diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/mkinfit.Rd | 11 | ||||
| -rw-r--r-- | man/schaefer07_complex_case.Rd | 39 |
2 files changed, 49 insertions, 1 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 640207ce..0e381afd 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -10,7 +10,7 @@ values. } \usage{ -mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, ...) +mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), lower = 0, upper = Inf, fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, ...) } \arguments{ \item{mkinmod}{ @@ -37,6 +37,15 @@ mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.in \code{\link{mkinmod}}). The default is to set the initial value of the first model variable to 100 and all others to 0. } + \item{lower}{ + Lower bounds for the parameters, passed to \code{\link{modFit}}. Defaults to 0 because + negative values to not make sense for the models currently created by \code{\link{mkinmod}}. + } + \item{upper}{ + Upper bounds for the parameters, passed to \code{\link{modFit}}. Defaults to \code{Inf}. Setting + non-infinite upper bounds has a strong impact on performance, and using a method like "L-BFGS-B" (by + specifying an additional \code{method} argument) is recommended. + } \item{fixed_parms}{ The names of parameters that should not be optimised but rather kept at the values specified in \code{parms.ini}. diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd new file mode 100644 index 00000000..2978e25d --- /dev/null +++ b/man/schaefer07_complex_case.Rd @@ -0,0 +1,39 @@ +\name{schaefer07_complex_case}
+\alias{schaefer07_complex_case}
+\encoding{latin1}
+\docType{data}
+\title{
+ Metabolism data set used for checking the software quality of KinGUI
+}
+\description{
+ This dataset was used for a comparison of KinGUI and ModelMaker to check the
+ software quality of KinGUI in the original publication (Schäfer et al., 2007).
+}
+\usage{data(schaefer07_complex_case)}
+\format{
+ A data frame with 8 observations on the following 6 variables.
+ \describe{
+ \item{\code{time}}{a numeric vector}
+ \item{\code{parent}}{a numeric vector}
+ \item{\code{A1}}{a numeric vector}
+ \item{\code{B1}}{a numeric vector}
+ \item{\code{C1}}{a numeric vector}
+ \item{\code{A2}}{a numeric vector}
+ }
+}
+\source{
+ Schäfer D, Mikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic
+ software tool for evaluations according to FOCUS degradation kinetics. In: Del
+ Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII
+ Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923. }
+\examples{
+data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+model <- mkinmod(
+ parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+ A1 = list(type = "SFO", to = "A2"),
+ B1 = list(type = "SFO"),
+ C1 = list(type = "SFO"),
+ A2 = list(type = "SFO"))
+\dontrun{mkinfit(model, data, plot=TRUE)}
+}
+\keyword{datasets}
|