diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinmod.Rd | 26 | ||||
| -rw-r--r-- | man/mkinpredict.Rd | 19 |
2 files changed, 33 insertions, 12 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index 63087d49..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)
@@ -15,10 +19,11 @@ 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", "IORE", "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 \code{to},
specifying names of variables to which a transfer is to be assumed in the
@@ -49,6 +54,17 @@ mkinmod(..., use_of_ff = "min", speclist = NULL) \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 } |