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-rw-r--r--inst/unitTests/runit.mkinmod.R74
1 files changed, 29 insertions, 45 deletions
diff --git a/inst/unitTests/runit.mkinmod.R b/inst/unitTests/runit.mkinmod.R
index a0e89968..38b07cd5 100644
--- a/inst/unitTests/runit.mkinmod.R
+++ b/inst/unitTests/runit.mkinmod.R
@@ -1,7 +1,7 @@
# $Id: runit.mkinmod.R 64 2010-09-01 13:33:51Z jranke $
-# Copyright (C) 2010 Johannes Ranke
-# Contact: mkin-devel@lists.berlios.de
+# Copyright (C) 2010-2012 Johannes Ranke
+# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -21,37 +21,25 @@
test.mkinmod.SFO <- function()
{
SFO.diffs <- c(
- parent = "d_parent = - k_parent_sink * parent"
+ parent = "d_parent = - k_parent * parent"
)
- SFO.parms <- c("k_parent_sink")
+ SFO.parms <- c("k_parent")
SFO.map <- list(parent = c(SFO = "parent"))
- SFO.coefmat <- matrix("- k_parent_sink", dimnames = list("parent", "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.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(
+ SFO.mkinmod <- mkinmod(
parent = list(type = "SFO")
)
- checkIdentical(SFO, SFO.3)
+ checkIdentical(SFO, SFO.mkinmod)
}
test.mkinmod.SFORB <- function()
{
SFORB.diffs <- c(
parent_free = paste(
- "d_parent_free = - k_parent_free_sink * parent_free",
+ "d_parent_free = - k_parent_free * parent_free",
"- k_parent_free_bound * parent_free",
"+ k_parent_bound_free * parent_bound"),
parent_bound = paste(
@@ -59,39 +47,39 @@ test.mkinmod.SFORB <- function()
"+ 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.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_sink - k_parent_free_bound", "k_parent_bound_free",
+ 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", to = NULL, sink=TRUE)
+ parent = list(type = "SFORB")
)
- checkIdentical(SFORB, SFORB.mkinmod)
+ #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"
+ 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_sink", "k_m1_sink", "k_parent_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_sink - k_parent_m1",
- "0", "k_parent_m1", "- k_m1_sink"), nrow=2, byrow=TRUE,
+ 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", sink=TRUE),
+ parent = list(type = "SFO", to = "m1"),
m1 = list(type = "SFO", sink=TRUE)
)
checkIdentical(SFO_SFO, SFO_SFO.mkinmod)
@@ -100,17 +88,17 @@ test.mkinmod.SFO_SFO <- function()
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"
+ 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_sink", "k_m1_sink", "k_m2_sink", "k_parent_m1", "k_parent_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_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,
+ 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)
@@ -127,19 +115,15 @@ 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"
+ 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", "k_m1_sink", "k_m2_sink",
- "f_to_m1", "f_to_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.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)
+ map = FOMC_SFO2.map)
class(FOMC_SFO2) <- "mkinmod"
FOMC_SFO2.mkinmod <- mkinmod(
parent = list(type = "FOMC", to = c("m1", "m2"), sink=TRUE),

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