diff options
Diffstat (limited to 'R/mkinerrmin.R')
| -rw-r--r-- | R/mkinerrmin.R | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R index 4137d33a..b28235a6 100644 --- a/R/mkinerrmin.R +++ b/R/mkinerrmin.R @@ -36,10 +36,11 @@ mkinerrmin <- function(fit, alpha = 0.05) suffixes = c("_mean", "_pred")) errdata <- errdata[order(errdata$time, errdata$name), ] - # Any value that is set to exactly zero is not really an observed value - # Remove those at time 0 - those are caused by the FOCUS recommendation - # to set metabolites occurring at time 0 to 0 - errdata <- subset(errdata, !(time == 0 & value_mean == 0)) + # Remove values at time zero for variables whose value for state.ini is fixed, + # as these will not have any effect in the optimization and should therefore not + # be counted as degrees of freedom. + fixed_initials = gsub("_0$", "", rownames(subset(fit$fixed, type = "state"))) + errdata <- subset(errdata, !(time == 0 & name %in% fixed_initials)) n.optim.overall <- length(parms.optim) @@ -71,11 +72,12 @@ mkinerrmin <- function(fit, alpha = 0.05) # Formation fractions are attributed to the target variable, so look # for source compartments with formation fractions for (source_var in fit$obs_vars) { + n.ff.source = length(grep(paste("^f", source_var, sep = "_"), + names(parms.optim))) + n.paths.source = length(fit$mkinmod$spec[[source_var]]$to) for (target_var in fit$mkinmod$spec[[source_var]]$to) { if (obs_var == target_var) { - n.ff.optim <- n.ff.optim + - length(grep(paste("^f", source_var, sep = "_"), - names(parms.optim))) + n.ff.optim <- n.ff.optim + n.ff.source/n.paths.source } } } |