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-rw-r--r--DESCRIPTION7
-rw-r--r--tests/test_FOCUS_2006_A.R2
-rw-r--r--tests/test_FOCUS_2006_A.Rout.save198
-rw-r--r--vignettes/Rplots.pdf815
4 files changed, 106 insertions, 916 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 5e5547a..18d5f9e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: kinfit
Type: Package
Title: Routines for fitting kinetic models to chemical degradation data
-Version: 1.1.12
-Date: 2013-11-27
+Version: 1.1.13
+Date: 2014-11-24
Author: Johannes Ranke, with contributions from Katrin Lindenberger
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Description: Simple calculation routines based on the FOCUS Kinetics
@@ -10,6 +10,9 @@ Description: Simple calculation routines based on the FOCUS Kinetics
included (no metabolite formation/decline or multicompartment kinetics).
Please note that no warranty is implied for correctness of results or
fitness for a particular purpose.
+ This package is not actively developed at the moment. Please check the mkin
+ package for an actively maintained package for kinetic evaluations of
+ degradation data
License: GPL
LazyLoad: yes
LazyData: yes
diff --git a/tests/test_FOCUS_2006_A.R b/tests/test_FOCUS_2006_A.R
index ff55174..3dc37f3 100644
--- a/tests/test_FOCUS_2006_A.R
+++ b/tests/test_FOCUS_2006_A.R
@@ -37,7 +37,7 @@ print(kinresults(fits)$stats, digits=5)
data(FOCUS_2006_D)
fits <- kinfit(FOCUS_2006_D, kinmodels = c("SFO", "FOMC"))
print(kinresults(fits)$results, digits=5)
-print(kinresults(fits)$stats, digits=5)
+print(kinresults(fits)$stats, digits=3)
data(FOCUS_2006_E)
fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP"))
diff --git a/tests/test_FOCUS_2006_A.Rout.save b/tests/test_FOCUS_2006_A.Rout.save
index 1b459f6..2b962a7 100644
--- a/tests/test_FOCUS_2006_A.Rout.save
+++ b/tests/test_FOCUS_2006_A.Rout.save
@@ -1,98 +1,100 @@
-
-R version 2.14.0 (2011-10-31)
-Copyright (C) 2011 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: i386-pc-mingw32/i386 (32-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> # $Id: test_FOCUS_2006_A.R 59 2010-07-28 12:29:15Z jranke $
->
-> # Copyright (C) 2008-2010 Johannes Ranke
-> # Contact: mkin-devel@lists.berlios.de
->
-> # This file is part of the R package kinfit
->
-> # kinfit 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/>
->
-> library(kinfit)
-> data(FOCUS_2006_A)
-> fits <- kinfit(FOCUS_2006_A, kinmodels = c("SFO", "HS"))
-> print(kinresults(fits)$results, digits=5)
- DT50 DT90
-SFO 18.624 61.868
-> print(kinresults(fits)$stats, digits=5)
- n.times df mean.means RSS err.min R2
-SFO 8 6 50.054 221.81 0.083848 0.9845
->
-> data(FOCUS_2006_B)
-> fits <- kinfit(FOCUS_2006_B, kinmodels = c("SFO", "FOMC", "DFOP"))
-> print(kinresults(fits)$results, digits=5)
- DT50 DT90
-SFO 8.8686 29.461
-FOMC 8.6834 30.754
-DFOP 8.6829 30.789
-> print(kinresults(fits)$stats, digits=5)
- n.times df mean.means RSS err.min R2
-SFO 8 6 35.015 30.656 0.044555 0.99713
-FOMC 8 5 35.015 28.583 0.045886 0.99733
-DFOP 8 4 35.015 28.550 0.049527 0.99733
->
-> data(FOCUS_2006_C)
-> fits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP"))
-> print(kinresults(fits)$results, digits=5)
- DT50 DT90
-SFO 2.2647 7.5233
-FOMC 1.7852 15.1479
-DFOP 1.8869 21.2507
-> print(kinresults(fits)$stats, digits=5)
- n.times df mean.means RSS err.min R2
-SFO 9 7 23.589 196.5334 0.158440 0.97136
-FOMC 9 6 23.589 31.0509 0.066568 0.99548
-DFOP 9 5 23.589 4.3627 0.026621 0.99936
->
-> data(FOCUS_2006_D)
-> fits <- kinfit(FOCUS_2006_D, kinmodels = c("SFO", "FOMC"))
-> print(kinresults(fits)$results, digits=5)
- DT50 DT90
-SFO 7.0776 23.511
-FOMC 6.9350 24.044
-> print(kinresults(fits)$stats, digits=5)
- n.times df mean.means RSS err.min R2
-SFO 9 7 39.523 207.63 0.064524 0.99194
-FOMC 9 6 39.523 205.45 0.067792 0.99202
->
-> data(FOCUS_2006_E)
-> fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP"))
-> print(kinresults(fits)$results, digits=5)
- DT50 DT90
-SFO 2.2647 7.5233
-FOMC 1.7852 15.1479
-DFOP 1.8869 21.2507
-> print(kinresults(fits)$stats, digits=5)
- n.times df mean.means RSS err.min R2
-SFO 9 7 23.589 196.5334 0.158440 0.97136
-FOMC 9 6 23.589 31.0509 0.066568 0.99548
-DFOP 9 5 23.589 4.3627 0.026621 0.99936
->
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # $Id: test_FOCUS_2006_A.R 59 2010-07-28 12:29:15Z jranke $
+>
+> # Copyright (C) 2008-2010 Johannes Ranke
+> # Contact: mkin-devel@lists.berlios.de
+>
+> # This file is part of the R package kinfit
+>
+> # kinfit 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/>
+>
+> library(kinfit)
+> data(FOCUS_2006_A)
+> fits <- kinfit(FOCUS_2006_A, kinmodels = c("SFO", "HS"))
+> print(kinresults(fits)$results, digits=5)
+ DT50 DT90
+SFO 18.624 61.868
+> print(kinresults(fits)$stats, digits=5)
+ n.times df mean.means RSS err.min R2
+SFO 8 6 50.054 221.81 0.083848 0.9845
+>
+> data(FOCUS_2006_B)
+> fits <- kinfit(FOCUS_2006_B, kinmodels = c("SFO", "FOMC", "DFOP"))
+> print(kinresults(fits)$results, digits=5)
+ DT50 DT90
+SFO 8.8686 29.461
+FOMC 8.6834 30.754
+DFOP 8.6829 30.789
+> print(kinresults(fits)$stats, digits=5)
+ n.times df mean.means RSS err.min R2
+SFO 8 6 35.015 30.656 0.044555 0.99713
+FOMC 8 5 35.015 28.583 0.045886 0.99733
+DFOP 8 4 35.015 28.550 0.049527 0.99733
+>
+> data(FOCUS_2006_C)
+> fits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP"))
+> print(kinresults(fits)$results, digits=5)
+ DT50 DT90
+SFO 2.2647 7.5233
+FOMC 1.7852 15.1479
+DFOP 1.8869 21.2507
+> print(kinresults(fits)$stats, digits=5)
+ n.times df mean.means RSS err.min R2
+SFO 9 7 23.589 196.5334 0.158440 0.97136
+FOMC 9 6 23.589 31.0509 0.066568 0.99548
+DFOP 9 5 23.589 4.3627 0.026621 0.99936
+>
+> data(FOCUS_2006_D)
+> fits <- kinfit(FOCUS_2006_D, kinmodels = c("SFO", "FOMC"))
+> print(kinresults(fits)$results, digits=5)
+ DT50 DT90
+SFO 7.0776 23.511
+FOMC 6.9350 24.044
+> print(kinresults(fits)$stats, digits=3)
+ n.times df mean.means RSS err.min R2
+SFO 9 7 39.5 208 0.0645 0.992
+FOMC 9 6 39.5 205 0.0678 0.992
+>
+> data(FOCUS_2006_E)
+> fits <- kinfit(FOCUS_2006_E, kinmodels = c("SFO", "FOMC", "DFOP"))
+> print(kinresults(fits)$results, digits=5)
+ DT50 DT90
+SFO 2.2647 7.5233
+FOMC 1.7852 15.1479
+DFOP 1.8869 21.2507
+> print(kinresults(fits)$stats, digits=5)
+ n.times df mean.means RSS err.min R2
+SFO 9 7 23.589 196.5334 0.158440 0.97136
+FOMC 9 6 23.589 31.0509 0.066568 0.99548
+DFOP 9 5 23.589 4.3627 0.026621 0.99936
+>
+> proc.time()
+ user system elapsed
+ 0.992 0.064 1.113
diff --git a/vignettes/Rplots.pdf b/vignettes/Rplots.pdf
deleted file mode 100644
index c52b7ab..0000000
--- a/vignettes/Rplots.pdf
+++ /dev/null
@@ -1,815 +0,0 @@
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