- 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, 14 insertions, 0 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index 163dc8d4..c9a6a51f 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -11,6 +11,20 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
   ep$SFORB <- vector()

   for (obs_var in obs_vars) {

     type = names(fit$mkinmod$map[[obs_var]])[1]  

+

+    # Get formation fractions if directly fitted, and calculate remaining fraction to sink

+    f_names = grep(paste("f", obs_var, sep = "_"), names(parms.all), value=TRUE)

+    f_values = parms.all[f_names]

+    f_to_sink = 1 - sum(f_values)

+    names(f_to_sink) = ifelse(type == "SFORB", 

+                            paste(obs_var, "free", "sink", sep = "_"), 

+                            paste(obs_var, "sink", sep = "_"))

+    for (f_name in f_names) {

+      ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]

+    }

+    ep$ff = append(ep$ff, f_to_sink)

+

+    # Get the rest

     if (type == "SFO") {

       k_names = grep(paste("k", obs_var, sep="_"), names(parms.all), value=TRUE)

       k_tot = sum(parms.all[k_names])