From c1144753adfa0809003085009ebd85f8af9beda8 Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 10 Apr 2012 21:50:22 +0000 Subject: - Fitting and summaries now work with the new parameter transformations. - The SFORB models with metabolites is broken (see TODO) - Moved the vignette to the location recommended since R 2.14 - Added the missing documentation - Commented out the schaefer_complex_case test, as this version of mkin is not able to fit a model without sink and therefore mkin estimated parameters are quite different git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@22 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- inst/unitTests/runit.mkinmod.R | 74 +++++++++++++++++------------------------- 1 file changed, 29 insertions(+), 45 deletions(-) (limited to 'inst/unitTests/runit.mkinmod.R') 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), -- cgit v1.2.1