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-rw-r--r--DESCRIPTION2
-rw-r--r--NEWS.md2
-rw-r--r--R/mkinsub.R6
-rw-r--r--R/plot.mkinfit.R8
-rw-r--r--build.log7
-rw-r--r--man/mkinsub.Rd13
-rw-r--r--man/plot.mkinfit.Rd3
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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