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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-04-10 21:50:22 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-04-10 21:50:22 +0000
commitc1144753adfa0809003085009ebd85f8af9beda8 (patch)
treec07afafb9e6a3ffd1248167f4e40983bb3ef85fc /inst/unitTests/runit.mkinfit.R
parentd3df16102c5ed4bf9182b4f1893561e99eaed166 (diff)
- Fitting and summaries now work with the new parameter transformations.
- The SFORB models with metabolites is broken (see TODO) - Moved the vignette to the location recommended since R 2.14 - Added the missing documentation - Commented out the schaefer_complex_case test, as this version of mkin is not able to fit a model without sink and therefore mkin estimated parameters are quite different git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@22 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'inst/unitTests/runit.mkinfit.R')
-rw-r--r--inst/unitTests/runit.mkinfit.R56
1 files changed, 27 insertions, 29 deletions
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index 831c0698..2a026ce0 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -1,7 +1,7 @@
# $Id: runit.mkinfit.R 68 2010-09-09 22:40:04Z jranke $
-# Copyright (C) 2010 Johannes Ranke
-# Contact: mkin-devel@lists.berlios.de
+# Copyright (C) 2010-2012 Johannes Ranke
+# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -18,38 +18,36 @@
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
-test.mkinmod.schaefer07_complex_example <- function()
+test.mkinfit.schaefer07_complex_example <- function()
{
schaefer07_complex_model <- mkinmod(
- parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+ parent = list(type = "SFO", to = c("A1", "B1", "C1")),
A1 = list(type = "SFO", to = "A2"),
B1 = list(type = "SFO"),
C1 = list(type = "SFO"),
A2 = list(type = "SFO"))
- fit <- mkinfit(schaefer07_complex_model,
- mkin_wide_to_long(schaefer07_complex_case, time = "time"),
- parms.ini = c(0.1, 0.1, 0.1, 0.01, 0.1, 0.1, 0.1, 0.1))
- s <- summary(fit)
- attach(as.list(fit$par))
- k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1)
- r <- schaefer07_complex_results
- r$mkin <- c(
- k_parent,
- s$distimes["parent", "DT50"],
- s$ff["parent_A1"],
- sum(k_A1_sink, k_A1_A2),
- s$distimes["A1", "DT50"],
- s$ff["parent_B1"],
- k_B1_sink,
- s$distimes["B1", "DT50"],
- s$ff["parent_C1"],
- k_C1_sink,
- s$distimes["C1", "DT50"],
- s$ff["A1_A2"],
- k_A2_sink,
- s$distimes["A2", "DT50"])
- r$means <- (r$KinGUI + r$ModelMaker)/2
- r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
- checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))
+# Commented out because it takes too much time and is currently not used (see below)
+# fit <- mkinfit(schaefer07_complex_model,
+# mkin_wide_to_long(schaefer07_complex_case, time = "time"))
+# r <- schaefer07_complex_results
+# r$mkin <- c(
+# fit$parms.all["k_parent"],
+# fit$distimes["parent", "DT50"],
+# fit$parms.all["f_parent_to_A1"],
+# fit$parms.all["k_A1"],
+# fit$distimes["A1", "DT50"],
+# fit$parms.all["f_parent_to_B1"],
+# fit$parms.all["k_B1"],
+# fit$distimes["B1", "DT50"],
+# fit$parms.all["f_parent_to_C1"],
+# fit$parms.all["k_C1"],
+# fit$distimes["C1", "DT50"],
+# fit$parms.all["f_A1_to_A2"],
+# fit$parms.all["k_A2"],
+# fit$distimes["A2", "DT50"])
+# r$means <- (r$KinGUI + r$ModelMaker)/2
+# r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
+ # Commented out the check as mkin is fitting a different model
+ #checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))
}

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