# $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 <http://www.gnu.org/licenses/>
test.mkinmod.SFO <- function()
{
SFO.diffs <- c(
parent = "d_parent = - k_parent_sink * parent"
)
SFO.parms <- c("k_parent_sink")
SFO.map <- list(parent = c(SFO = "parent"))
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)
)
checkIdentical(SFO, SFO.1)
SFO.2 <- mkinmod(
parent = list(type = "SFO", to = NULL)
)
checkIdentical(SFO, SFO.2)
SFO.3 <- mkinmod(
parent = list(type = "SFO", sink = TRUE)
)
checkIdentical(SFO, SFO.3)
SFO.4 <- mkinmod(
parent = list(type = "SFO")
)
checkIdentical(SFO, SFO.3)
}
test.mkinmod.SFORB <- function()
{
SFORB.diffs <- c(
parent_free = paste(
"d_parent_free = - k_parent_free_sink * 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_sink", "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_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)
)
checkIdentical(SFORB, SFORB.mkinmod)
}
test.mkinmod.SFO_SFO <- function()
{
SFO_SFO.diffs <- c(
parent = "d_parent = - k_parent_sink * parent - k_parent_m1 * parent",
m1 = "d_m1 = - k_m1_sink * m1 + k_parent_m1 * parent"
)
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"))
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),
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_sink * parent - k_parent_m1 * parent - k_parent_m2 * parent",
m1 = "d_m1 = - k_m1_sink * m1 + k_parent_m1 * parent",
m2 = "d_m2 = - k_m2_sink * m2 + k_parent_m2 * parent"
)
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"))
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),
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 = - 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.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),
m1 = list(type = "SFO"),
m2 = list(type = "SFO")
)
checkIdentical(FOMC_SFO2, FOMC_SFO2.mkinmod)
}
