From 38f9e15f0c972c1516ae737a2bca8d7789581bbd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Oct 2016 09:19:21 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/reference/mkinmod.html | 206 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 206 insertions(+) create mode 100644 docs/reference/mkinmod.html (limited to 'docs/reference/mkinmod.html') diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html new file mode 100644 index 00000000..9dd8fca0 --- /dev/null +++ b/docs/reference/mkinmod.html @@ -0,0 +1,206 @@ + + + + + + + + +mkinmod. mkin + + + + + + + + + + + + + + + + + + + + + + + + +
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+

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+ +

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.

+ + + 
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 + 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. +
+
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

+
+ +
+

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.

+
+ +
+

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, + 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 + 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", ...)
+SFO <- mkinmod(parent = list(type = "SFO"))
+
+# One parent compound, one metabolite, both single first order
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
Successfully compiled differential equation model from auto-generated C code.

+## Not run: ------------------------------------
+# # The above model used to be specified like this, before the advent of mkinsub()
+# SFO_SFO <- mkinmod(
+#   parent = list(type = "SFO", to = "m1"),
+#   m1 = list(type = "SFO"))
+# 
+# # Show details of creating the C function
+# SFO_SFO <- mkinmod(
+#   parent = mkinsub("SFO", "m1"),
+#   m1 = mkinsub("SFO"), verbose = TRUE)
+# 
+# # 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"),
+#                            M2 = mkinsub("SFO"),
+#                            use_of_ff = "max", quiet = TRUE)
+# 
+# fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
+#                           synthetic_data_for_UBA_2014[[12]]$data,
+#                           quiet = TRUE)
+## ---------------------------------------------
+
+
+

Author

+ + Johannes Ranke + +
+
+ + +
+ + + -- cgit v1.2.1