From 08cae49345c048fdbb69befc5a3b3f7966836223 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 16 Oct 2015 16:31:29 +0200
Subject: Full compound names in models that are shown in the plot

---
 DESCRIPTION         |  2 +-
 NEWS.md             |  2 ++
 R/mkinsub.R         |  6 +++---
 R/plot.mkinfit.R    |  8 ++++++--
 build.log           |  7 +------
 man/mkinsub.Rd      | 13 ++++++++++++-
 man/plot.mkinfit.Rd |  3 ++-
 7 files changed, 27 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 06b212c7..365a325f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
 Version: 0.9-40.900
-Date: 2015-07-22
+Date: 2015-10-16
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/NEWS.md b/NEWS.md
index fbe95d11..cfaccc7a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
 
 ### Minor changes
 
+- Make it possible to specify arbitrary strings as names for the compounds in `mkinmod`, and show them in the plot
+
 - Use an index.r file to group help topics in static documentation
 
 ## mkin 0.9-40 (2015-07-21)
diff --git a/R/mkinsub.R b/R/mkinsub.R
index f92af54b..99c3ea20 100644
--- a/R/mkinsub.R
+++ b/R/mkinsub.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2014 Johannes Ranke
+# Copyright (C) 2014,2015 Johannes Ranke
 # Portions of this code are copyright (C) 2013 Eurofins Regulatory AG
 # Contact: jranke@uni-bremen.de
 
@@ -16,8 +16,8 @@
 
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <http://www.gnu.org/licenses/>
-mkinsub <- function(submodel, to = NULL, sink = TRUE)
+mkinsub <- function(submodel, to = NULL, sink = TRUE, full_name = NA)
 {
-  return(list(type = submodel, to = to, sink = sink))
+  return(list(type = submodel, to = to, sink = sink, full_name = full_name))
 }
 # vim: set ts=2 sw=2 expandtab:
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 31746fb8..f8ee600e 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2014 Johannes Ranke
+# Copyright (C) 2010-2015 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -76,7 +76,11 @@ plot.mkinfit <- function(x, fit = x,
   }
   matlines(out$time, out[obs_vars], col = col_obs[obs_vars], lty = lty_obs[obs_vars])
   if (legend == TRUE) {
-    legend(lpos, inset= inset, legend = obs_vars,
+    legend_names = lapply(names(fit$mkinmod$spec), function(x) {
+                            if (is.na(fit$mkinmod$spec[[x]]$full_name)) x
+                            else fit$mkinmod$spec[[x]]$full_name
+      })
+    legend(lpos, inset= inset, legend = legend_names,
       col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars])
   }
   # Show residuals if requested
diff --git a/build.log b/build.log
index 9968573e..c3b0aa75 100644
--- a/build.log
+++ b/build.log
@@ -2,9 +2,4 @@
 * preparing ‘mkin’:
 * checking DESCRIPTION meta-information ... OK
 * installing the package to build vignettes
-* creating vignettes ... OK
-* checking for LF line-endings in source and make files
-* checking for empty or unneeded directories
-* looking to see if a ‘data/datalist’ file should be added
-* building ‘mkin_0.9-40.tar.gz’
-
+* creating vignettes ...
\ No newline at end of file
diff --git a/man/mkinsub.Rd b/man/mkinsub.Rd
index 9eeffda0..352c4097 100644
--- a/man/mkinsub.Rd
+++ b/man/mkinsub.Rd
@@ -8,7 +8,7 @@
   \code{\link{mkinmod}}.
 }
 \usage{
-mkinsub(submodel, to = NULL, sink = TRUE)
+mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
 }
 \arguments{
   \item{submodel}{
@@ -23,6 +23,12 @@ mkinsub(submodel, to = NULL, sink = TRUE)
     Should a pathway to sink be included in the model in addition to the 
     pathways to other state variables?
   }
+  \item{full_name}{
+    An optional name to be used e.g. for plotting fits performed with the model.
+    You can use non-ASCII characters here, but then your R code will not be
+    portable, \emph{i.e.} may produce unintended plot results on other
+    operating systems or system configurations.
+  }
 }
 \value{
   A list for use with \code{\link{mkinmod}}.
@@ -40,5 +46,10 @@ SFO_SFO <- mkinmod(
 SFO_SFO.2 <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
+
+# Now supplying full names
+SFO_SFO.2 <- mkinmod(
+  parent = mkinsub("SFO", "m1", full_name = "Test compound"),
+  m1 = mkinsub("SFO", full_name = "Metabolite M1"))
 }
 
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index f26aac4c..494dc38d 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -82,7 +82,8 @@
 \examples{
 # One parent compound, one metabolite, both single first order, path from
 # parent to sink included
-SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
+                   m1 = mkinsub("SFO", full = "Metabolite M1" ))
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 plot(fit)
 }
-- 
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