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.

transform_odeparms(parms, mkinmod, +

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 + + + + + + + + + + + + + + + + + + + + + + +

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` transformation, the parameter names and - the information if the pathway to sink is included in the model. - - transform_rates - - Boolean specifying if kinetic rate constants should be transformed in the + the information if the pathway to sink is included in the model.
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 and the break point tb - of the HS model. - - transform_fractions - - Boolean specifying if formation fractions constants should be transformed in the + of the HS model.
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 `ilr` - transformation. - - + transformation.

Value

@@ -162,10 +170,10 @@ parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"))

#> Successfully compiled differential equation model from auto-generated C code.

# Fit the model to the FOCUS example dataset D using defaults fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) -summary(fit, data=FALSE) # See transformed and backtransformed parameters

#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:57:59 2016 -#> Date of summary: Thu Dec 8 07:57:59 2016 +summary(fit, data=FALSE) # See transformed and backtransformed parameters

#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:24 2017 +#> Date of summary: Fri May 5 12:46:24 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -173,7 +181,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.621 s +#> Fitted with method Port using 153 model solutions performed in 0.61 s #> #> Weighting: none #> @@ -207,7 +215,7 @@ #> parent_0 1.00000 0.6075 -0.06625 -0.1701 #> log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 #> log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 -#> log_k_m1_sink -0.17006 -0.6253 0.47163 1.0000 +#> log_k_m1_sink -0.17006 -0.6253 0.47164 1.0000 #> #> Residual standard error: 3.211 on 36 degrees of freedom #> @@ -239,10 +247,10 @@ #> m1 131.761 437.70

fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) -summary(fit.2, data=FALSE)

#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:58:01 2016 -#> Date of summary: Thu Dec 8 07:58:01 2016 +summary(fit.2, data=FALSE)

#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:26 2017 +#> Date of summary: Fri May 5 12:46:26 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -250,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 327 model solutions performed in 1.419 s +#> Fitted with method Port using 352 model solutions performed in 1.437 s #> #> Weighting: none #> @@ -329,10 +337,10 @@ m1 = list(type = "SFO"), use_of_ff = "max")

#> Successfully compiled differential equation model from auto-generated C code.

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

#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:58:02 2016 -#> Date of summary: Thu Dec 8 07:58:02 2016 +summary(fit.ff, data = FALSE)

#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:27 2017 +#> Date of summary: Fri May 5 12:46:27 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -340,7 +348,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.814 s +#> Fitted with method Port using 185 model solutions performed in 0.776 s #> #> Weighting: none #> @@ -413,10 +421,10 @@ use_of_ff = "max")

#> Successfully compiled differential equation model from auto-generated C code.

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

#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:58:03 2016 -#> Date of summary: Thu Dec 8 07:58:03 2016 +summary(fit.ff.2, data = FALSE)

#> mkin version: 0.9.45.2 +#> R version: 3.4.0 +#> Date of fit: Fri May 5 12:46:28 2017 +#> Date of summary: Fri May 5 12:46:28 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -424,7 +432,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.436 s +#> Fitted with method Port using 104 model solutions performed in 0.433 s #> #> Weighting: none #> @@ -463,7 +471,7 @@ #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper -#> parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> parent_0 84.79000 28.600 3.938e-27 78.78000 90.80000 #> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 #> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 #> -- cgit v1.2.1