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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-12 19:10:32 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-12 19:10:32 +0200
commit36bc31c52cbe4b686f5562e21ee110380481dff8 (patch)
treef872beb978159d6f69b60505030fc1beedc1b747 /man
parent20f235860c3d5a9c6319c516637021e02ecb6cae (diff)
Another documentation update
Diffstat (limited to 'man')
-rw-r--r--man/mkinfit.Rd19
1 files changed, 8 insertions, 11 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 5a2b3e53..b8d44fba 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -94,12 +94,11 @@ differential equations is based on the spectral decomposition of the
coefficient matrix in cases that this is 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 "deSolve" if a compiler is present,
-and "eigen" if no compiler is present and the model can be expressed using
-eigenvalues and eigenvectors. This argument is passed on to the helper
-function \code{\link{mkinpredict}}.}
+implemented for relatively simple degradation models. The default is
+"auto", which uses "analytical" if possible, otherwise "deSolve" if a
+compiler is present, and "eigen" if no compiler is present and the model
+can be expressed using eigenvalues and eigenvectors. This argument is
+passed on to the helper function \code{\link{mkinpredict}}.}
\item{method.ode}{The solution method passed via \code{\link{mkinpredict}}
to \code{\link{ode}} in case the solution type is "deSolve". The default
@@ -154,11 +153,9 @@ the error model. If the error model is "const", unweighted nonlinear
least squares fitting ("OLS") is selected. If the error model is "obs", or
"tc", the "d_3" algorithm is selected.
-The algorithm "d_3" will directly minimize the negative log-likelihood and
-\itemize{
-\item independently - also use the three step algorithm described below. The
-fit with the higher likelihood is returned.
-}
+The algorithm "d_3" will directly minimize the negative log-likelihood
+and independently also use the three step algorithm described below.
+The fit with the higher likelihood is returned.
The algorithm "direct" will directly minimize the negative log-likelihood.

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