importFrom stringr str_trim str_split
+#'
+#' @keywords internal
+#'
+set_time_sim <- function(project_path, run_path, start_date, end_date) {
+  time_sim <- read_lines(paste0(project_path,'/time.sim'), lazy = FALSE)
+
+  if(xor(is.null(start_date), is.null(end_date))) {
+    stop("'start_date' and 'end_date' must be provided together!")
+  } else if (!is.null(start_date)) {
+    ## Determine required date indices for writing to time.sim
+    start_date <- ymd(start_date)
+    end_date   <- ymd(end_date)
+    time_interval <- interval(start_date, end_date)
+    start_year    <- year(int_start(time_interval))
+    start_jdn     <- yday(int_start(time_interval))
+    end_year      <- year(int_end(time_interval))
+    end_jdn       <- yday(int_end(time_interval))
+
+    time_sim[3] <- c(start_jdn, start_year, end_jdn, end_year, 0) %>%
+      sprintf("%10d",.) %>%
+      paste(., collapse = "")
+  }
+
+  write_lines(time_sim, paste0(run_path,'/time.sim'))
+}

SWATdoctR.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

man/build_model_run.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{build_model_run}
+\alias{build_model_run}
+\title{Generate folder structure for parallel SWAT execution}
+\usage{
+build_model_run(project_path)
+}
+\arguments{
+\item{project_path}{Path to the SWAT project folder (i.e. TxtInOut)}
+}
+\description{
+Generate folder structure for parallel SWAT execution
+}

man/find_swat_exe.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{find_swat_exe}
+\alias{find_swat_exe}
+\title{Find the SWAT+ executable file and trigger error if 0 or more than 1
+file are found.}
+\usage{
+find_swat_exe(project_path, os)
+}
+\arguments{
+\item{project_path}{Path to the SWAT+ project folder (i.e. TxtInOut).}
+
+\item{os}{Text string that defines the operating system}
+}
+\description{
+Find the SWAT+ executable file and trigger error if 0 or more than 1
+file are found.
+}
+\keyword{internal}

man/get_os.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{get_os}
+\alias{get_os}
+\title{Identify the operating system.
+The function was written by Will Lowe and was copied from here:
+https://conjugateprior.org/2015/06/identifying-the-os-from-r/}
+\usage{
+get_os()
+}
+\description{
+Identify the operating system.
+The function was written by Will Lowe and was copied from here:
+https://conjugateprior.org/2015/06/identifying-the-os-from-r/
+}
+\keyword{internal}

man/read_mgt.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{read_mgt}
+\alias{read_mgt}
+\title{Read SWAT+ management output file and return the read output in a tibble}
+\usage{
+read_mgt(run_path)
+}
+\arguments{
+\item{run_path}{Path to the folder where simulations are performed}
+}
+\description{
+Read SWAT+ management output file and return the read output in a tibble
+}
+\keyword{internal}

man/read_tbl.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{read_tbl}
+\alias{read_tbl}
+\title{Read SWAT+ output that is arranged in a tabular format (most outputs)
+and return the read output table in a tibble format}
+\usage{
+read_tbl(out_file, run_path)
+}
+\arguments{
+\item{out_file}{Name of the output file that should be read.}
+
+\item{run_path}{Path to the folder where simulations are performed}
+}
+\description{
+Read SWAT+ output that is arranged in a tabular format (most outputs)
+and return the read output table in a tibble format
+}
+\keyword{internal}

man/run_os.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{run_os}
+\alias{run_os}
+\title{Add './' to run the exe on unix systems}
+\usage{
+run_os(exe, os)
+}
+\arguments{
+\item{exe}{Text string that defines the name of the executable file}
+
+\item{os}{Text string that defines the operating system}
+}
+\description{
+Add './' to run the exe on unix systems
+}
+\keyword{internal}

man/run_swat_verification.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{run_swat_verification}
+\alias{run_swat_verification}
+\title{Run simulations for model verification}
+\usage{
+run_swat_verification(
+  project_path,
+  outputs = c("wb", "mgt", "plt"),
+  start_date = NULL,
+  end_date = NULL,
+  years_skip = NULL,
+  keep_folder = FALSE
+)
+}
+\arguments{
+\item{project_path}{Character string, path to the SWAT+ project folder
+(i.e. TxtInOut).}
+
+\item{outputs}{Define the outputs that should be read after the simulation
+run. The outputs that are defined here depend on the verification steps
+that should be performed on the outputs.}
+
+\item{start_date}{(optional) Start date of the SWAT simulation. Provided as
+character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+in the form yyyymmdd, or in Date format.}
+
+\item{end_date}{(optional) End date of the SWAT simulation. Provided as
+character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+in the form yyyymmdd, or in Date format.}
+
+\item{years_skip}{(optional) Integer value to define the number of simulation
+years that are skipped before writing SWAT model outputs.}
+
+\item{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}.
+\code{Default = FALSE}}
+}
+\value{
+Returns the simulation results for the defined output variables as a
+  list of tibbles.
+}
+\description{
+This function allows to run a SWAT2012 project in R.
+Basic settings for the SWAT run such as the simulation period or the time
+interval for the outputs can be done directly. SWAT simulation outputs can be
+defined that are returned in a 'tidy' format in R. Functionality such as model
+parametrization, parallel execution of simulations, or incremental saving of
+simulation runs is provided.
+}

man/set_print_prt.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{set_print_prt}
+\alias{set_print_prt}
+\title{Read and set SWAT+ print.prt file write the updated print.prt and the original file
+as a backup 'print_backup.prt'}
+\usage{
+set_print_prt(project_path, run_path, outputs, years_skip)
+}
+\arguments{
+\item{project_path}{Path to the SWAT project folder (i.e. TxtInOut)}
+
+\item{run_path}{Path to the folder where simulations are performed}
+
+\item{outputs}{Define the outputs that should be read after the simulation
+run. The outputs that are defined here depend on the verification steps
+that should be performed on the outputs.}
+
+\item{years_skip}{(optional) Integer value to define the number of simulation
+years that are skipped before writing SWAT model outputs.}
+}
+\description{
+Read and set SWAT+ print.prt file write the updated print.prt and the original file
+as a backup 'print_backup.prt'
+}
+\keyword{internal}

man/set_time_sim.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_swat_verify.R
+\name{set_time_sim}
+\alias{set_time_sim}
+\title{Read and set SWAT+ time.sim file write the updated time.sim and the original file
+as a backup 'time_backup.sim'}
+\usage{
+set_time_sim(project_path, run_path, start_date, end_date)
+}
+\arguments{
+\item{project_path}{Path to the SWAT project folder (i.e. TxtInOut)}
+
+\item{run_path}{Path to the folder where simulations are performed}
+
+\item{start_date}{(optional) Start date of the SWAT simulation. Provided as
+character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+in the form yyyymmdd, or in Date format.}
+
+\item{end_date}{(optional) End date of the SWAT simulation. Provided as
+character string in any ymd format (e.g. 'yyyy-mm-dd'), numeric value
+in the form yyyymmdd, or in Date format.}
+}
+\description{
+Read and set SWAT+ time.sim file write the updated time.sim and the original file
+as a backup 'time_backup.sim'
+}
+\keyword{internal}