diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/mkin_wide_to_long.R | 4 | ||||
| -rw-r--r-- | R/mkinerrmin.R | 4 | ||||
| -rw-r--r-- | R/mkinfit.R | 3 | ||||
| -rw-r--r-- | R/mkinresplot.R | 1 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 23 | ||||
| -rw-r--r-- | R/transform_odeparms.R | 20 | ||||
| -rw-r--r-- | vignettes/examples.Rnw | 3 |
8 files changed, 52 insertions, 10 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index c76ca01..4b9e663 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: mkin Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data -Version: 0.9-10 -Date: 2013-02-16 +Version: 0.9-11 +Date: 2013-02-17 Author: Johannes Ranke, Katrin Lindenberger, René Lehmann Maintainer: Johannes Ranke <jranke@uni-bremen.de> Description: Calculation routines based on the FOCUS Kinetics Report (2006). diff --git a/R/mkin_wide_to_long.R b/R/mkin_wide_to_long.R index 8ec05ef..8e4ec60 100644 --- a/R/mkin_wide_to_long.R +++ b/R/mkin_wide_to_long.R @@ -1,6 +1,6 @@ # $Id$
-# Copyright (C) 2010 Johannes Ranke
+# Copyright (C) 2010-2013 Johannes Ranke
# Contact: mkin-devel@lists.berlios.de
# This file is part of the R package mkin
@@ -17,7 +17,7 @@ # You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
-
+utils::globalVariables(c("name", "value"))
mkin_wide_to_long <- function(wide_data, time = "t")
{
colnames <- names(wide_data)
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R index c278647..49538e3 100644 --- a/R/mkinerrmin.R +++ b/R/mkinerrmin.R @@ -1,6 +1,6 @@ # $Id$
-# Copyright (C) 2010-2012 Johannes Ranke
+# Copyright (C) 2010-2013 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -17,7 +17,7 @@ # You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
-
+utils::globalVariables(c("name"))
mkinerrmin <- function(fit, alpha = 0.05)
{
parms.optim <- fit$parms.all
diff --git a/R/mkinfit.R b/R/mkinfit.R index 411cb40..e084cf1 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -1,6 +1,6 @@ # $Id$
-# Copyright (C) 2010-2012 Johannes Ranke
+# Copyright (C) 2010-2013 Johannes Ranke
# Contact: jranke@uni-bremen.de
# The summary function is an adapted and extended version of summary.modFit
# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
@@ -20,6 +20,7 @@ # You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
+utils::globalVariables(c("name", "value"))
mkinfit <- function(mkinmod, observed,
parms.ini = "auto",
diff --git a/R/mkinresplot.R b/R/mkinresplot.R index b348278..b45b26f 100644 --- a/R/mkinresplot.R +++ b/R/mkinresplot.R @@ -17,6 +17,7 @@ # You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
+utils::globalVariables(c("variable", "residual"))
mkinresplot <- function (object, obs_vars = vector(),
xlab = "Time", ylab = "Residual",
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index b47678b..fa1d805 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -1,3 +1,26 @@ +# $Id: $ + +# Copyright (C) 2010-2013 Johannes Ranke +# Contact: jranke@uni-bremen.de +# The summary function is an adapted and extended version of summary.modFit +# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn +# inspired by summary.nls.lm + +# 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/> +utils::globalVariables(c("type", "variable", "observed")) plot.mkinfit <- function(x, fit = x, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)), diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index 8b39874..f56478f 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -1,3 +1,23 @@ +# $Id$
+
+# Copyright (C) 2010-2013 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/>
+
transform_odeparms <- function(parms, mod_vars) {
# Set up container for transformed parameters
transparms <- parms
diff --git a/vignettes/examples.Rnw b/vignettes/examples.Rnw index 24e1b57..784eddf 100644 --- a/vignettes/examples.Rnw +++ b/vignettes/examples.Rnw @@ -123,7 +123,6 @@ The following code defines example dataset L2 from the FOCUS kinetics report, p. 287
<<FOCUS_2006_L2_data, echo=TRUE, eval=TRUE>>=
-library("mkin")
FOCUS_2006_L2 = data.frame(
t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
parent = c(96.1, 91.8, 41.4, 38.7,
@@ -203,7 +202,6 @@ The following code defines example dataset L3 from the FOCUS kinetics report, p. 290
<<FOCUS_2006_L3_data, echo=TRUE, eval=TRUE>>=
-library("mkin")
FOCUS_2006_L3 = data.frame(
t = c(0, 3, 7, 14, 30, 60, 91, 120),
parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
@@ -252,7 +250,6 @@ The following code defines example dataset L4 from the FOCUS kinetics report, p. 293
<<FOCUS_2006_L4_data, echo=TRUE, eval=TRUE>>=
-library("mkin")
FOCUS_2006_L4 = data.frame(
t = c(0, 3, 7, 14, 30, 60, 91, 120),
parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
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