From 47030f0342b66b1520b8a20844a0569d492d188e Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 31 Jan 2019 15:32:20 +0100
Subject: Export to CAKE study file

---
 NAMESPACE          |  1 +
 R/CAKE_export.R    | 80 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 man/CAKE_export.Rd | 73 +++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 154 insertions(+)
 create mode 100644 R/CAKE_export.R
 create mode 100644 man/CAKE_export.Rd

diff --git a/NAMESPACE b/NAMESPACE
index cc6b24e9..fc812f46 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,3 +26,4 @@ importFrom(methods, signature)
 importFrom(R6, R6Class)
 importFrom(grDevices, dev.cur)
 importFrom(plyr, join)
+importFrom(utils, write.table)
diff --git a/R/CAKE_export.R b/R/CAKE_export.R
new file mode 100644
index 00000000..db9caa8d
--- /dev/null
+++ b/R/CAKE_export.R
@@ -0,0 +1,80 @@
+# 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))
+  }
+
+}
diff --git a/man/CAKE_export.Rd b/man/CAKE_export.Rd
new file mode 100644
index 00000000..3a3da4d0
--- /dev/null
+++ b/man/CAKE_export.Rd
@@ -0,0 +1,73 @@
+\name{CAKE_export}
+\alias{CAKE_export}
+\title{
+  Export a list of datasets in wide format to a CAKE study file
+}
+\description{
+  In addition to the datasets, the pathways in the degradation
+  model can be specified as well.
+}
+\usage{
+CAKE_export(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")
+}
+\arguments{
+  \item{ds}{
+    A named list of datasets in long format as compatible with
+    \code{\link{mkinfit}}.
+  }
+  \item{map}{
+    A character vector with CAKE compartment names (Parent, A1, ...),
+    named with the names used in the list of datasets.
+  }
+  \item{links}{
+    An optional character vector of target compartments, named with
+    the names of the source compartments. In order to make this
+    easier, the names are used as in the datasets supplied.
+  }
+  \item{filename}{
+    Where to write the result. Should end in .csf in order to be compatible
+    with CAKE.
+  }
+  \item{path}{
+    An optional path to the output file.
+  }
+  \item{overwrite}{
+    If TRUE, existing files are overwritten.
+  }
+  \item{study}{
+    The name of the study.
+  }
+  \item{description}{
+    An optional description.
+  }
+  \item{time_unit}{
+    The time unit for the residue data.
+  }
+  \item{res_unit}{
+    The unit used for the residues.
+  }
+  \item{comment}{
+    An optional comment.
+  }
+  \item{date}{
+    The date of file creation.
+  }
+  \item{optimiser}{
+    Can be OLS or IRLS.
+  }
+}
+\value{
+  The function is called for its side effect.
+}
+\author{
+  Johannes Ranke
+}
-- 
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