diff options
Diffstat (limited to 'man/transform_odeparms.Rd')
| -rw-r--r-- | man/transform_odeparms.Rd | 19 |
1 files changed, 11 insertions, 8 deletions
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 710b0875..f38bb051 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -23,9 +23,9 @@ backtransform_odeparms( \item{parms}{Parameters of kinetic models as used in the differential equations.} -\item{mkinmod}{The kinetic model of class \code{\link{mkinmod}}, containing +\item{mkinmod}{The kinetic model of class \link{mkinmod}, containing the names of the model variables that are needed for grouping the -formation fractions before \code{\link{ilr}} transformation, the parameter +formation fractions before \link{ilr} transformation, the parameter names and the information if the pathway to sink is included in the model.} \item{transform_rates}{Boolean specifying if kinetic rate constants should @@ -38,10 +38,13 @@ models and the break point tb of the HS model.} \item{transform_fractions}{Boolean specifying if formation fractions constants should be transformed in the model specification used in the fitting for better compliance with the assumption of normal distribution -of the estimator. The default (TRUE) is to do transformations. The g -parameter of the DFOP and HS models are also transformed, as they can also -be seen as compositional data. The transformation used for these -transformations is the \code{\link{ilr}} transformation.} +of the estimator. The default (TRUE) is to do transformations. +The g parameter of the DFOP model is also seen as a fraction. +If a single fraction is transformed (g parameter of DFOP or only a single +target variable e.g. a single metabolite plus a pathway to sink), a +logistic transformation is used \code{\link[stats:Logistic]{stats::qlogis()}}. In other cases, i.e. if +two or more formation fractions need to be transformed whose sum cannot +exceed one, the \link{ilr} transformation is used.} \item{transparms}{Transformed parameters of kinetic models as used in the fitting procedure.} @@ -55,12 +58,12 @@ restricted values to the full scale of real numbers. For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, -the \code{\link{ilr}} transformation is used. +the \link{ilr} transformation is used. } \details{ The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. -This is no problem for the internal use in \code{\link{mkinfit}}. +This is no problem for the internal use in \link{mkinfit}. } \examples{ |