- Update the TODO list, setting some requirements for version 1.0

- Check that initial values specified using parms.ini are actually needed for the model, stop otherwise
- List all formation fractions in the same place in the summary, also if they were fitted in the model
- Include an FOMC model coupled to two metabolites in the unit tests
- Some updates needed because of the above
- Update of static documentation including the vignettes
- Update of the mkin vignettes in the vignettes directory



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@82 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 8 insertions, 31 deletions

diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
index 784054b..278560d 100644
--- a/inst/unitTests/runit.mkinfit.R
+++ b/inst/unitTests/runit.mkinfit.R
@@ -295,42 +295,19 @@ test.mkinfit.schaefer07_complex_example <- function()
   checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))

 } # }}}

 

-# Test deSolve based fit to Schaefer 2007 data against solution from conference paper {{{

-test.mkinfit.schaefer07_complex_example <- function()

+# Test deSolve based fit to Schaefer 2007 using FOMC for parent (eigenvalue based solution not possible)

+# and skipping B1 because of its high scatter {{{

+test.mkinfit.schaefer07_complex_example_2 <- function()

 {

-  schaefer07_complex_model <- mkinmod(

-    parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),

+  schaefer07_complex_model_2 <- mkinmod(

+    parent = list(type = "FOMC", to = c("A1", "C1")),

     A1 = list(type = "SFO", to = "A2"),

-    B1 = list(type = "SFO"),

     C1 = list(type = "SFO"),

     A2 = list(type = "SFO"))

   

-  # Works fine with n.outtimes = 1000 but takes too much time

-  #   fit <- mkinfit(schaefer07_complex_model, 

-  #     mkin_wide_to_long(schaefer07_complex_case, time = "time"), 

-  #     n.outtimes = 1000, solution_type = "deSolve")

-  #   s <- summary(fit)

-  #   r <- schaefer07_complex_results

-  #   attach(as.list(fit$parms.all))

-  #   k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1)

-  #   r$mkin <- c(

-  #     k_parent,

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

-  #     s$ff["parent_A1"],

-  #     sum(k_A1_sink, k_A1_A2),

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

-  #     s$ff["parent_B1"],

-  #     k_B1_sink,

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

-  #     s$ff["parent_C1"],

-  #     k_C1_sink,

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

-  #     s$ff["A1_A2"],

-  #     k_A2_sink,

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

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

-  #   r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))

-  #   checkIdentical(r$mkin.deviation < 10, rep(TRUE, length(r$mkin.deviation)))

+   fit <- mkinfit(schaefer07_complex_model_2, 

+     mkin_wide_to_long(schaefer07_complex_case, time = "time"))

+   checkTrue(fit$ssr < 122)

 } # }}}

 

 # vim: set foldmethod=marker ts=2 sw=2 expandtab: