From c4e8498ee688fff1e1b2df1a7a65f888cb0d9d84 Mon Sep 17 00:00:00 2001 From: jranke Date: Wed, 25 Apr 2012 10:33:53 +0000 Subject: - 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 --- inst/unitTests/runit.mkinfit.R | 1 + inst/unitTests/runit.mkinpredict.R | 86 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 inst/unitTests/runit.mkinpredict.R (limited to 'inst') diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index a06e4ff1..2030f852 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 00000000..997857ce --- /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 + +# 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: -- cgit v1.2.1