Fix mkinfit for a special situation

See NEWS.md: When the parent was not the (only) variable with the
highest value out of all variables in the observed data, it could
happen that the initial value (state.ini) was not initialised.

3 files changed, 10 insertions, 8 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 3898f69a..e8b7195d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for fitting kinetic models with one or more state
   variables to chemical degradation data
 Version: 0.9-33
-Date: 2014-08-19
+Date: 2014-08-20
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/NEWS.md b/NEWS.md
index a24c31bc..d05c2095 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,6 +8,8 @@
 
 - `mkinfit()`: The internally fitted parameter for `g` was named `g_ilr` even when `transform_fractions=FALSE`
 
+- `mkinfit()`: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.
+
 ## MINOR CHANGES
 
 - The formatting of differential equations in the summary was improved by wrapping overly long lines
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 92c8f8bf..0f488ec8 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -41,11 +41,11 @@ mkinfit <- function(mkinmod, observed,
   trace_parms = FALSE,

   ...)

 {

-  # Check mkinmod and generate a model for the variable whithe the highest value

+  # Check mkinmod and generate a model for the variable whith the highest value

   # if a suitable string is given

   parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB") 

-  presumed_parent_name = observed[which.max(observed$value), "name"]

   if (class(mkinmod) != "mkinmod") {

+    presumed_parent_name = observed[which.max(observed$value), "name"]

     if (mkinmod[[1]] %in% parent_models_available) {

       speclist <- list(list(type = mkinmod, sink = TRUE))

       names(speclist) <- presumed_parent_name

@@ -153,14 +153,14 @@ mkinfit <- function(mkinmod, observed,
   }

 

   # Set default for state.ini if appropriate

+  parent_name = names(mkinmod$spec)[[1]]

   if (state.ini[1] == "auto") {

-    presumed_parent_time_0 = subset(observed, 

-                                    time == 0 & name == presumed_parent_name)$value

-    presumed_parent_time_0_mean = mean(presumed_parent_time_0, na.rm = TRUE)

-    if (is.na(presumed_parent_time_0_mean)) {

+    parent_time_0 = subset(observed, time == 0 & name == parent_name)$value

+    parent_time_0_mean = mean(parent_time_0, na.rm = TRUE)

+    if (is.na(parent_time_0_mean)) {

       state.ini = c(100, rep(0, length(mkinmod$diffs) - 1))

     } else {

-      state.ini = c(presumed_parent_time_0_mean, rep(0, length(mkinmod$diffs) - 1))

+      state.ini = c(parent_time_0_mean, rep(0, length(mkinmod$diffs) - 1))

     }

   }