diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinfit.Rd | 18 | ||||
| -rw-r--r-- | man/transform_odeparms.Rd | 35 |
2 files changed, 44 insertions, 9 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 0c5d76a9..839580a1 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -23,6 +23,8 @@ mkinfit(mkinmod, observed, method.ode = "lsoda", method.modFit = "Marq", control.modFit = list(), + transform_rates = TRUE, + transform_fractions = TRUE, plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, @@ -102,6 +104,22 @@ mkinfit(mkinmod, observed, Additional arguments passed to the optimisation method used by \code{\link{modFit}}. } + \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 + as k1 and k2 rate constants for the DFOP and HS models. + } + \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. + } \item{plot}{ Should the observed values and the numerical solutions be plotted at each stage of the optimisation? diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 999beaaf..e251cf62 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -13,20 +13,37 @@ negative, the \code{\link{ilr}} transformation is used. } \usage{ -transform_odeparms(parms, mod_vars) -backtransform_odeparms(transparms, mod_vars) +transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE) +backtransform_odeparms(transparms, mod_vars, + transform_rates = TRUE, transform_fractions = TRUE) } \arguments{ \item{parms}{ - Parameters of kinetic models as used in the differential equations. -} + Parameters of kinetic models as used in the differential equations. + } \item{transparms}{ - Transformed parameters of kinetic models as used in the fitting procedure. -} + Transformed parameters of kinetic models as used in the fitting procedure. + } \item{mod_vars}{ - Names of the state variables in the kinetic model. These are used for - grouping the formation fractions before \code{\link{ilr}} transformation. -} + Names of the state variables in the kinetic model. These are used for + grouping the formation fractions before \code{\link{ilr}} transformation. + } + \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 + as k1 and k2 rate constants for the DFOP and HS models. + } + \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. + } } \value{ A vector of transformed or backtransformed parameters with the same names |