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/mkinmod.html | 135 ++++++++++++++++++++++---------------------- 1 file changed, 66 insertions(+), 69 deletions(-) (limited to 'docs/reference/mkinmod.html') diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f592af1c..2eefdc2e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -8,11 +8,13 @@ Function to set up a kinetic model with one or more state variables — mkinmod • mkin + + @@ -32,18 +34,17 @@ - - + + + @@ -114,7 +115,6 @@ For the definition of model types and their parameters, the equations given News - @@ -136,49 +136,47 @@ For the definition of model types and their parameters, the equations given
- -

The function usually takes several expressions, each assigning a compound name to - a list, specifying the kinetic model type and reaction or transfer to other - observed compartments. Instead of specifying several expressions, a list - of lists can be given in the speclist argument.

-

For the definition of model types and their parameters, the equations given - in the FOCUS and NAFTA guidance documents are used.

- +

The function usually takes several expressions, each assigning a compound +name to a list, specifying the kinetic model type and reaction or transfer +to other observed compartments. Instead of specifying several expressions, a +list of lists can be given in the speclist argument.

- 
mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
- + 
mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
+  verbose = FALSE)
+

Arguments

- + - + - + @@ -186,44 +184,46 @@ For the definition of model types and their parameters, the equations given - +
...

For each observed variable, a list has to be specified as an argument, containing - at least a component type, specifying the type of kinetics to use - for the variable. Currently, single first order kinetics "SFO", - indeterminate order rate equation kinetics "IORE", or - single first order with reversible binding "SFORB" are implemented for all - variables, while - "FOMC", "DFOP" and "HS" can additionally be chosen for the first - variable which is assumed to be the source compartment. - Additionally, each component of the list can include a character vector to, - specifying names of variables to which a transfer is to be assumed in the - model. - If the argument use_of_ff is set to "min" (default) and the model for - the compartment is "SFO" or "SFORB", an additional component of the list - can be "sink=FALSE" effectively fixing the flux to sink to zero.

For each observed variable, a list has to be specified as an +argument, containing at least a component type, specifying the type +of kinetics to use for the variable. Currently, single first order +kinetics "SFO", indeterminate order rate equation kinetics "IORE", or +single first order with reversible binding "SFORB" are implemented for all +variables, while "FOMC", "DFOP" and "HS" can additionally be chosen for +the first variable which is assumed to be the source compartment. +Additionally, each component of the list can include a character vector +to, specifying names of variables to which a transfer is to be +assumed in the model. If the argument use_of_ff is set to "min" +(default) and the model for the compartment is "SFO" or "SFORB", an +additional component of the list can be "sink=FALSE" effectively fixing +the flux to sink to zero.
use_of_ff

Specification of the use of formation fractions in the model equations and, if - applicable, the coefficient matrix. If "min", a minimum use of formation - fractions is made in order to avoid fitting the product of formation fractions - and rate constants. If "max", formation fractions are always used.

Specification of the use of formation fractions in the +model equations and, if applicable, the coefficient matrix. If "min", a +minimum use of formation fractions is made in order to avoid fitting the +product of formation fractions and rate constants. If "max", formation +fractions are always used.
speclist

The specification of the observed variables and their submodel types and - pathways can be given as a single list using this argument. Default is NULL.

The specification of the observed variables and their +submodel types and pathways can be given as a single list using this +argument. Default is NULL.
quiet
verbose

If TRUE, passed to cfunction if applicable to give - detailed information about the C function being built.

If TRUE, passed to cfunction if +applicable to give detailed information about the C function being built.
- -

Value

-

A list of class mkinmod for use with mkinfit, containing

-
diffs

A vector of string representations of differential equations, - one for each modelling variable.

-
parms

A vector of parameter names occurring in the differential equations.

-
map

A list containing named character vectors for each observed variable, specifying - the modelling variables by which it is represented.

-
use_of_ff

The content of use_of_ff is passed on in this list component.

-
coefmat

The coefficient matrix, if the system of differential equations can be - represented by one.

+

Value

- +

A list of class mkinmod for use with mkinfit, + containing, among others,

+
diffs

A vector of string representations of differential equations, one for + each modelling variable.

+
map

A list containing named character vectors for each observed variable, + specifying the modelling variables by which it is represented.

+
use_of_ff

The content of use_of_ff is passed on in this list component.

+
coefmat

The coefficient matrix, if the system of differential equations can be + represented by one.

+
ll

The likelihood function, taking the parameter vector as the first argument.

+ +

Details

+ +

For the definition of model types and their parameters, the equations given +in the FOCUS and NAFTA guidance documents are used.

Note

-

The IORE submodel is not well tested (yet). When using this model for metabolites, - you may want to read the second note in the help page to - mkinfit.

- +

The IORE submodel is not well tested for metabolites. When using this + model for metabolites, you may want to read the second note in the help + page to mkinfit.

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and - Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, +

FOCUS (2006) “Guidance Document on Estimating Persistence + and Degradation Kinetics from Environmental Fate Studies on Pesticides in + EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental - Media

- + Evaluating and Calculating Degradation Kinetics in Environmental Media

Examples

- 
# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
+    

+# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
 SFO <- mkinmod(parent = list(type = "SFO"))
 
 # One parent compound, one metabolite, both single first order
@@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file663b71dc323f.c 2> file663b71dc323f.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file59d942b9ac06.c 2> file59d942b9ac06.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
@@ -260,7 +260,7 @@ For the definition of model types and their parameters, the equations given
 #>  17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
 #>  18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
 #>  19: }
#> Successfully compiled differential equation model from auto-generated C code.

-# If we have several parallel metabolites 
+# If we have several parallel metabolites
 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
 m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
                            M1 = mkinsub("SFO"),
@@ -276,13 +276,10 @@ For the definition of model types and their parameters, the equations given
     
Contents

     
 
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