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-rw-r--r--man/ilr.Rd8
-rw-r--r--man/mkinpredict.Rd63
-rw-r--r--man/summary.mkinfit.Rd11
-rw-r--r--man/transform_odeparms.Rd51
4 files changed, 117 insertions, 16 deletions
diff --git a/man/ilr.Rd b/man/ilr.Rd
index fef0d29..8bf7a72 100644
--- a/man/ilr.Rd
+++ b/man/ilr.Rd
@@ -17,22 +17,16 @@
vectors with all elements being greater than zero.
}
}
-\details{
-}
\value{
The result of the forward or backward transformation. The returned components always
sum to 1 for the case of the inverse log-ratio transformation.
}
\references{
-%% ~put references to the literature/web site here ~
+ Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248
}
\author{
René Lehmann and Johannes Ranke
}
-\note{
-%% ~~further notes~~
-}
-
\seealso{
Other implementations are in R packages \code{compositions} and \code{robCompositions}.
}
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
new file mode 100644
index 0000000..af37f7c
--- /dev/null
+++ b/man/mkinpredict.Rd
@@ -0,0 +1,63 @@
+\name{mkinpredict}
+\alias{mkinpredict}
+\title{
+ Produce predictions from a kinetic model using specifc parameters
+}
+\description{
+ This function produces a time series for all the observed variables in a kinetic model
+ as specified by \code{\link{mkinmod}}, using a specific set of kinetic parameters and
+ initial values for the state variables.
+}
+\usage{
+mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-06, ...)
+}
+\arguments{
+ \item{mkinmod}{
+ A kinetic model as produced by \code{\link{mkinmod}}.
+}
+ \item{odeparms}{
+ A numeric vector specifying the parameters used in the kinetic model, which is generally
+ defined as a set of ordinary differential equations.
+}
+ \item{odeini}{
+ A numeric vectory containing the initial values of the state variables of the model. Note
+ that the state variables can differ from the observed variables, for example in the case
+ of the SFORB model.
+}
+ \item{outtimes}{
+ A numeric vector specifying the time points for which model predictions should be
+ generated.
+}
+ \item{solution_type}{
+ The method that should be used for producing the predictions. This should
+ generally be "analytical" if there is only one observed variable, and usually
+ "deSolve" in the case of several observed variables. The third possibility "eigen"
+ is faster but produces results that the author believes to be less accurate.
+}
+ \item{map_output}{
+ Boolean to specify if the output should list values for the observed variables (default)
+ or for all state variables (if set to FALSE).
+}
+ \item{atol}{
+ Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-6 as in
+ \code{\link{lsoda}}.
+}
+ \item{\dots}{
+ Further arguments passed to the ode solver in case such a solver is used.
+}
+}
+\value{
+ A matrix in the same format as the output of \code{\link{ode}}.
+}
+\author{
+ Johannes Ranke
+}
+\examples{
+ SFO <- mkinmod(degradinol = list(type = "SFO"))
+ mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")
+ mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "eigen")
+ mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20)
+ mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20, method = "rk4")
+ mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), (1:200)/10)
+}
+\keyword{ manip }
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index b3e7862..59b988a 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -11,8 +11,8 @@
and residual values.
}
\usage{
-\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, ff = TRUE, ...)
-\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), tval = TRUE, ...)
+\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, ...)
+\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), ...)
}
\arguments{
@@ -28,16 +28,9 @@
\item{distimes}{
logical, indicating whether DT50 and DT90 values should be included.
}
- \item{ff}{
- logical, indicating whether formation fractions should be included.
-}
\item{digits}{
Number of digits to use for printing
}
- \item{tval}{
- Should the test statistic of the t-test for parameter significance be
- printed? Defaults to \code{TRUE}. Saves vertical space if set to \code{FALSE}.
-}
\item{\dots}{
optional arguments passed to methods like \code{print}.
}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
new file mode 100644
index 0000000..cc1c8f7
--- /dev/null
+++ b/man/transform_odeparms.Rd
@@ -0,0 +1,51 @@
+\name{transform_odeparms}
+\alias{transform_odeparms}
+\alias{backtransform_odeparms}
+\title{
+ Functions to transform and backtransform kinetic parameters for fitting
+}
+\description{
+ The transformations are intended to map parameters that should only take
+ on restricted values to the full scale of real numbers. For kinetic rate
+ constants and other paramters that can only take on positive values, a
+ simple log transformation is used. For compositional parameters, such as
+ the formations fractions that should always sum up to 1 and can not be
+ negative, the \code{\link{ilr}} transformation is used.
+}
+\usage{
+transform_odeparms(parms, mod_vars)
+backtransform_odeparms(transparms, mod_vars)
+}
+\arguments{
+ \item{parms}{
+ Parameters of kinetic models as used in the differential equations.
+}
+ \item{transparms}{
+ Transformed parameters of kinetic models as used in the fitting procedure.
+}
+ \item{mod_vars}{
+ Names of the state variables in the kinetic model. These are used for
+ grouping the formation fractions before \code{\link{ilr}} transformation.
+}
+}
+\value{
+ A vector of transformed or backtransformed parameters with the same names
+ as the original parameters.
+}
+\author{
+ Johannes Ranke
+}
+\examples{
+SFO_SFO <- mkinmod(
+ parent = list(type = "SFO", to = "m1", sink = TRUE),
+ m1 = list(type = "SFO"))
+# Fit the model to the FOCUS example dataset D using defaults
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+summary(fit, data=FALSE) # See transformed and backtransformed parameters
+initials <- fit$start$initial
+transformed <- fit$start$transformed
+names(initials) <- names(transformed) <- rownames(fit$start)
+transform_odeparms(initials, c("parent", "m1"))
+backtransform_odeparms(transformed, c("parent", "m1"))
+}
+\keyword{ manip }

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