- Transferred some testing code from test.R to unit tests for mkinpredict

- Fixed the output format of mkinpredict to be uniform across solution types



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@33 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

4 files changed, 92 insertions, 6 deletions

diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index be43b0e..493c578 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -57,8 +57,8 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de
           evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")),
           evalparse(paste("k", parent.name, "sink", sep="_")))
     )
-    out <- cbind(outtimes, o)
-    dimnames(out) <- list(outtimes, c("time", sub("_free", "", parent.name)))
+    out <- data.frame(outtimes, o)
+    names(out) <- c("time", sub("_free", "", parent.name))
   }
   if (solution_type == "eigen") {
     coefmat.num <- matrix(sapply(as.vector(mkinmod$coefmat), evalparse), 
@@ -70,8 +70,8 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de
     }
     o <- matrix(mapply(f.out, outtimes), 
       nrow = length(mod_vars), ncol = length(outtimes))
-    dimnames(o) <- list(mod_vars, outtimes)
-    out <- cbind(time = outtimes, t(o))
+    out <- data.frame(outtimes, t(o))
+    names(out) <- c("time", mod_vars)
   } 
   if (solution_type == "deSolve") {
     mkindiff <- function(t, state, parms) {
diff --git a/TODO b/TODO
index a7503bd..fb8b80d 100644
--- a/TODO
+++ b/TODO
@@ -1,9 +1,8 @@
 Must have:
-- Fix remaining problem with the schaefer complex test data (test.R)
 - Adapt mkinplot function
 
 Nice to have:
-- Make unit tests for mkinpredict, comparing different solution types
+- Fix remaining problem with the schaefer complex test data (test.R: fit.2.eigen)
 - Calculate confidence intervals for parameters assuming normal distribution
 - Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved
 - Add unit tests for mkinfit
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index a06e4ff..2030f85 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -257,4 +257,5 @@ test.mkinfit.schaefer07_complex_example <- function()
   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)))

 } # }}}

+

 # vim: set foldmethod=marker ts=2 sw=2 expandtab:

diff --git a/inst/unitTests/runit.mkinpredict.R b/inst/unitTests/runit.mkinpredict.R
new file mode 100644
index 0000000..997857c
--- /dev/null
+++ b/inst/unitTests/runit.mkinpredict.R
@@ -0,0 +1,86 @@
+# $Id: jranke $

+

+# Copyright (C) 2012 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/>

+

+# Check solution types for SFO {{{

+test.SFO_solution_types <- function()

+{

+  ot = seq(0, 100, by = 1)

+  SFO <- mkinmod(parent = list(type = "SFO"))

+  SFO.analytical <- round(subset(mkinpredict(SFO, c(k_parent_sink = 0.1),

+        c(parent = 100), ot, solution_type = "analytical"), time == 100), digits=5)

+  SFO.deSolve <- round(subset(mkinpredict(SFO, c(k_parent_sink = 0.1),

+        c(parent = 100), ot, solution_type = "deSolve"), time == 100), digits=5)

+  SFO.eigen <- round(subset(mkinpredict(SFO, c(k_parent_sink = 0.1),

+        c(parent = 100), ot, solution_type = "eigen"), time == 100), digits=5)

+

+  checkEquals(SFO.analytical, SFO.deSolve)

+  checkEquals(SFO.analytical, SFO.eigen)

+} # }}}

+

+# Check model specification and solution types for SFO_SFO {{{

+# Relative Tolerance is 0.01%

+# Do not use time 0, as eigenvalue based solution does not give 0 at time 0 for metabolites

+# and relative tolerance is thus not met

+test.SFO_solution_types <- function()

+{

+  tol = 0.01

+  SFO_SFO.1 <- mkinmod(parent = list(type = "SFO", to = "m1"),

+         m1 = list(type = "SFO"), use_of_ff = "min")

+  SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"),

+         m1 = list(type = "SFO"), use_of_ff = "max")

+

+  ot = seq(0, 100, by = 1)

+  r.1.e <- subset(mkinpredict(SFO_SFO.1, 

+             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1), 

+             c(parent = 100, m1 = 0), ot, solution_type = "eigen"), 

+                 time %in% c(1, 10, 50, 100))

+  r.1.d <- subset(mkinpredict(SFO_SFO.1, 

+             c(k_parent_m1 = 0.1, k_parent_sink = 0.1, k_m1_sink = 0.1), 

+             c(parent = 100, m1 = 0), ot, solution_type = "deSolve"), 

+                 time %in% c(1, 10, 50, 100))

+

+  r.2.e <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1), 

+	    c(parent = 100, m1 = 0), ot, solution_type = "eigen"),

+                  time %in% c(1, 10, 50, 100))

+  r.2.d <- subset(mkinpredict(SFO_SFO.2, c(k_parent = 0.2, f_parent_to_m1 = 0.5, k_m1 = 0.1), 

+	    c(parent = 100, m1 = 0), ot, solution_type = "deSolve"),

+                  time %in% c(1, 10, 50, 100))

+

+  # Compare eigen and deSolve for minimum use of formation fractions

+  dev.1.e_d.percent = 100 * (r.1.e[-1] - r.1.d[-1])/r.1.e[-1]

+  dev.1.e_d.percent = as.numeric(unlist((dev.1.e_d.percent)))

+  dev.1.e_d.percent = ifelse(is.na(dev.1.e_d.percent), 0, dev.1.e_d.percent)

+  checkIdentical(dev.1.e_d.percent < tol, rep(TRUE, length(dev.1.e_d.percent)))

+

+  # Compare eigen and deSolve for maximum use of formation fractions

+  dev.2.e_d.percent = 100 * (r.1.e[-1] - r.1.d[-1])/r.1.e[-1]

+  dev.2.e_d.percent = as.numeric(unlist((dev.2.e_d.percent)))

+  dev.2.e_d.percent = ifelse(is.na(dev.2.e_d.percent), 0, dev.2.e_d.percent)

+  checkIdentical(dev.2.e_d.percent < tol, rep(TRUE, length(dev.2.e_d.percent)))

+

+  # Compare minimum and maximum use of formation fractions

+  dev.1_2.e.percent = 100 * (r.1.e[-1] - r.2.e[-1])/r.1.e[-1]

+  dev.1_2.e.percent = as.numeric(unlist((dev.1_2.e.percent)))

+  dev.1_2.e.percent = ifelse(is.na(dev.1_2.e.percent), 0, dev.1_2.e.percent)

+  checkIdentical(dev.1_2.e.percent < tol, rep(TRUE, length(dev.1_2.e.percent)))

+

+} # }}}

+

+# vim: set foldmethod=marker ts=2 sw=2 expandtab: