Bugfix release version 0.9-31

2 files changed, 37 insertions, 28 deletions

diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R
index 671bcaab..9ebac6a4 100644
--- a/R/mkinerrmin.R
+++ b/R/mkinerrmin.R
@@ -48,6 +48,7 @@ mkinerrmin <- function(fit, alpha = 0.05)
     n.optim = errmin.overall$n.optim, df = errmin.overall$df)

   rownames(errmin) <- "All data"

 

+  # The degrees of freedom are counted according to FOCUS kinetics (2011, p. 164)

   for (obs_var in fit$obs_vars)

   {

     errdata.var <- subset(errdata, name == obs_var)

@@ -57,21 +58,31 @@ mkinerrmin <- function(fit, alpha = 0.05)
 

     # Rate constants are attributed to the source variable

     n.k.optim <- length(grep(paste("^k", obs_var, sep="_"), names(parms.optim)))

-

-    # Formation fractions are attributed to the target variable

-    n.ff.optim <- length(grep(paste("^f", ".*", obs_var, "$", sep=""), names(parms.optim)))

+    n.k.optim <- n.k.optim + length(grep(paste("^log_k", obs_var, sep="_"), 

+                                         names(parms.optim)))

+

+    n.ff.optim <- 0

+    # Formation fractions are attributed to the target variable, so look

+    # for source compartments with formation fractions

+    for (source_var in fit$obs_vars) {

+      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.optim <- n.k.optim + n.initials.optim + n.ff.optim

 

     # FOMC, DFOP and HS parameters are only counted if we are looking at the

     # first variable in the model which is always the source variable

     if (obs_var == fit$obs_vars[[1]]) {

-      if ("alpha" %in% names(parms.optim)) n.optim <- n.optim + 1

-      if ("beta" %in% names(parms.optim)) n.optim <- n.optim + 1

-      if ("k1" %in% names(parms.optim)) n.optim <- n.optim + 1

-      if ("k2" %in% names(parms.optim)) n.optim <- n.optim + 1

-      if ("g" %in% names(parms.optim)) n.optim <- n.optim + 1

-      if ("tb" %in% names(parms.optim)) n.optim <- n.optim + 1

+      special_parms = c("alpha", "log_alpha", "beta", "log_beta", 

+                        "k1", "log_k1", "k2", "log_k2", 

+                        "g", "g_ilr", "tb", "log_tb")

+      n.optim <- n.optim + length(intersect(special_parms, names(parms.optim)))

     }

 

     # Calculate and add a line to the results

diff --git a/R/mkinfit.R b/R/mkinfit.R
index b7ca1d74..c6e13b97 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -105,26 +105,24 @@ mkinfit <- function(mkinmod, observed,
     if (parmname == "tb") parms.ini[parmname] = 5

     if (parmname == "g") parms.ini[parmname] = 0.5

   }

-  # Default values for formation fractions in case they are used

-  if (mkinmod$use_of_ff == "max") {

-    for (box in mod_vars) {

-      f_names <- mkinmod$parms[grep(paste0("^f_", box), mkinmod$parms)]

-      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.")

-        }

-        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

+  # Default values for formation fractions in case they are present

+  for (box in mod_vars) {

+    f_names <- mkinmod$parms[grep(paste0("^f_", box), mkinmod$parms)]

+    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.")

+      }

+      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

     }

   }