Export to CAKE study file

1 files changed, 80 insertions, 0 deletions

diff --git a/R/CAKE_export.R b/R/CAKE_export.R
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+++ b/R/CAKE_export.R
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+# Copyright (C) 2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+CAKE_export <- function(ds, map = c(parent = "Parent"),
+  links = NA,
+  filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
+  study = "Codlemone aerobic soil degradation",
+  description = "",
+  time_unit = "days",
+  res_unit = "% AR",
+  comment = "Created using mkin::CAKE_export",
+  date = Sys.Date(),
+  optimiser = "IRLS")
+{
+  file <- file.path(path, filename)
+  if (file.exists(file) & !overwrite) stop(file, " already exists, stopping")
+  csf <- file(file, encoding = "latin1", open = "w+")
+  on.exit(close(csf))
+
+  add <- function(x) cat(paste0(x, "\r\n"), file = csf, append = TRUE)
+  add0 <- function(x) cat(x, file = csf, append = TRUE)
+
+  add("[FileInfo]")
+  add("CAKE-Version: 3.3 (Release)")
+  add(paste("Name:", study))
+  add(paste("Description:", description))
+  add(paste("MeasurementUnits:", res_unit))
+  add(paste("TimeUnits:", time_unit))
+  add(paste("Comments:", comment))
+  add(paste("Date:", date))
+  add(paste("Optimiser:", optimiser))
+  add("")
+
+  add("[Data]")
+
+  for (i in seq_along(ds)) {
+    add(paste("NewDataSet:", names(ds)[i]))
+    d <- mkin_long_to_wide(ds[[i]])
+    names(d) <- c("Time", map[names(d)[-1]])
+    write.table(d, csf,
+      sep = "\t", col.names = TRUE,
+      row.names = FALSE,
+      quote = FALSE, eol = "\r\n", na = "")
+    add("")
+  }
+
+  if (!is.na(links)) {
+    add("")
+    add("[Model]")
+    add(paste0("ParentCompartment: Parent\t", names(map)[1], "\t", names(map)[1]))
+    for (name in names(map)[-1]) {
+      add(paste0("Compartment: ", map[name], "\t", name, "\t", name))
+    }
+    for (li in names(links)) {
+      add(paste0("Link: ", map[li], "\t", map[links[li]], "\t0.5\t0\t1\tFree\tExplicit"))
+    }
+
+  }
+
+  add("")
+  add("[ComponentNames]")
+  for (name in names(map)) {
+    add(paste0(map[name], ":", name))
+  }
+
+}