diff options
Diffstat (limited to 'man/transform_odeparms.Rd')
| -rw-r--r-- | man/transform_odeparms.Rd | 20 |
1 files changed, 10 insertions, 10 deletions
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index c6034424..71c179d7 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -5,7 +5,7 @@ Functions to transform and backtransform kinetic parameters for fitting } \description{ - The transformations are intended to map parameters that should only take + The transformations are intended to map parameters that should only take on restricted values to the full scale of real numbers. For kinetic rate constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as @@ -17,9 +17,9 @@ This is no problem for the internal use in \code{\link{mkinfit}}. } \usage{ -transform_odeparms(parms, mkinmod, +transform_odeparms(parms, mkinmod, transform_rates = TRUE, transform_fractions = TRUE) -backtransform_odeparms(transparms, mkinmod, +backtransform_odeparms(transparms, mkinmod, transform_rates = TRUE, transform_fractions = TRUE) } \arguments{ @@ -32,22 +32,22 @@ backtransform_odeparms(transparms, mkinmod, \item{mkinmod}{ The kinetic model of class \code{\link{mkinmod}}, containing the names of the model variables that are needed for grouping the formation fractions - before \code{\link{ilr}} transformation, the parameter names and - the information if the pathway to sink is included in the model. + before \code{\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 be transformed in the model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. If TRUE, also - alpha and beta parameters of the FOMC model are log-transformed, as well + assumption of normal distribution of the estimator. If TRUE, also + alpha and beta parameters of the FOMC model are log-transformed, as well as k1 and k2 rate constants for the DFOP and HS 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 + 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. @@ -70,7 +70,7 @@ summary(fit, data=FALSE) # See transformed and backtransformed parameters \dontrun{ fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE) -summary(fit.2, data=FALSE) +summary(fit.2, data=FALSE) } initials <- fit$start$value |