From 075fb65b2a114e804cfa3f8d8d68c933b5f8eb04 Mon Sep 17 00:00:00 2001
From: mrustl <michael.rustler@kompetenz-wasser.de>
Date: Thu, 30 May 2024 16:25:15 +0200
Subject: [PATCH] Add read_atmosph() for importing ATMOSPH.in data

---
 DESCRIPTION         |  2 +-
 NAMESPACE           |  4 ++++
 R/read_atmosph.R    | 54 +++++++++++++++++++++++++++++++++++++++++++++
 man/read_atmosph.Rd | 20 +++++++++++++++++
 4 files changed, 79 insertions(+), 1 deletion(-)
 create mode 100644 R/read_atmosph.R
 create mode 100644 man/read_atmosph.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index fa48168..9312ae0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -43,5 +43,5 @@ Remotes:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index 9386989..6e179e7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,6 +8,7 @@ export(get_output_meta)
 export(get_units_list)
 export(prepare_atmosphere_input)
 export(read_alevel)
+export(read_atmosph)
 export(read_meta_general)
 export(read_runinf)
 export(read_solute)
@@ -31,9 +32,12 @@ importFrom(magrittr,"%>%")
 importFrom(readr,fwf_widths)
 importFrom(readr,read_delim)
 importFrom(readr,read_fwf)
+importFrom(readr,read_table)
 importFrom(rlang,.data)
+importFrom(stats,setNames)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_pad)
+importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_split)
diff --git a/R/read_atmosph.R b/R/read_atmosph.R
new file mode 100644
index 0000000..536dc15
--- /dev/null
+++ b/R/read_atmosph.R
@@ -0,0 +1,54 @@
+#' Read ATMOSPH.in
+#'
+#' @param path path to ATMOSPH.in (default: system.file("extdata/model/test/ATMOSPH.in",
+#' package = "kwb.hydrus1d"))
+#'
+#' @return list with atmospheric config parameter sublist and time series sublist
+#' @export
+#' @importFrom readr read_table
+#' @importFrom stringr str_remove str_trim str_split
+#' @importFrom stats setNames
+#'
+read_atmosph <- function(path = system.file("extdata/model/test/ATMOSPH.in",
+                                            package = "kwb.hydrus1d")) {
+
+atm <- readLines(path)
+
+idx_headers <- grep("\\s+tAtm\\s+", atm)
+idx_start <- idx_headers + 1
+idx_end <- grep("end\\*\\*\\*", atm) - 1
+
+idx_config_start <- grep("ATMOSPHERIC INFORMATION", atm) + 1
+idx_config_end <- idx_headers - 1
+
+config_names_vars <- lapply(1:6, function(i) {
+  atm[idx_config_start:idx_config_end][i] %>%
+    stringr::str_remove("\\(MaxAL = number of atmospheric data-records\\)") %>%
+    stringr::str_remove("\\(max. allowed pressure head at the soil surface\\)") %>%
+    stringr::str_trim(side = "both") %>%
+    stringr::str_split("\\s+", simplify = TRUE) %>%
+    as.vector()
+})
+
+
+atm_config <- stats::setNames(sapply(c(config_names_vars[[2]], config_names_vars[[4]], config_names_vars[[6]]),
+                                     list),
+                              nm = c(config_names_vars[[1]], config_names_vars[[3]], config_names_vars[[5]]))
+
+
+atm_names <-  stringr::str_trim(atm[idx_headers], side = "both") %>%
+  stringr::str_split("\\s+", simplify = TRUE) %>%
+  as.vector()
+
+a_file <- tempfile()
+
+atm[idx_start:idx_end] %>%
+  stringr::str_trim(side = "both") %>%
+  writeLines(a_file)
+
+atm_dat <- readr::read_table(a_file, col_names = FALSE)
+names(atm_dat)[seq_along(atm_names)] <- atm_names
+
+list(config = atm_config,
+     data = atm_dat)
+}
diff --git a/man/read_atmosph.Rd b/man/read_atmosph.Rd
new file mode 100644
index 0000000..5001a46
--- /dev/null
+++ b/man/read_atmosph.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_atmosph.R
+\name{read_atmosph}
+\alias{read_atmosph}
+\title{Read ATMOSPH.in}
+\usage{
+read_atmosph(
+  path = system.file("extdata/model/test/ATMOSPH.in", package = "kwb.hydrus1d")
+)
+}
+\arguments{
+\item{path}{path to ATMOSPH.in (default: system.file("extdata/model/test/ATMOSPH.in",
+package = "kwb.hydrus1d"))}
+}
+\value{
+list with atmospheric config parameter sublist and time series sublist
+}
+\description{
+Read ATMOSPH.in
+}