#' Import concentration data from HYDRUS 2D output
#'
#' This function imports concentration data from a simulation successfully run
#' in HYDRUS 2D. Use 'h3d_' functions to import HYDRUS 3D results. Simulation
#' results ('Mesh Information' and 'Concentrations') have to be exported to
#' ASCII prior to running this function using the HYDRUS 2D/3D GUI
#' ('Results' --> 'Convert Output to ASCII').
#' @param path Path to HYDRUS 2D project containing 'MESHTRIA.TXT' and
#' 'CONC<n>.TXT' with <n> being 1, 2, ...,
#' @return
#' Returns a tibble with 5 columns.
#' 'timestep': 'Print Times' in units defined in HYDRUS 'Time Information',
#' 'x': x-coordinate of mesh node,
#' 'y': y-coordinate of mesh node,
#' 'parameter': 'concentrationX' for concentration (concentration1,
#' concentration2, ..., concentration7),
#' 'value': numerical value in units defined in HYDRUS [-].
#' @family
#' HYDRUS 2D functions
#' @references
#' https://www.pc-progress.com/downloads/Pgm_Hydrus3D2/HYDRUS3D%20User%20Manual.pdf
#' @author
#' Jan Knappe, \email{jan.knappe@@gmail.com}
#' @import
#' dplyr tidyr stringr readr tibble purrr
#' @export
#' @examples
#' h2d_concentratio(path = "data")
#'
#' \dontrun{
#' h2d_concentratio(path = "CONC1.TXT")
#' h2d_concentratio(path = "Project/CONC1.TXT")
#' }
h2d_concentration <- function(path) {
#
# Preamble
# ~~~~~~~~~~~~~~~~
#
# path name of mesh file
meshFile <-
if (substring(path, nchar(path)) == "/") {
# path provided with trailing '/'
paste0(path, "MESHTRIA.TXT")
} else {
# path provided without trailing '/'
paste0(path, "/MESHTRIA.TXT")
}
#
# correct path if provided without trailing '/'
if (!(substring(path, nchar(path)) == "/")) {
path <- paste0(path, "/")
}
#
# find all concentration files in path (max = 7)
files <-
list.files(path = path, pattern = "Conc[1-7].TXT")
#
# Error handling
# ~~~~~~~~~~~~~~~~
#
# project folder must exists
if (!dir.exists(path)) {
stop("Can't find path to HYDRUS project. Does variable 'path' point to an existing HYDRUS project?")
}
# MESHTRIA.TXT must exist in the project folder
if (!file.exists(meshFile)) {
stop("HYDRUS project folder does not contain mesh information. Export mesh information through the HYDRUS GUI.")
}
# simulation results must exist in the project folder
if (!length(files == 0)) {
stop("HYDRUS project folder does not contain concentration data. Export simulation results through the HYDRUS GUI.")
}
#
# Function
# ~~~~~~~~~~~~~~~~
#
# import node coordinates
nodes <-
h2d_nodes(path = path)
#
# import data
input <-
files %>%
map(function(x) { # x = concentration files
readChar(paste0(path, x), nchars = file.info(paste0(path, x))$size) %>%
str_replace_all(pattern = " ", "\r\n") %>%
read_csv(col_names = "value") %>%
# flag parameter from source file
mutate(parameter = paste0("concentration", str_extract(x, "[1-7]"))) %>%
# extract timestep information
mutate(timestep = ifelse(value %in% "Time", lead(value, 2), NA)) %>%
fill(timestep) %>%
# remove non-data rows
mutate(remove = ifelse(value %in% "Time", TRUE, FALSE),
remove = ifelse(lag(value, 1) %in% "Time", TRUE, remove),
remove = ifelse(lag(value, 2) %in% "Time", TRUE, remove)) %>%
filter(!remove) %>%
select(-remove) %>%
# parse to numeric
mutate(timestep = as.numeric(timestep),
value = as.numeric(value)) %>%
# add nodeID information
group_by(timestep) %>%
mutate(nodeID = row_number(timestep)) %>%
ungroup()
}) %>%
bind_rows()
#
# join with node coordinates
result <-
input %>%
left_join(nodes,
by = "nodeID") %>%
select(timestep, x, y, parameter, value)
#
result
}
#~~~~~~~~
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