From ccc70e82af4ba435f0a71ba1ae4e0e92045c3852 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 5 May 2017 12:46:31 +0200 Subject: Static docs except articles rebuilt with current pkgdown --- docs/reference/mkinmod.html | 100 +++++++++++++++++++++++++------------------- 1 file changed, 56 insertions(+), 44 deletions(-) (limited to 'docs/reference/mkinmod.html') diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 1343abcc..de9815d4 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,8 +6,7 @@ - - — mkinmod • mkin +Function to set up a kinetic model with one or more state variables — mkinmod • mkin @@ -26,12 +25,14 @@ - + + + @@ -71,6 +72,9 @@
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Calculation of time weighted average concentrations with mkin +
  • @@ -96,8 +100,7 @@
    -

    -

    +

    Function to set up a kinetic model with one or more state variables

    @@ -105,58 +108,67 @@ 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 +

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

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

    Arguments

    -
    -
    ...
    -
    - For each observed variable, a list has to be specified as an argument, containing + + + + + + + + + + + + + + + + + + + + + + +
    ...

    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 + 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 + "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 + 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. - -

    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. -
    -
    quiet
    -
    - Should messages be suppressed? -
    -
    verbose
    -
    - If TRUE, passed to cfunction if applicable to give - detailed information about the C function being built. -
    - + 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.

    quiet

    Should messages be suppressed?

    verbose

    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.

    +

    Note

    @@ -170,8 +182,8 @@ 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://focus.jrc.ec.europa.eu/dk

    -

    NAFTA Technical Working Group on Pesticides (not dated) Guidance for + http://esdac.jrc.europa.eu/projects/degradation-kinetics

    +

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

    @@ -193,7 +205,7 @@ SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)
    #> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file2ac5b2884c1.c 2> file2ac5b2884c1.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file70ea30edf42a.c 2> file70ea30edf42a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: -- cgit v1.2.1