- 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

3 files changed, 27 insertions, 2 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index 163dc8d..c9a6a51 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])

diff --git a/R/mkinfit.R b/R/mkinfit.R
index b80be97..cf018f0 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -28,6 +28,8 @@ mkinfit <- function(mkinmod, observed,
   fixed_parms = NULL,

   fixed_initials = names(mkinmod$diffs)[-1],

   solution_type = "auto",

+  method.modFit = "Marq",

+  control.modFit = list(),

   plot = FALSE, quiet = FALSE,

   err = NULL, weight = "none", scaleVar = FALSE,

   atol = 1e-8, rtol = 1e-10, n.outtimes = 100,

@@ -45,6 +47,13 @@ mkinfit <- function(mkinmod, observed,
 

   # Define starting values for parameters where not specified by the user

   if (parms.ini[[1]] == "auto") parms.ini = vector()

+

+  # Prevent inital parameter specifications that are not in the model

+  wrongpar.names <- setdiff(names(parms.ini), mkinmod$parms)

+  if (length(wrongpar.names) > 0) {

+    stop("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "), " not used in the model")

+  }

+

   defaultpar.names <- setdiff(mkinmod$parms, names(parms.ini))

   for (parmname in defaultpar.names) {

     # Default values for rate constants, depending on the parameterisation

@@ -168,7 +177,7 @@ mkinfit <- function(mkinmod, observed,
     }

     return(mC)

   }

-  fit <- modFit(cost, c(state.ini.optim, parms.optim), ...)

+  fit <- modFit(cost, c(state.ini.optim, parms.optim), method = method.modFit, control = control.modFit, ...)

 

   # We need to return some more data for summary and plotting

   fit$solution_type <- solution_type

@@ -203,6 +212,7 @@ mkinfit <- function(mkinmod, observed,
   fit$data <- data[order(data$variable, data$time), ]

   fit$atol <- atol

   fit$rtol <- rtol

+

   # Return all backtransformed parameters for summary

   fit$bparms.optim <- bparms.optim 

   fit$bparms.fixed <- bparms.fixed

@@ -239,7 +249,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
   dimnames(param) <- list(pnames, c("Estimate", "Std. Error", "Lower", "Upper"))

 

   blci <- buci <- numeric()

-  # Only use lower end of CI for one parameter at a time

+  # Only transform boundaries of CI for one parameter at a time

   for (pname in pnames) {

     par.lower <- par.upper <- object$par

     par.lower[pname] <- param[pname, "Lower"]

diff --git a/R/mkinmod.R b/R/mkinmod.R
index adfd9ea..09deea4 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -26,6 +26,7 @@ mkinmod <- function(..., use_of_ff = "min")
   # Check if any of the names of the observed variables contains any other

   for (obs_var in obs_vars) {

     if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other")

+    if (grepl("_to_", obs_var)) stop("Sorry, names of observed variables can not contain _to_")

   }

 

   if (!use_of_ff %in% c("min", "max"))