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

2 files changed, 78 insertions, 11 deletions

diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index df09cc64..831c0698 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -1,3 +1,23 @@
+# $Id: runit.mkinfit.R 68 2010-09-09 22:40:04Z 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.schaefer07_complex_example <- function()

 {

   schaefer07_complex_model <- mkinmod(

@@ -17,16 +37,16 @@ test.mkinmod.schaefer07_complex_example <- function()
   r$mkin <- c(

     k_parent,

     s$distimes["parent", "DT50"],

-    k_parent_A1/k_parent,

+    s$ff["parent_A1"],

     sum(k_A1_sink, k_A1_A2),

     s$distimes["A1", "DT50"],

-    k_parent_B1/k_parent,

+    s$ff["parent_B1"],

     k_B1_sink,

     s$distimes["B1", "DT50"],

-    k_parent_C1/k_parent,

+    s$ff["parent_C1"],

     k_C1_sink,

     s$distimes["C1", "DT50"],

-    k_A1_A2/(k_A1_A2 + k_A1_sink),

+    s$ff["A1_A2"],

     k_A2_sink,

     s$distimes["A2", "DT50"])

   r$means <- (r$KinGUI + r$ModelMaker)/2

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

+

 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),