mkin (version 0.9-31)

transform_odeparms: Functions to transform and backtransform kinetic parameters for fitting

Description

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 the formations fractions that should always sum up to 1 and can not be negative, the ilr transformation is used.

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 mkinfit.

Usage

transform_odeparms(parms, mkinmod, 
                   transform_rates = TRUE, transform_fractions = TRUE)
backtransform_odeparms(transparms, mkinmod, 
                       transform_rates = TRUE, transform_fractions = TRUE)

Arguments

parms

Parameters of kinetic models as used in the differential equations.

transparms

Transformed parameters of kinetic models as used in the fitting procedure.

mkinmod

The kinetic model of class mkinmod, containing the names of the model variables that are needed for grouping the formation fractions before ilr transform

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 th

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 transforma

Value

• A vector of transformed or backtransformed parameters with the same names as the original parameters.

Examples

SFO_SFO <- mkinmod(
  parent = list(type = "SFO", to = "m1", sink = TRUE),
  m1 = list(type = "SFO"))
# Fit the model to the FOCUS example dataset D using defaults
fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)
summary(fit, data=FALSE) # See transformed and backtransformed parameters
summary(fit.2, data=FALSE) 
initials <- fit$start$value
names(initials) <- rownames(fit$start)
transformed <- fit$start_transformed$value
names(transformed) <- rownames(fit$start_transformed)
transform_odeparms(initials, SFO_SFO)
backtransform_odeparms(transformed, SFO_SFO)

# The case of formation fractions
SFO_SFO.ff <- mkinmod(
  parent = list(type = "SFO", to = "m1", sink = TRUE),
  m1 = list(type = "SFO"),
  use_of_ff = "max")

fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)
summary(fit.ff, data = FALSE)
initials <- c("f_parent_to_m1" = 0.5)
transformed <- transform_odeparms(initials, SFO_SFO.ff)
backtransform_odeparms(transformed, SFO_SFO.ff)

# And without sink
SFO_SFO.ff.2 <- mkinmod(
  parent = list(type = "SFO", to = "m1", sink = FALSE),
  m1 = list(type = "SFO"),
  use_of_ff = "max")


fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)
summary(fit.ff.2, data = FALSE)