From af2e1540cdad2fd00bb6216a38a754ff748629ad Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Oct 2019 02:10:08 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/transform_odeparms.html | 119 ++++++++++++++++++--------------- 1 file changed, 64 insertions(+), 55 deletions(-) (limited to 'docs/reference/transform_odeparms.html') diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index b1a952d9..4d88a03e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -8,11 +8,13 @@ Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin + + @@ -32,21 +34,19 @@ - - + + + @@ -117,7 +117,6 @@ The transformation of sets of formation fractions is fragile, as it supposes News - @@ -139,71 +138,80 @@ The transformation of sets of formation fractions is fragile, as it supposes
- -

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.

- +

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.

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

Parameters of kinetic models as used in the differential +equations.
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.

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 - 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.

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 - 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.

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.

transparms

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

Value

-

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

+

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

+

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 mkinfit.

+

Functions

+ +

Examples

- 
SFO_SFO <- mkinmod(
+    

+SFO_SFO <- mkinmod(
   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)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
@@ -278,15 +286,16 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> k_parent   0.0635    0.00521   12.19 2.91e-14  0.0538  0.075
 #> k_m1       0.0148    0.00182    8.13 8.81e-10  0.0115  0.019
 #> sigma      8.2229    0.94323    8.72 1.73e-10  6.3060 10.140
# }
+