- 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

1 files changed, 0 insertions, 134 deletions

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 <http://www.gnu.org/licenses/>

-

-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)

-}