diff options
Diffstat (limited to 'vignettes/FOCUS_Z.Rmd')
| -rw-r--r-- | vignettes/FOCUS_Z.Rmd | 17 |
1 files changed, 9 insertions, 8 deletions
diff --git a/vignettes/FOCUS_Z.Rmd b/vignettes/FOCUS_Z.Rmd index b1ac7d42..951d5eee 100644 --- a/vignettes/FOCUS_Z.Rmd +++ b/vignettes/FOCUS_Z.Rmd @@ -20,6 +20,7 @@ vignette: > ```{r, include = FALSE} require(knitr) +options(digits = 5) opts_chunk$set(engine='R', tidy = FALSE) ``` @@ -64,11 +65,10 @@ summary(m.Z.2a, data = FALSE)$bpar As obvious from the parameter summary (the \texttt{bpar} component of the summary), the kinetic rate constant from parent compound Z to sink -is negligible. Accordingly, the exact magnitude of the fitted parameter -\texttt{log k\_Z0\_sink} is ill-defined and the covariance matrix is not -returned (not shown, would be visible in the complete summary). -This suggests, in agreement with the analysis in the FOCUS kinetics report, to -simplify the model by removing the pathway to sink. +is very small and the t-test for this parameter suggests that it is +not significantly different from zero. This suggests, in agreement with the +analysis in the FOCUS kinetics report, to simplify the model by removing the +pathway to sink. A similar result can be obtained when formation fractions are used in the model formulation: @@ -85,11 +85,12 @@ summary(m.Z.2a.ff, data = FALSE)$bpar Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is -practically unity. Again, the covariance matrix is not returned as the model is +practically unity. Here, the covariance matrix used for the calculation +of confidence intervals is not returned as the model is overparameterised. -The simplified model is obtained by setting the list component \texttt{sink} to -\texttt{FALSE}.\footnote{If the model formulation without formation fractions +A simplified model is obtained by removing the pathway to the sink. +\footnote{If the model formulation without formation fractions is used, the same effect can be obtained by fixing the parameter \texttt{k\_Z\_sink} to a value of zero.} |