[Pomp-commits] r634 - in pkg: . inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 27 23:17:56 CEST 2012
Author: kingaa
Date: 2012-03-27 23:17:56 +0200 (Tue, 27 Mar 2012)
New Revision: 634
Modified:
pkg/.Rinstignore
pkg/inst/doc/bsmc-ricker-flat-prior.rda
pkg/inst/doc/intro_to_pomp.Rnw
pkg/inst/doc/intro_to_pomp.pdf
pkg/inst/doc/manual.pdf
Log:
- put inst/doc/*.rda files into .Rinstignore
- improve 'bsmc' section in intro vignette
Modified: pkg/.Rinstignore
===================================================================
--- pkg/.Rinstignore 2012-03-27 20:57:54 UTC (rev 633)
+++ pkg/.Rinstignore 2012-03-27 21:17:56 UTC (rev 634)
@@ -1,2 +1,3 @@
inst/doc/Makefile
inst/doc/fullnat.bst
+inst/doc/(.+?)\.rda$
Modified: pkg/inst/doc/bsmc-ricker-flat-prior.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw 2012-03-27 20:57:54 UTC (rev 633)
+++ pkg/inst/doc/intro_to_pomp.Rnw 2012-03-27 21:17:56 UTC (rev 634)
@@ -1386,24 +1386,24 @@
First, we draw a sample from our prior distribution.
Here, we'll use uniform priors on two model parameters ($\log{r}$ and $\sigma$), leaving the others fixed at their true values.
-<<bsmc-example-flat-prior-1,echo=F,eval=F>>=
+<<bsmc-example-flat-prior-1,echo=F,eval=T>>=
require(pomp)
data(ricker)
-set.seed(136872209L)
@
We'll use 10,000 particles, so we'll need that many samples from the prior distribution.
<<bsmc-example-flat-prior-2,eval=F>>=
+set.seed(136872209L)
Np <- 10000
-params <- parmat(coef(ricker),nrep=Np)
-params["log.r",] <- runif(n=Np,min=2,max=5)
-params["sigma",] <- runif(n=Np,min=0.1,max=1)
+prior1 <- parmat(coef(ricker),nrep=Np)
+prior1["log.r",] <- runif(n=Np,min=2,max=5)
+prior1["sigma",] <- runif(n=Np,min=0.1,max=1)
@
Now \code{params} holds these 10,000 samples.
The following runs the sequential Monte Carlo algorithm.
Note that, by specifying \code{transform=TRUE}, we cause the estimation to proceed on the transformed scale.
<<bsmc-example-flat-prior-3,eval=F>>=
-fit <- bsmc(ricker,params=params,transform=TRUE,
- est=c("log.r","log.sigma"),smooth=0.2)
+ fit1 <- bsmc(ricker,params=prior1,transform=TRUE,
+ est=c("log.r","log.sigma"),smooth=0.2)
@
<<bsmc-example-flat-prior-eval,eval=T,echo=F>>=
binary.file <- "bsmc-ricker-flat-prior.rda"
@@ -1413,40 +1413,42 @@
<<bsmc-example-flat-prior-1>>
<<bsmc-example-flat-prior-2>>
<<bsmc-example-flat-prior-3>>
- save(fit,file=binary.file,compress="xz")
+ save(fit1,file=binary.file,compress="xz")
}
@
Fig.~\ref{fig:bsmc-example-flat-prior} shows the results of this computation.
Obtain the posterior means of the parameters by doing
<<bsmc-example-flat-prior-coef>>=
-signif(coef(fit),digits=2)
+signif(coef(fit1),digits=2)
@
Note that these are reported on the natural (i.e., untransformed) scale.
\begin{figure}
<<bsmc-example-flat-prior-plot,fig=T,pdf=F,png=T,height=6,width=6,echo=F>>=
- plot(fit,thin=5000)
+ plot(fit1,thin=5000)
@
\caption{
Results of \code{bsmc} on the Ricker model.
The off-diagonal panels show 5000 samples from the prior (grey) and posterior (blue) distributions.
The diagonal panels show histograms of the marginal posterior distributions for each of the parameters.
Note that these are shown on the transformed scale.
- This plot was produced by executing \code{plot(fit,thin=5000)}.
+ This plot was produced by executing \code{plot(fit1,thin=5000)}.
\label{fig:bsmc-example-flat-prior}
}
\end{figure}
To repeat the procedure with log-normal priors on $r$ and $\sigma$, one might do the following.
<<bsmc-example-normal-prior>>=
+set.seed(90348704L)
+Np <- 10000
+prior2 <- parmat(coef(ricker),nrep=Np)
## normal prior on log.r
-params["log.r",] <- rnorm(n=Np,mean=coef(ricker,"log.r"),sd=3)
+prior2["log.r",] <- rnorm(n=Np,mean=4,sd=3)
## log-normal prior on sigma
-params["sigma",] <- rlnorm(n=Np,meanlog=log(coef(ricker,"sigma")),
- sdlog=5)
-fit <- bsmc(ricker,params=params,transform=TRUE,
+prior2["sigma",] <- rlnorm(n=Np,meanlog=log(0.5),sdlog=5)
+fit2 <- bsmc(ricker,params=prior2,transform=TRUE,
est=c("log.r","log.sigma"),smooth=0.2)
-signif(coef(fit),digits=2)
+signif(coef(fit2),digits=2)
@
Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/manual.pdf
===================================================================
--- pkg/inst/doc/manual.pdf 2012-03-27 20:57:54 UTC (rev 633)
+++ pkg/inst/doc/manual.pdf 2012-03-27 21:17:56 UTC (rev 634)
@@ -225,14 +225,12 @@
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 634
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