[Pomp-commits] r1202 - pkg/pomp pkg/pomp/man www/content www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 11 20:57:35 CEST 2015
Author: kingaa
Date: 2015-06-11 20:57:35 +0200 (Thu, 11 Jun 2015)
New Revision: 1202
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/man/csnippet.Rd
pkg/pomp/man/pomp.Rd
www/content/NEWS.html
www/vignettes/pomp.pdf
Log:
- update and improve documentation
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-06-11 11:56:42 UTC (rev 1201)
+++ pkg/pomp/DESCRIPTION 2015-06-11 18:57:35 UTC (rev 1202)
@@ -1,7 +1,7 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.67-1
+Version: 0.67-2
Date: 2015-06-11
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
Modified: pkg/pomp/man/csnippet.Rd
===================================================================
--- pkg/pomp/man/csnippet.Rd 2015-06-11 11:56:42 UTC (rev 1201)
+++ pkg/pomp/man/csnippet.Rd 2015-06-11 18:57:35 UTC (rev 1202)
@@ -89,11 +89,20 @@
}
\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}.
- \item The goal of a these snippets is the computation of the values of the transformed parameters. The value of transformed parameter \code{x} should be assigned to variable \code{Tx}.
+ \item The parameter transformation mapping a parameter vector from the scale used by the model codes to another scale is specified using the \code{toEstimationScale} argument whilst the transformation mapping a parameter vector from the alternative scale to that on which the model is defined is specified with the \code{fromEstimationScale} argument.
+ \item The goal of these snippets is the computation of the values of the transformed parameters. The value of transformed parameter \code{x} should be assigned to variable \code{Tx}.
\item Time-, state-, and covariate-dependent transformations are not allowed. Therefore, neither the time, nor any state variables, nor any of the covariates will be available in the context within which a parameter transformation snippet is executed.
}
}
+\section{Rules for writing \code{initializer} snippets}{
+ \enumerate{
+ \item The goal of a this snippet is the construction of a state vector, i.e., the setting of the dynamical states at time \eqn{t_0}{\code{t0}}.
+ \item In addition to the parameters and covariates (if any), the variable \code{t}, containing the time of the observation, will be defined in the context in which the snippet is executed.
+ \item \strong{NB:} The \code{statenames} argument plays a particularly important role when the initializer is specified using a \code{Csnippet}.
+ In particular, every state variable must be named in \code{statenames}.
+ \strong{Failure to follow this rule will result in undefined behavior.}
+ }
+}
\section{Viewing the generated C code}{
It can be useful to view the C code generated by calling \code{pomp} with one or more \code{Csnippet} arguments.
To do so, set \code{options(verbose=TRUE)} before calling \code{pomp}.
Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd 2015-06-11 11:56:42 UTC (rev 1201)
+++ pkg/pomp/man/pomp.Rd 2015-06-11 18:57:35 UTC (rev 1202)
@@ -126,11 +126,19 @@
}
}
\item{initializer}{
- optional function of prototype \preformatted{initializer(params,t0,\dots)} that yields initial conditions for the state process when given a vector, \code{params}, of parameters.
+ The initializer gives the parameterization of the initial state of the unobserved Markov process.
+ Specifically, given a vector of parameters, \code{params} and an initial time, \code{t0}, the initializer determines the state vector at time \code{t0}.
By default, any parameters in \code{params}, the names of which end in \dQuote{\code{.0}}, are assumed to be initial values of states.
To initialize the unobserved state process, these are simply copied over as initial conditions.
The names of the resulting state variables are obtained by dropping the \dQuote{\code{.0}} suffix.
+
+ A custom initializer can be supplied here in one of two formats:
+ \enumerate{
+ \item as an \R function of prototype \preformatted{initializer(params,t0,\dots)} that yields initial conditions for the state process when given a vector, \code{params}, of parameters.
+ \item as a snippet of C code (via \code{\link{Csnippet}}).
+ See the \code{\link{Csnippet}} help for rules on writing a custom initializer.
+ }
}
\item{rprior}{
optional; function drawing a sample from a prior distribution on parameters.
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-06-11 11:56:42 UTC (rev 1201)
+++ www/content/NEWS.html 2015-06-11 18:57:35 UTC (rev 1202)
@@ -7,6 +7,19 @@
<h2>News for package ‘pomp’</h2>
+<h3>Changes in <span class="pkg">pomp</span> version 0.67-1</h3>
+
+
+<ul>
+<li><p> A 'pomp' object's initializer can now be specified as a Csnippet.
+</p>
+</li>
+<li><p> The default initializer is now considerably faster.
+</p>
+</li></ul>
+
+
+
<h3>Changes in <span class="pkg">pomp</span> version 0.66-4</h3>
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-06-11 11:56:42 UTC (rev 1201)
+++ www/vignettes/pomp.pdf 2015-06-11 18:57:35 UTC (rev 1202)
@@ -1,43 +1,33 @@
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[TRUNCATED]
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