[Pomp-commits] r359 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 4 18:10:27 CEST 2010
Author: kingaa
Date: 2010-10-04 18:10:27 +0200 (Mon, 04 Oct 2010)
New Revision: 359
Removed:
pkg/man/euler.Rd
Log:
- remove documentation for removed plugins
Deleted: pkg/man/euler.Rd
===================================================================
--- pkg/man/euler.Rd 2010-10-04 16:07:03 UTC (rev 358)
+++ pkg/man/euler.Rd 2010-10-04 16:10:27 UTC (rev 359)
@@ -1,117 +0,0 @@
-\name{euler}
-\alias{euler.simulate}
-\alias{onestep.simulate}
-\alias{onestep.density}
-\keyword{internal}
-\title{Plug-ins for dynamical models based on stochastic Euler algorithms}
-\description{
- Plug-in facilities for implementing discrete-time Markov processes and continuous-time Markov processes using the Euler algorithm.
- These can be used in the \code{rprocess} and \code{dprocess} slots of \code{pomp}.
-}
-\usage{
-euler.simulate(xstart, times, params, step.fun, delta.t, \dots,
- statenames = character(0), paramnames = character(0),
- covarnames = character(0), zeronames = character(0),
- tcovar, covar, PACKAGE)
-onestep.simulate(xstart, times, params, step.fun, \dots,
- statenames = character(0), paramnames = character(0),
- covarnames = character(0), zeronames = character(0),
- tcovar, covar, PACKAGE)
-onestep.density(x, times, params, dens.fun, \dots,
- statenames = character(0), paramnames = character(0),
- covarnames = character(0), tcovar, covar, log = FALSE,
- PACKAGE)
-}
-\arguments{
- \item{xstart}{
- Matrix (dimensions \code{nvar} x \code{nrep}) of states at initial time \code{times[1]}.
- }
- \item{x}{
- Matrix (dimensions \code{nvar} x \code{nrep} x \code{ntimes}) of states at times \code{times}.
- }
- \item{times}{
- Vector of times (length \code{ntimes}) at which states are required or given.
- }
- \item{params}{
- Matrix containing parameters of the model.
- The \code{nrep} columns of \code{params} correspond to those of \code{xstart}.
- }
- \item{step.fun}{
- This can be either an R function or the name of a compiled, dynamically loaded native function containing the model simulator.
- It should be written to take a single Euler step from a single point in state space.
- If it is a native function, it must be of type \dQuote{pomp_onestep_sim} as defined in the header \dQuote{pomp.h}, which is included with the package.
- For details on how to write such codes, see Details.
- }
- \item{dens.fun}{
- This can be either an R function or a compiled, dynamically loaded native function containing the model transition log probability density function.
- This function will be called to compute the log likelihood of the actual Euler steps.
- It must be of type \dQuote{pomp_onestep_pdf} as defined in the header \dQuote{pomp.h}, which is included with the package.
- For details on how to write such codes, see Details.
- }
- \item{delta.t}{
- Time interval of Euler steps.
- }
- \item{statenames, paramnames, covarnames}{
- Names of state variables, parameters, covariates, in the order they will be expected by the routine named in \code{step.fun} and \code{dens.fun}.
- This information is only used when the latter are implemented as compiled native functions.
- }
- \item{zeronames}{
- Names of additional variables which will be zeroed before each time in \code{times}.
- These are useful, e.g., for storing accumulations of state variables.
- }
- \item{covar, tcovar}{
- Matrix of covariates and times at which covariates are measured.
- }
- \item{log}{
- logical; if TRUE, log probabilities are given.
- }
- \item{\dots}{
- if \code{step.fun} (or \code{dens.fun}) is an R function, then additional arguments will be passed to it.
- If \code{step.fun} (or \code{dens.fun}) is a native routine, then additional arguments are ignored.
- }
- \item{PACKAGE}{
- an optional argument that specifies to which dynamically loaded library we restrict the search for the native routines.
- If this is \dQuote{base}, we search in the R executable itself.
- }
-}
-\details{
- \code{onestep.simulate} assumes that a single call to \code{step.fun} will advance the state process from one time to the next.
- \code{euler.simulate} will take multiple Euler steps, each of size at most \code{delta.t} (see below for information on how the actual Euler step size is chosen) to get from one time to the next.
-
- \code{onestep.density} assumes that no state transitions occure between consecutive times.
-
- If \code{step.fun} is written as an R function, it must have at least the arguments \code{x}, \code{t}, \code{params}, \code{delta.t}, and \code{\dots}.
- On a call to this function, \code{x} will be a named vector of state variables, \code{t} a scalar time, and \code{params} a named vector of parameters.
- The length of the Euler step will be \code{delta.t}.
- If the argument \code{covars} is included and a covariate table has been included in the \code{pomp} object, then on a call to this function, \code{covars} will be filled with the values, at time \code{t}, of the covariates.
- This is accomplished via interpolation of the covariate table.
- Additional arguments may be given: these will be filled by the correspondingly-named elements in the \code{userdata} slot of the \code{pomp} object (see \code{\link{pomp}}).
-
- If \code{step.fun} is written in a native language, it must be a function of type "pomp_onestep_sim" as specified in the header "pomp.h" included with the package (see the directory "include" in the installed package directory).
-
- If \code{dens.fun} is written as an R function, it must have at least the arguments \code{x1}, \code{x2}, \code{t1}, \code{t2}, \code{params}, and \code{\dots}.
- On a call to this function, \code{x1} and \code{x2} will be named vectors of state variables at times \code{t1} and \code{t2}, respectively.
- The named vector \code{params} contains the parameters.
- If the argument \code{covars} is included and a covariate table has been included in the \code{pomp} object, then on a call to this function, \code{covars} will be filled with the values, at time \code{t1}, of the covariates.
- This is accomplished via interpolation of the covariate table.
- As above, any additional arguments will be filled by the correspondingly-named elements in the \code{userdata} slot of the \code{pomp} object (see \code{\link{pomp}}).
-
- If \code{dens.fun} is written in a native language, it must be a function of type "pomp_onestep_pdf" as defined in the header "pomp.h" included with the package (see the directory "include" in the installed package directory).
-}
-\value{
- \code{euler.simulate} and \code{onestep.simulate} each return a \code{nvar} x \code{nrep} x \code{ntimes} array, where \code{nvar} is the number of state variables, \code{nrep} is the number of replicate simulations (= number of columns of \code{xstart} and \code{params}), and \code{ntimes} is the length of \code{times}.
- If \code{x} is this array, \code{x[,,1]} will be identical to \code{xstart}; the rownames of \code{x} and \code{xstart} will also coincide.
-
- \code{onestep.density} returns a \code{nrep} x \code{ntimes-1} array.
- If \code{f} is this array, \code{f[i,j]} is the likelihood of a transition from \code{x[,i,j]} to \code{x[,i,j+1]} in exactly one Euler step of duration \code{times[j+1]-times[j]}.
-}
-\author{Aaron A. King \email{kingaa at umich dot edu}}
-\seealso{\code{\link{eulermultinom}}, \code{\link{pomp}}}
-\examples{
-## an example showing how to use these functions to implement a seasonal SIR model is contained
-## in the 'examples' directory
-\dontrun{
-edit(file=system.file("examples/euler_sir.R",package="pomp"))
-}
-}
-\keyword{models}
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