[Pomp-commits] r1146 - pkg/pomp pkg/pomp/man www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 23 13:59:14 CET 2015
Author: kingaa
Date: 2015-03-23 13:59:14 +0100 (Mon, 23 Mar 2015)
New Revision: 1146
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/man/csnippet.Rd
www/vignettes/pomp.pdf
Log:
- document Csnippets for rprior and dprior
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-03-23 12:59:09 UTC (rev 1145)
+++ pkg/pomp/DESCRIPTION 2015-03-23 12:59:14 UTC (rev 1146)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.63-2
-Date: 2015-03-16
+Version: 0.63-3
+Date: 2015-03-23
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
person(given=c("Edward","L."),family="Ionides",role=c("aut")),
Modified: pkg/pomp/man/csnippet.Rd
===================================================================
--- pkg/pomp/man/csnippet.Rd 2015-03-23 12:59:09 UTC (rev 1145)
+++ pkg/pomp/man/csnippet.Rd 2015-03-23 12:59:14 UTC (rev 1146)
@@ -50,7 +50,8 @@
}
\section{Rules for writing \code{dmeasure} snippets}{
\enumerate{
- \item The goal of such a snippet is to fill the \code{lik} variable with the likelihood of the data given the state. Alternatively, if \code{give_log=1}, \code{lik} should be filled with the log likelihood.
+ \item The goal of such a snippet is to fill the \code{lik} variable with the likelihood of the data given the state.
+ Alternatively, if \code{give_log=1}, \code{lik} should be filled with the log likelihood.
\item In addition to the states, parameters, covariates (if any), and observables, the variable \code{t}, containing the time of the observation, will be defined in the context in which the snippet is executed.
}
}
@@ -68,6 +69,24 @@
\item As with the other C snippets, all states, parameters and covariates, as well as the current time, \code{t}, will be defined in the context within which the snippet is executed.
}
}
+\section{Rules for writing \code{rprior} snippets}{
+ \enumerate{
+ \item The goal of such a snippet is the replacement of parameters with values drawn from the prior distribution.
+ \item Within the context in which the snippet will be evaluated, only the parameters will be defined.
+ \item Hyperparameters can be included in the ordinary parameter list.
+ Obviously, hyperparameters should not be replaced with random draws.
+ }
+}
+\section{Rules for writing \code{dprior} snippets}{
+ \enumerate{
+ \item The goal of such a snippet is computation of the prior probability density, or the log of same, at a given point in parameter space.
+ This scalar value should be returned in the variable \code{lik}.
+ When \code{give_log=1}, the user should return the log of the prior probability density.
+ \item Within the context in which the snippet will be evaluated, only the parameters and \code{give_log} will be defined.
+ \item Hyperparameters can be included in the ordinary parameter list.
+ Obviously, hyperparameters should not be replaced with random draws.
+ }
+}
\section{Rules for writing parameter transformation snippets}{
\enumerate{
\item The parameter transformation mapping a parameter vector from the scale defined by the model codes to another scale is specified as the \code{parameter.inv.transform} whilst the transformation mapping a parameter vector from the alternative scale to that on which the model is defined is specified as the \code{parameter.transform}.
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-03-23 12:59:09 UTC (rev 1145)
+++ www/vignettes/pomp.pdf 2015-03-23 12:59:14 UTC (rev 1146)
@@ -1,54 +1,37 @@
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[TRUNCATED]
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