From 86c48be3a34d7d9a43f136719535555d184cbf60 Mon Sep 17 00:00:00 2001 From: jranke Date: Sun, 17 Feb 2013 20:18:28 +0000 Subject: - 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 --- DESCRIPTION | 4 ++-- R/mkin_wide_to_long.R | 4 ++-- R/mkinerrmin.R | 4 ++-- R/mkinfit.R | 3 ++- R/mkinresplot.R | 1 + R/plot.mkinfit.R | 23 +++++++++++++++++++++++ R/transform_odeparms.R | 20 ++++++++++++++++++++ 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 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 - +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 - +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 +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 +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 +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 + 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 <>= -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 <>= -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 <>= -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)) -- cgit v1.2.1