From 1718d434efae26de02754c6622c43f4dc9e624b9 Mon Sep 17 00:00:00 2001 From: jranke Date: Thu, 15 Mar 2012 15:54:14 +0000 Subject: Update kinfit and mkin to the latest version published on BerliOS. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- inst/unitTests/runit.mkinmod.R | 61 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 54 insertions(+), 7 deletions(-) (limited to 'inst/unitTests/runit.mkinmod.R') diff --git a/inst/unitTests/runit.mkinmod.R b/inst/unitTests/runit.mkinmod.R index 44d9ffb5..a0e89968 100644 --- a/inst/unitTests/runit.mkinmod.R +++ b/inst/unitTests/runit.mkinmod.R @@ -1,3 +1,23 @@ +# $Id: runit.mkinmod.R 64 2010-09-01 13:33:51Z jranke $ + +# Copyright (C) 2010 Johannes Ranke +# Contact: mkin-devel@lists.berlios.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( @@ -5,7 +25,9 @@ test.mkinmod.SFO <- function() ) SFO.parms <- c("k_parent_sink") SFO.map <- list(parent = c(SFO = "parent")) - SFO <- list(diffs = SFO.diffs, parms = SFO.parms, map = SFO.map) + SFO.coefmat <- matrix("- k_parent_sink", dimnames = list("parent", "parent")) + SFO <- list(diffs = SFO.diffs, parms = SFO.parms, map = SFO.map, + coefmat = SFO.coefmat) class(SFO) <- "mkinmod" SFO.1 <- mkinmod( parent = list(type = "SFO", to = NULL, sink = TRUE) @@ -39,7 +61,13 @@ test.mkinmod.SFORB <- function() ) SFORB.parms <- c("k_parent_free_sink", "k_parent_free_bound", "k_parent_bound_free") SFORB.map <- list(parent = c(SFORB = "parent_free", SFORB = "parent_bound")) - SFORB <- list(diffs = SFORB.diffs, parms = SFORB.parms, map = SFORB.map) + vars <- paste("parent", c("free", "bound"), sep="_") + SFORB.coefmat <- matrix( + c("- k_parent_free_sink - 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", to = NULL, sink=TRUE) @@ -55,7 +83,12 @@ test.mkinmod.SFO_SFO <- function() ) SFO_SFO.parms <- c("k_parent_sink", "k_m1_sink", "k_parent_m1") SFO_SFO.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1")) - SFO_SFO <- list(diffs = SFO_SFO.diffs, parms = SFO_SFO.parms, map = SFO_SFO.map) + vars <- c("parent", "m1") + SFO_SFO.coefmat <- matrix(c("- k_parent_sink - k_parent_m1", + "0", "k_parent_m1", "- k_m1_sink"), 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", sink=TRUE), @@ -73,7 +106,14 @@ test.mkinmod.SFO_SFO2 <- function() ) SFO_SFO2.parms <- c("k_parent_sink", "k_m1_sink", "k_m2_sink", "k_parent_m1", "k_parent_m2") SFO_SFO2.map <- list(parent = c(SFO = "parent"), m1 = c(SFO = "m1"), m2 = c(SFO = "m2")) - SFO_SFO2 <- list(diffs = SFO_SFO2.diffs, parms = SFO_SFO2.parms, map = SFO_SFO2.map) + vars <- c("parent", "m1", "m2") + SFO_SFO2.coefmat <- matrix( + c("- k_parent_sink - k_parent_m1 - k_parent_m2", "0", "0", + "k_parent_m1", "- k_m1_sink", "0", + "k_parent_m2", "0", "- k_m2_sink"), 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), @@ -90,9 +130,16 @@ test.mkinmod.FOMC_SFO2 <- function() m1 = "d_m1 = - k_m1_sink * m1 + f_to_m1 * (alpha/beta) * ((time/beta) + 1)^-1 * parent", m2 = "d_m2 = - k_m2_sink * m2 + (1 - f_to_m1) * f_to_m2 * (alpha/beta) * ((time/beta) + 1)^-1 * parent" ) - FOMC_SFO2.parms <- c("alpha", "beta", "k_m1_sink", "k_m2_sink", "f_to_m1", "f_to_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) + FOMC_SFO2.parms <- c("alpha", "beta", "k_m1_sink", "k_m2_sink", + "f_to_m1", "f_to_m2") + FOMC_SFO2.map <- list(parent = c(FOMC = "parent"), + m1 = c(SFO = "m1"), + m2 = c(SFO = "m2")) + FOMC_SFO2.ff <- c( + m1 = "f_to_m1", + m2 = "(1 - f_to_m1) * f_to_m2") + FOMC_SFO2 <- list(diffs = FOMC_SFO2.diffs, parms = FOMC_SFO2.parms, + map = FOMC_SFO2.map, ff = FOMC_SFO2.ff) class(FOMC_SFO2) <- "mkinmod" FOMC_SFO2.mkinmod <- mkinmod( parent = list(type = "FOMC", to = c("m1", "m2"), sink=TRUE), -- cgit v1.2.1