diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2014-07-02 18:38:39 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2014-07-02 18:38:39 +0200 |
| commit | 9728f72ac3fde73051c85b124d14fdc6406e6cfb (patch) | |
| tree | 83ba06976c2b144e96784eab7a9140468c95e90e /R/mkinfit.R | |
| parent | a75c5f01d346cd7e2bbb3f01a98bc16bdca972e5 (diff) | |
Do not introduce formation fractions for singular pathways
- As a consequence, we do not need implicit formation fractions in
mkinfit
Diffstat (limited to 'R/mkinfit.R')
| -rw-r--r-- | R/mkinfit.R | 39 |
1 files changed, 16 insertions, 23 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 0e643ac7..b7ca1d74 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -106,32 +106,25 @@ mkinfit <- function(mkinmod, observed, if (parmname == "g") parms.ini[parmname] = 0.5
}
# Default values for formation fractions in case they are used
- f_fixed_implicit = numeric(0)
if (mkinmod$use_of_ff == "max") {
for (box in mod_vars) {
f_names <- mkinmod$parms[grep(paste0("^f_", box), mkinmod$parms)]
- # When we have no sink and only one pathway, we get an implicitly
- # fixed parameter which we need in the model
- if (!mkinmod$spec[[box]]$sink && length(f_names) == 1) {
- if (f_names %in% names(parms.ini) && parms.ini[f_names] != 1) {
- message("Setting ", f_names, " to 1")
- parms.ini[f_names] = 1
+ if (length(f_names) > 0) {
+ # We need to differentiate between default and specified fractions
+ # and set the unspecified to 1 - sum(specified)/n_unspecified
+ f_default_names <- intersect(f_names, defaultpar.names)
+ f_specified_names <- setdiff(f_names, defaultpar.names)
+ sum_f_specified = sum(parms.ini[f_specified_names])
+ if (sum_f_specified > 1) {
+ stop("Starting values for the formation fractions originating from ",
+ box, " sum up to more than 1.")
}
- defaultpar.names <- setdiff(defaultpar.names, f_names)
- f_fixed_implicit[f_names] = 1
- }
- f_default_names <- intersect(f_names, defaultpar.names)
- f_specified_names <- setdiff(f_names, defaultpar.names)
- sum_f_specified = sum(parms.ini[f_specified_names])
- if (sum_f_specified > 1) {
- stop("Starting values for the formation fractions originating from ",
- box, " sum up to more than 1.")
- }
- if (mkinmod$spec[[box]]$sink) n_unspecified = length(f_default_names) + 1
- else {
- n_unspecified = length(f_default_names)
+ if (mkinmod$spec[[box]]$sink) n_unspecified = length(f_default_names) + 1
+ else {
+ n_unspecified = length(f_default_names)
+ }
+ parms.ini[f_default_names] <- (1 - sum_f_specified) / n_unspecified
}
- parms.ini[f_default_names] <- (1 - sum_f_specified) / n_unspecified
}
}
@@ -226,7 +219,7 @@ mkinfit <- function(mkinmod, observed, transform_fractions = transform_fractions)
# Solve the system with current transformed parameter values
- out <- mkinpredict(mkinmod, c(parms, f_fixed_implicit),
+ out <- mkinpredict(mkinmod, parms,
odeini, outtimes,
solution_type = solution_type,
method.ode = method.ode,
@@ -245,7 +238,7 @@ mkinfit <- function(mkinmod, observed, if(plot) {
outtimes_plot = seq(min(observed$time), max(observed$time), length.out=100)
- out_plot <- mkinpredict(mkinmod, c(parms, f_fixed_implicit),
+ out_plot <- mkinpredict(mkinmod, parms,
odeini, outtimes_plot,
solution_type = solution_type,
method.ode = method.ode,
|