aboutsummaryrefslogtreecommitdiff
path: root/man/mkinfit.Rd
diff options
context:
space:
mode:
Diffstat (limited to 'man/mkinfit.Rd')
-rw-r--r--man/mkinfit.Rd23
1 files changed, 17 insertions, 6 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 17e0a112..0c8e48f1 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -14,10 +14,10 @@ mkinfit(mkinmod, observed,
parms.ini = "auto",
state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)),
fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1],
- eigen = FALSE,
+ solution_type = "auto",
plot = FALSE, quiet = FALSE, err = NULL, weight = "none",
scaleVar = FALSE,
- atol = 1e-6, ...)
+ atol = 1e-6, n.outtimes, ...)
}
\arguments{
\item{mkinmod}{
@@ -53,11 +53,16 @@ mkinfit(mkinmod, observed,
The names of model variables for which the initial state at time 0 should be excluded
from the optimisation. Defaults to all state variables except for the first one.
}
- \item{eigen}{
- Should the solution of the system of differential equations be based on the
+ \item{solution_type}{
+ If set to "eigen", the solution of the system of differential equations is based on the
spectral decomposition of the coefficient matrix in cases that this is
- possible? Be aware that the results may differ from the results returned using
- the ode solver.
+ possible. If set to "deSolve", a numerical ode solver from package
+ \code{\link{deSolve}} is used. If set to "analytical", an analytical solution
+ of the model is used. This is only implemented for simple degradation experiments
+ with only one state variable, i.e. with no metabolites. The default is "auto",
+ which uses "analytical" if possible, otherwise "eigen" if the model can be expressed
+ using eigenvalues and eigenvectors, and finally "deSolve" for the remaining
+ models (time dependence of degradation rates and metabolites).
}
\item{plot}{
Should the observed values and the numerical solutions be plotted at each stage
@@ -81,6 +86,12 @@ mkinfit(mkinmod, observed,
Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-6 as in
\code{\link{lsoda}}.
}
+ \item{n.outtimes}{
+ The length of the dataseries that is produced by the model prediction
+ function \code{\link{mkinpredict}}. This impacts the accuracy of
+ the numerical solver if that is used (see \code{solution} argument.
+ The default value is 100.
+ }
\item{\dots}{
Further arguments that will be passed to \code{\link{modFit}}.
}

Contact - Imprint