diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/FOMC.solution.Rd | 2 | ||||
| -rw-r--r-- | man/IORE.solution.Rd | 34 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 6 | ||||
| -rw-r--r-- | man/mkinmod.Rd | 27 | ||||
| -rw-r--r-- | man/mkinpredict.Rd | 19 | ||||
| -rw-r--r-- | man/mkinsub.Rd | 44 |
6 files changed, 119 insertions, 13 deletions
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd index d04d34e1..f4a26e41 100644 --- a/man/FOMC.solution.Rd +++ b/man/FOMC.solution.Rd @@ -44,6 +44,6 @@ FOMC.solution(t, parent.0, alpha, beta) Technology} \bold{24}, 1032-1038
}
\examples{
- \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2)}
+ \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))}
}
\keyword{ manip }
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd new file mode 100644 index 00000000..65dac9a7 --- /dev/null +++ b/man/IORE.solution.Rd @@ -0,0 +1,34 @@ +\name{IORE.solution}
+\Rdversion{1.1}
+\alias{IORE.solution}
+\title{ Indeterminate order rate equation kinetics }
+\description{
+ Function describing exponential decline from a defined starting value, with
+ a concentration dependent rate constant.
+}
+\usage{
+ IORE.solution(t, parent.0, k.iore, N)
+}
+\arguments{
+ \item{t}{ Time. }
+ \item{parent.0}{ Starting value for the response variable at time zero. }
+ \item{k.iore}{ Rate constant. Note that this depends on the concentration units used. }
+ \item{N}{ Exponent describing the nonlinearity of the rate equation }
+}
+\note{
+ The solution of the IORE kinetic model reduces to the
+ \code{\link{SFO.solution}} if N = 1.
+}
+\value{
+ The value of the response variable at time \code{t}.
+}
+\references{
+ NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+ Evaluating and Calculating Degradation Kinetics in Environmental
+ Media
+}
+\examples{
+ \dontrun{plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
+ ylim = c(0, 100))}
+}
+\keyword{ manip }
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index f4174c29..9c82f5ff 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -216,6 +216,12 @@ mkinfit(mkinmod, observed, Gao). A similar implemention can also be found in CAKE 2.0, which is the other GUI derivative of mkin, sponsored by Syngenta. } +\note{ + When using the "IORE" submodel for metabolites, fitting with + "transform_rates = TRUE" (the default) often leads to failures of the + numerical ODE solver. In this situation it may help to switch off the + internal rate transformation. +} \author{ Johannes Ranke } diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index 76127c58..e6749ded 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -4,9 +4,13 @@ Function to set up a kinetic model with one or more state variables.
}
\description{
- The function takes a specification, consisting of a list of the observed variables
- in the data. Each observed variable is again represented by a list, specifying the
- kinetic model type and reaction or transfer to other observed compartments.
+ 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.
}
\usage{
mkinmod(..., use_of_ff = "min", speclist = NULL)
@@ -15,7 +19,8 @@ mkinmod(..., use_of_ff = "min", speclist = NULL) \item{...}{
For each observed variable, a list has to be specified as an argument, containing
at least a component \code{type}, specifying the type of kinetics to use
- for the variable. Currently, single first order kinetics "SFO" or
+ 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
@@ -46,7 +51,19 @@ mkinmod(..., use_of_ff = "min", speclist = NULL) \item{map}{ A list containing named character vectors for each observed variable, specifying
the modelling variables by which it is represented. }
\item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. }
- \item{coefmat}{ The coefficient matrix, if the system of differential equations can be represented by one. }
+ \item{coefmat}{ The coefficient matrix, if the system of differential equations can be
+ represented by one. }
+}
+\references{
+ FOCUS (2006) \dQuote{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,
+ \url{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
}
\author{
Johannes Ranke
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index 97db90e3..7d8979e4 100644 --- a/man/mkinpredict.Rd +++ b/man/mkinpredict.Rd @@ -65,21 +65,25 @@ } \examples{ SFO <- mkinmod(degradinol = list(type = "SFO")) + # Compare solution types mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "analytical") mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, + solution_type = "deSolve") + mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "eigen") - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, - solution_type = "analytical")[20,] - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - atol = 1e-20)[20,] - # The integration method does not make a lot of difference + # Compare integration methods to analytical solution mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - atol = 1e-20, method = "ode45")[20,] + solution_type = "analytical")[21,] mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - atol = 1e-20, method = "rk4")[20,] + method = "lsoda")[21,] + mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, + method = "ode45")[21,] + mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, + method = "rk4")[21,] + # rk4 is not as precise here # The number of output times used to make a lot of difference until the # default for atol was adjusted @@ -87,5 +91,6 @@ seq(0, 20, by = 0.1))[201,] mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.01))[2001,] + } \keyword{ manip } diff --git a/man/mkinsub.Rd b/man/mkinsub.Rd new file mode 100644 index 00000000..637a671c --- /dev/null +++ b/man/mkinsub.Rd @@ -0,0 +1,44 @@ +\name{mkinsub} +\alias{mkinsub} +\title{ + Function to set up a kinetic submodel for one state variable +} +\description{ + This is a convenience function to set up the lists used as arguments for + \code{\link{mkinmod}}. +} +\usage{ +mkinsub(type, to = NULL, sink = TRUE) +} +\arguments{ + \item{type}{ + Character vector of length one to specify the submodel type. See + \code{\link{mkinmod}} for the list of allowed submodel names. + } + \item{to}{ + Vector of the names of the state variable to which a transformation + shall be included in the model. + } + \item{sink}{ + Should a pathway to sink be included in the model in addition to the + pathways to other state variables? + } +} +\value{ + A list for use with \code{\link{mkinmod}}. +} +\author{ + Johannes Ranke +} +\examples{ +# One parent compound, one metabolite, both single first order. +SFO_SFO <- mkinmod( + parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO")) + +# The same model using mkinsub +SFO_SFO.2 <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) +} + |