- Added the examples vignette to the kinfit package

- Added calls to utils::globalVariables to make
  R CMD check pass cleanly without NOTES



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@62 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

8 files changed, 52 insertions, 10 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index c76ca01e..4b9e6635 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 8ec05ef2..8e4ec604 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 c2786476..49538e37 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 411cb40c..e084cf1a 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 b3482789..b45b26fe 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 b47678ba..fa1d805c 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 8b39874e..f56478f1 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 24e1b57c..784eddfc 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))