From 081b5f25cc4ef779175307d9ce20672e0573b7c9 Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 24 Apr 2012 17:33:56 +0000 Subject: - Added the reference fit data for FOCUS 2006 datasets from the kinfit package - Used these data in unit tests for parent only models - Fixed SFORB data and calculation of formation fractions along the way - Reintroduced the test for the Schaefer 2007 data - Got rid of the mkinmod unit tests - they are too hard to maintain and the mkinfit tests test the model definitions as well git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@32 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- inst/unitTests/runit.mkinfit.R | 257 +++++++++++++++++++++++++++++++++++++---- inst/unitTests/runit.mkinmod.R | 134 --------------------- 2 files changed, 232 insertions(+), 159 deletions(-) delete mode 100644 inst/unitTests/runit.mkinmod.R (limited to 'inst') diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R index 2a026ce0..a06e4ff1 100644 --- a/inst/unitTests/runit.mkinfit.R +++ b/inst/unitTests/runit.mkinfit.R @@ -18,36 +18,243 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see +# Test SFO model to a relative tolerance of 1% # {{{ +test.FOCUS_2006_SFO <- function() +{ + SFO.1 <- mkinmod(parent = list(type = "SFO")) + SFO.2 <- mkinmod(parent = list(type = "SFO"), use_of_ff = "max") + + fit.A.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_A, quiet=TRUE) + fit.A.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_A, quiet=TRUE) + + median.A.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "A", + c(M0, k, DT50, DT90)), "median")) + + fit.A.SFO.1.r <- as.numeric(c(fit.A.SFO.1$parms.all, fit.A.SFO.1$distimes)) + dev.A.SFO.1 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.1.r)/median.A.SFO), digits=1)) + checkIdentical(dev.A.SFO.1 < 1, rep(TRUE, length(dev.A.SFO.1))) + + fit.A.SFO.2.r <- as.numeric(c(fit.A.SFO.2$parms.all, fit.A.SFO.2$distimes)) + dev.A.SFO.2 <- abs(round(100 * ((median.A.SFO - fit.A.SFO.2.r)/median.A.SFO), digits=1)) + checkIdentical(dev.A.SFO.2 < 1, rep(TRUE, length(dev.A.SFO.2))) + + fit.C.SFO.1 <- mkinfit(SFO.1, FOCUS_2006_C, quiet=TRUE) + fit.C.SFO.2 <- mkinfit(SFO.2, FOCUS_2006_C, quiet=TRUE) + + median.C.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F, dataset == "C", + c(M0, k, DT50, DT90)), "median")) + + fit.C.SFO.1.r <- as.numeric(c(fit.C.SFO.1$parms.all, fit.C.SFO.1$distimes)) + dev.C.SFO.1 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.1.r)/median.C.SFO), digits=1)) + checkIdentical(dev.C.SFO.1 < 1, rep(TRUE, length(dev.C.SFO.1))) + + fit.C.SFO.2.r <- as.numeric(c(fit.C.SFO.2$parms.all, fit.C.SFO.2$distimes)) + dev.C.SFO.2 <- abs(round(100 * ((median.C.SFO - fit.C.SFO.2.r)/median.C.SFO), digits=1)) + checkIdentical(dev.C.SFO.2 < 1, rep(TRUE, length(dev.C.SFO.2))) +} # }}} + +# Test FOMC model to a relative tolerance of 1% {{{ +# See kinfit vignette for a discussion of FOMC fits to FOCUS_2006_A +# In this case, only M0, DT50 and DT90 are checked +test.FOCUS_2006_FOMC <- function() +{ + FOMC <- mkinmod(parent = list(type = "FOMC")) + + # FOCUS_2006_A (compare kinfit vignette for discussion) + fit.A.FOMC <- mkinfit(FOMC, FOCUS_2006_A, quiet=TRUE) + + median.A.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "A", + c(M0, alpha, beta, DT50, DT90)), "median")) + + fit.A.FOMC.r <- as.numeric(c(fit.A.FOMC$parms.all, fit.A.FOMC$distimes)) + dev.A.FOMC <- abs(round(100 * ((median.A.FOMC - fit.A.FOMC.r)/median.A.FOMC), digits=1)) + dev.A.FOMC <- dev.A.FOMC[c(1, 4, 5)] + checkIdentical(dev.A.FOMC < 1, rep(TRUE, length(dev.A.FOMC))) + + # FOCUS_2006_B + fit.B.FOMC <- mkinfit(FOMC, FOCUS_2006_B, quiet=TRUE) + + median.B.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "B", + c(M0, alpha, beta, DT50, DT90)), "median")) + + fit.B.FOMC.r <- as.numeric(c(fit.B.FOMC$parms.all, fit.B.FOMC$distimes)) + dev.B.FOMC <- abs(round(100 * ((median.B.FOMC - fit.B.FOMC.r)/median.B.FOMC), digits=1)) + dev.B.FOMC <- dev.B.FOMC[c(1, 4, 5)] + checkIdentical(dev.B.FOMC < 1, rep(TRUE, length(dev.B.FOMC))) + + # FOCUS_2006_C + fit.C.FOMC <- mkinfit(FOMC, FOCUS_2006_C, quiet=TRUE) + + median.C.FOMC <- as.numeric(lapply(subset(FOCUS_2006_FOMC_ref_A_to_F, dataset == "C", + c(M0, alpha, beta, DT50, DT90)), "median")) + + fit.C.FOMC.r <- as.numeric(c(fit.C.FOMC$parms.all, fit.C.FOMC$distimes)) + dev.C.FOMC <- abs(round(100 * ((median.C.FOMC - fit.C.FOMC.r)/median.C.FOMC), digits=1)) + dev.C.FOMC <- dev.C.FOMC[c(1, 4, 5)] + checkIdentical(dev.C.FOMC < 1, rep(TRUE, length(dev.C.FOMC))) +} # }}} + +# Test DFOP model, tolerance of 1% with the exception of f parameter for A {{{ +test.FOCUS_2006_DFOP <- function() +{ + DFOP <- mkinmod(parent = list(type = "DFOP")) + + # FOCUS_2006_A + fit.A.DFOP <- mkinfit(DFOP, FOCUS_2006_A, quiet=TRUE) + fit.A.DFOP <- mkinfit(DFOP, FOCUS_2006_A, quiet=TRUE, plot=TRUE) + + median.A.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A", + c(M0, k1, k2, f, DT50, DT90)), "median")) + + fit.A.DFOP.r <- as.numeric(c(fit.A.DFOP$parms.all, fit.A.DFOP$distimes)) + dev.A.DFOP <- abs(round(100 * ((median.A.DFOP - fit.A.DFOP.r)/median.A.DFOP), digits=1)) + # about 6.7% deviation for parameter f, the others are < 0.1% + checkIdentical(dev.A.DFOP < c(1, 1, 1, 10, 1, 1), rep(TRUE, length(dev.A.DFOP))) + + # FOCUS_2006_B + fit.B.DFOP <- mkinfit(DFOP, FOCUS_2006_B, quiet=TRUE) + + median.B.DFOP <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", + c(M0, k1, k2, f, DT50, DT90)), "median")) + + fit.B.DFOP.r <- as.numeric(c(fit.B.DFOP$parms.all, fit.B.DFOP$distimes)) + dev.B.DFOP <- abs(round(100 * ((median.B.DFOP - fit.B.DFOP.r)/median.B.DFOP), digits=1)) + # about 0.6% deviation for parameter f, the others are <= 0.1% + checkIdentical(dev.B.DFOP < 1, rep(TRUE, length(dev.B.DFOP))) +} # }}} + +# Test HS model to a relative tolerance of 1% excluding Mathematica values {{{ +# as they are unreliable +test.FOCUS_2006_HS <- function() +{ + HS <- mkinmod(parent = list(type = "HS")) + + # FOCUS_2006_A + fit.A.HS <- mkinfit(HS, FOCUS_2006_A, quiet=TRUE) + + median.A.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "A", + c(M0, k1, k2, tb, DT50, DT90)), "median")) + + fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, fit.A.HS$distimes)) + dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1)) + # about 6.7% deviation for parameter f, the others are < 0.1% + checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS))) + + # FOCUS_2006_B + fit.B.HS <- mkinfit(HS, FOCUS_2006_B, quiet=TRUE) + + median.B.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "B", + c(M0, k1, k2, tb, DT50, DT90)), "median")) + + fit.B.HS.r <- as.numeric(c(fit.B.HS$parms.all, fit.B.HS$distimes)) + dev.B.HS <- abs(round(100 * ((median.B.HS - fit.B.HS.r)/median.B.HS), digits=1)) + # < 10% deviation for M0, k1, DT50 and DT90, others are problematic + dev.B.HS <- dev.B.HS[c(1, 2, 5, 6)] + checkIdentical(dev.B.HS < 10, rep(TRUE, length(dev.B.HS))) + + # FOCUS_2006_C + fit.C.HS <- mkinfit(HS, FOCUS_2006_C, quiet=TRUE) + + median.C.HS <- as.numeric(lapply(subset(FOCUS_2006_HS_ref_A_to_F, dataset == "C", + c(M0, k1, k2, tb, DT50, DT90)), "median")) + + fit.A.HS.r <- as.numeric(c(fit.A.HS$parms.all, fit.A.HS$distimes)) + dev.A.HS <- abs(round(100 * ((median.A.HS - fit.A.HS.r)/median.A.HS), digits=1)) + # deviation <= 0.1% + checkIdentical(dev.A.HS < 1, rep(TRUE, length(dev.A.HS))) +} # }}} + +# Test SFORB model against DFOP solutions to a relative tolerance of 1% # {{{ +test.FOCUS_2006_SFORB <- function() +{ + SFORB <- mkinmod(parent = list(type = "SFORB")) + + # FOCUS_2006_A + fit.A.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_A, quiet=TRUE) + fit.A.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_A, solution_type = "deSolve", quiet=TRUE) + + median.A.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "A", + c(M0, k1, k2, DT50, DT90)), "median")) + + fit.A.SFORB.1.r <- as.numeric(c( + parent_0 = fit.A.SFORB.1$parms.all[[1]], + k1 = fit.A.SFORB.1$SFORB[[1]], + k2 = fit.A.SFORB.1$SFORB[[2]], + fit.A.SFORB.1$distimes)) + dev.A.SFORB.1 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.1.r)/median.A.SFORB), digits=1)) + # The first Eigenvalue is a lot different from k1 in the DFOP fit + # The explanation is that the dataset is simply SFO + dev.A.SFORB.1 <- dev.A.SFORB.1[c(1, 3, 4, 5)] + checkIdentical(dev.A.SFORB.1 < 1, rep(TRUE, length(dev.A.SFORB.1))) + + fit.A.SFORB.2.r <- as.numeric(c( + parent_0 = fit.A.SFORB.2$parms.all[[1]], + k1 = fit.A.SFORB.2$SFORB[[1]], + k2 = fit.A.SFORB.2$SFORB[[2]], + fit.A.SFORB.2$distimes)) + dev.A.SFORB.2 <- abs(round(100 * ((median.A.SFORB - fit.A.SFORB.2.r)/median.A.SFORB), digits=1)) + # The first Eigenvalue is a lot different from k1 in the DFOP fit + # The explanation is that the dataset is simply SFO + dev.A.SFORB.2 <- dev.A.SFORB.2[c(1, 3, 4, 5)] + checkIdentical(dev.A.SFORB.2 < 1, rep(TRUE, length(dev.A.SFORB.2))) + + # FOCUS_2006_B + fit.B.SFORB.1 <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE) + fit.B.SFORB.2 <- mkinfit(SFORB, FOCUS_2006_B, solution_type = "deSolve", quiet=TRUE) + + median.B.SFORB <- as.numeric(lapply(subset(FOCUS_2006_DFOP_ref_A_to_B, dataset == "B", + c(M0, k1, k2, DT50, DT90)), "median")) + + fit.B.SFORB.1.r <- as.numeric(c( + parent_0 = fit.B.SFORB.1$parms.all[[1]], + k1 = fit.B.SFORB.1$SFORB[[1]], + k2 = fit.B.SFORB.1$SFORB[[2]], + fit.B.SFORB.1$distimes)) + dev.B.SFORB.1 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.1.r)/median.B.SFORB), digits=1)) + checkIdentical(dev.B.SFORB.1 < 1, rep(TRUE, length(dev.B.SFORB.1))) + + fit.B.SFORB.2.r <- as.numeric(c( + parent_0 = fit.B.SFORB.2$parms.all[[1]], + k1 = fit.B.SFORB.2$SFORB[[1]], + k2 = fit.B.SFORB.2$SFORB[[2]], + fit.B.SFORB.2$distimes)) + dev.B.SFORB.2 <- abs(round(100 * ((median.B.SFORB - fit.B.SFORB.2.r)/median.B.SFORB), digits=1)) + checkIdentical(dev.B.SFORB.2 < 1, rep(TRUE, length(dev.B.SFORB.2))) +} # }}} + +# Test eigenvalue based fit to Schaefer 2007 data against solution from conference paper {{{ test.mkinfit.schaefer07_complex_example <- function() { schaefer07_complex_model <- mkinmod( - parent = list(type = "SFO", to = c("A1", "B1", "C1")), + parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE), A1 = list(type = "SFO", to = "A2"), B1 = list(type = "SFO"), C1 = list(type = "SFO"), A2 = list(type = "SFO")) -# 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))) -} + fit <- mkinfit(schaefer07_complex_model, + mkin_wide_to_long(schaefer07_complex_case, time = "time")) + s <- summary(fit) + r <- schaefer07_complex_results + attach(as.list(fit$parms.all)) + k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1) + r$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))) +} # }}} +# vim: set foldmethod=marker ts=2 sw=2 expandtab: diff --git a/inst/unitTests/runit.mkinmod.R b/inst/unitTests/runit.mkinmod.R deleted file mode 100644 index 38b07cd5..00000000 --- a/inst/unitTests/runit.mkinmod.R +++ /dev/null @@ -1,134 +0,0 @@ -# $Id: runit.mkinmod.R 64 2010-09-01 13:33:51Z jranke $ - -# Copyright (C) 2010-2012 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 - -test.mkinmod.SFO <- function() -{ - SFO.diffs <- c( - parent = "d_parent = - k_parent * parent" - ) - SFO.parms <- c("k_parent") - SFO.map <- list(parent = c(SFO = "parent")) - SFO.coefmat <- matrix("- k_parent", dimnames = list("parent", "parent")) - SFO <- list(diffs = SFO.diffs, parms = SFO.parms, map = SFO.map, - coefmat = SFO.coefmat) - class(SFO) <- "mkinmod" - SFO.mkinmod <- mkinmod( - parent = list(type = "SFO") - ) - checkIdentical(SFO, SFO.mkinmod) -} - -test.mkinmod.SFORB <- function() -{ - SFORB.diffs <- c( - parent_free = paste( - "d_parent_free = - k_parent_free * parent_free", - "- k_parent_free_bound * parent_free", - "+ k_parent_bound_free * parent_bound"), - parent_bound = paste( - "d_parent_bound =", - "+ k_parent_free_bound * parent_free", - "- k_parent_bound_free * parent_bound") - ) - SFORB.parms <- c("k_parent_free", "k_parent_free_bound", "k_parent_bound_free") - SFORB.map <- list(parent = c(SFORB = "parent_free", SFORB = "parent_bound")) - vars <- paste("parent", c("free", "bound"), sep="_") - SFORB.coefmat <- matrix( - c("- k_parent_free - k_parent_free_bound", "k_parent_bound_free", - "k_parent_free_bound", "- k_parent_bound_free"), nrow=2, byrow=TRUE, - dimnames=list(vars, vars)) - SFORB <- list(diffs = SFORB.diffs, parms = SFORB.parms, - map = SFORB.map, coefmat = SFORB.coefmat) - class(SFORB) <- "mkinmod" - SFORB.mkinmod <- mkinmod( - parent = list(type = "SFORB") - ) - #checkIdentical(SFORB, SFORB.mkinmod) -} - -test.mkinmod.SFO_SFO <- function() -{ - SFO_SFO.diffs <- c( - parent = "d_parent = - k_parent * parent", - m1 = "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1" - ) - SFO_SFO.parms <- c("k_parent", "f_parent_to_m1", "k_m1") - SFO_SFO.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1")) - vars <- c("parent", "m1") - SFO_SFO.coefmat <- matrix(c("- k_parent", - "0", "f_parent_to_m1 * k_parent", "- k_m1"), nrow=2, byrow=TRUE, - dimnames=list(vars, vars)) - SFO_SFO <- list(diffs = SFO_SFO.diffs, parms = SFO_SFO.parms, - map = SFO_SFO.map, coefmat = SFO_SFO.coefmat) - class(SFO_SFO) <- "mkinmod" - SFO_SFO.mkinmod <- mkinmod( - parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO", sink=TRUE) - ) - checkIdentical(SFO_SFO, SFO_SFO.mkinmod) -} - -test.mkinmod.SFO_SFO2 <- function() -{ - SFO_SFO2.diffs <- c( - parent = "d_parent = - k_parent * parent", - m1 = "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1", - m2 = "d_m2 = + f_parent_to_m2 * k_parent * parent - k_m2 * m2" - ) - SFO_SFO2.parms <- c("k_parent", "f_parent_to_m1", "f_parent_to_m2", "k_m1", "k_m2") - SFO_SFO2.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"), m2 = c(SFO = "m2")) - vars <- c("parent", "m1", "m2") - SFO_SFO2.coefmat <- matrix( - c("- k_parent", "0", "0", - "f_parent_to_m1 * k_parent", "- k_m1", "0", - "f_parent_to_m2 * k_parent", "0", "- k_m2"), nrow=3, byrow=TRUE, - dimnames=list(vars, vars)) - SFO_SFO2 <- list(diffs = SFO_SFO2.diffs, parms = SFO_SFO2.parms, - map = SFO_SFO2.map, coefmat = SFO_SFO2.coefmat) - class(SFO_SFO2) <- "mkinmod" - SFO_SFO2.mkinmod <- mkinmod( - parent = list(type = "SFO", to = c("m1", "m2"), sink=TRUE), - m1 = list(type = "SFO", sink=TRUE), - m2 = list(type = "SFO", sink=TRUE) - ) - checkIdentical(SFO_SFO2, SFO_SFO2.mkinmod) -} - -test.mkinmod.FOMC_SFO2 <- function() -{ - FOMC_SFO2.diffs <- c( - parent = "d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent", - m1 = "d_m1 = + f_parent_to_m1 * (alpha/beta) * ((time/beta) + 1)^-1 * parent - k_m1 * m1", - m2 = "d_m2 = + f_parent_to_m2 * (alpha/beta) * ((time/beta) + 1)^-1 * parent - k_m2 * m2" - ) - FOMC_SFO2.parms <- c("alpha", "beta", "f_parent_to_m1", "f_parent_to_m2", "k_m1", "k_m2") - FOMC_SFO2.map <- list(parent = c(FOMC = "parent"), - m1 = c(SFO = "m1"), - m2 = c(SFO = "m2")) - FOMC_SFO2 <- list(diffs = FOMC_SFO2.diffs, parms = FOMC_SFO2.parms, - map = FOMC_SFO2.map) - class(FOMC_SFO2) <- "mkinmod" - FOMC_SFO2.mkinmod <- mkinmod( - parent = list(type = "FOMC", to = c("m1", "m2"), sink=TRUE), - m1 = list(type = "SFO"), - m2 = list(type = "SFO") - ) - checkIdentical(FOMC_SFO2, FOMC_SFO2.mkinmod) -} -- cgit v1.2.1