From f30472ecd2afea6bd2153b8ad2bb2f663f3a2742 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 25 Aug 2014 10:39:40 +0200 Subject: Bug fix and unit tests for mkinerrmin See NEWS.md for details --- inst/unitTests/runit.mkinerrmin.R | 62 +++++++++++++++++++++++++++++++++++++++ inst/unitTests/runit.mkinfit.R | 38 +----------------------- 2 files changed, 63 insertions(+), 37 deletions(-) create mode 100644 inst/unitTests/runit.mkinerrmin.R (limited to 'inst/unitTests') diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R new file mode 100644 index 00000000..56a33ff9 --- /dev/null +++ b/inst/unitTests/runit.mkinerrmin.R @@ -0,0 +1,62 @@ +# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{ +# and check chi2 error values against values obtained with mkin 0.33 +test.FOCUS_2006_D_SFO_SFO <- function() +{ + 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") + + fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D) + fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", FOCUS_2006_D) + fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D) + fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D) + + FOCUS_2006_D_results_schaefer07_means <- c( + parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34) + + r.1.e <- c(fit.1.e$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]]) + r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]]) + r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]]) + r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$distimes[[1]]) + + dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e + checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3)) + dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d + checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3)) + dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e + checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3)) + dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d + checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3)) + + round(mkinerrmin(fit.2.e), 4) + round(mkinerrmin(fit.2.d), 4) + + errmin.FOCUS_2006_D_rounded = data.frame( + err.min = c(0.0640, 0.0646, 0.0469), + n.optim = c(4, 2, 2), + df = c(15, 7, 8), + row.names = c("All data", "parent", "m1")) + checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4), + errmin.FOCUS_2006_D_rounded) +} # }}} + +# Test SFO_SFO model with FOCUS_2006_E against values obtained with mkin 0.33 {{{ +test.FOCUS_2006_E_SFO_SFO <- function() +{ + SFO_SFO.2 <- mkinmod(parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO"), use_of_ff = "max") + + fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_E) + + round(mkinerrmin(fit.2.e), 4) + errmin.FOCUS_2006_E_rounded = data.frame( + err.min = c(0.1544, 0.1659, 0.1095), + n.optim = c(4, 2, 2), + df = c(13, 7, 6), + row.names = c("All data", "parent", "m1")) + checkEqualsNumeric(round(mkinerrmin(fit.2.e), 4), + errmin.FOCUS_2006_E_rounded) +} # }}} + + diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index fdbc86e0..8eefb995 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -1,6 +1,4 @@ -# $Id: runit.mkinfit.R 68 2010-09-09 22:40:04Z jranke $ - -# Copyright (C) 2010-2013 Johannes Ranke +# Copyright (C) 2010-2014 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -189,40 +187,6 @@ test.FOCUS_2006_SFORB <- function() checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2))) } # }}} -# Test SFO_SFO model with FOCUS_2006_D against Schaefer 2007 paper, tolerance = 1% # {{{ -test.FOCUS_2006_D_SFO_SFO <- function() -{ - 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") - - fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D) - fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", FOCUS_2006_D) - fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D) - SFO <- mkinmod(parent = list(type = "SFO")) - f.SFO <- mkinfit(SFO, FOCUS_2006_D) - fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D) - fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D) - - FOCUS_2006_D_results_schaefer07_means <- c( - parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34) - - r.1.e <- c(fit.1.e$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]]) - r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]]) - r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]]) - r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$distimes[[1]]) - - dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e - checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3)) - dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d - checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3)) - dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e - checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3)) - dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d - checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3)) -} # }}} - # Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{ test.mkinfit.schaefer07_complex_example <- function() { -- cgit v1.2.1