Set implicit formation fraction to 1 even if set otherwise in parms.ini

1 files changed, 8 insertions, 6 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index ae30be43..8ad91981 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -110,6 +110,14 @@ mkinfit <- function(mkinmod, observed,
   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)) warning("Setting ", f_names, " to 1")

+        parms.ini[f_names] = 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])

@@ -119,13 +127,7 @@ mkinfit <- function(mkinmod, observed,
       }

       if (mkinmod$spec[[box]]$sink) n_unspecified = length(f_default_names) + 1

       else {

-        # When we have no sink and only one pathway, we get an implicitly

-        # fixed parameter which we need in the model

         n_unspecified = length(f_default_names)

-        if (length(f_names) == 1) {

-          f_fixed_implicit[f_names] = 1

-          fixed_parms = c(fixed_parms, f_names)

-        }

       }

       parms.ini[f_default_names] <- (1 - sum_f_specified) / n_unspecified

     }