[Pomp-commits] r644 - in pkg: . R inst inst/doc inst/include man src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 5 21:43:12 CEST 2012
Author: kingaa
Date: 2012-04-05 21:43:12 +0200 (Thu, 05 Apr 2012)
New Revision: 644
Modified:
pkg/DESCRIPTION
pkg/R/bsmc.R
pkg/R/compare-mif.R
pkg/inst/NEWS
pkg/inst/doc/advanced_topics_in_pomp.pdf
pkg/inst/doc/intro_to_pomp.Rnw
pkg/inst/doc/intro_to_pomp.pdf
pkg/inst/doc/manual.pdf
pkg/inst/include/pomp.h
pkg/man/bsmc.Rd
pkg/src/pomp.h
pkg/tests/bbs.Rout.save
Log:
- point estimates are posterior medians instead of means
- fix bug in compare.mif when transform=T
- modify/improve/repair plot method for 'bsmcd.pomp' objects
- change 'inline's to 'static inline's in pomp.h
- fix up vignettes
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-04 12:39:27 UTC (rev 643)
+++ pkg/DESCRIPTION 2012-04-05 19:43:12 UTC (rev 644)
@@ -2,7 +2,7 @@
Type: Package
Title: Statistical inference for partially observed Markov processes
Version: 0.41-2
-Date: 2012-04-04
+Date: 2012-04-05
Revision: $Rev$
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
Maintainer: Aaron A. King <kingaa at umich.edu>
Modified: pkg/R/bsmc.R
===================================================================
--- pkg/R/bsmc.R 2012-04-04 12:39:27 UTC (rev 643)
+++ pkg/R/bsmc.R 2012-04-05 19:43:12 UTC (rev 644)
@@ -334,8 +334,8 @@
## prior <- partrans(object,prior,dir="forward")
## }
- ## replace parameters with point estimate (posterior mean)
- coef(object,transform=transform) <- apply(params,1,mean)
+ ## replace parameters with point estimate (posterior median)
+ coef(object,transform=transform) <- apply(params,1,median)
new(
"bsmcd.pomp",
@@ -357,29 +357,37 @@
setMethod("$",signature(x="bsmcd.pomp"),function (x,name) slot(x,name))
-bsmc.plot <- function (prior, post, est, breaks, thin, ...) {
- prior <- t(prior[est,sample.int(n=ncol(prior),size=min(thin,ncol(prior)))])
- post <- t(post[est,sample.int(n=ncol(post),size=min(thin,ncol(post)))])
+bsmc.plot <- function (prior, post, pars, thin, ...) {
+ p1 <- sample.int(n=ncol(prior),size=min(thin,ncol(prior)))
+ p2 <- sample.int(n=ncol(post),size=min(thin,ncol(post)))
+ if (!all(pars%in%rownames(prior))) {
+ missing <- which(!(pars%in%rownames(prior)))
+ stop("unrecognized parameters: ",paste(sQuote(pars[missing]),collapse=","))
+
+ }
+ prior <- t(prior[pars,])
+ post <- t(post[pars,])
all <- rbind(prior,post)
pairs(
all,
- labels=est,
+ labels=pars,
panel=function (x, y, ...) { ## prior, posterior pairwise scatterplot
op <- par(new=TRUE)
on.exit(par(op))
i <- which(x[1]==all[1,])
j <- which(y[1]==all[1,])
- points(x,y,pch=20,col=rgb(0.85,0.85,0.85,0.1),xlim=range(all[,i]),ylim=range(all[,j]))
- points(post[,i],post[,j],pch=20,col=rgb(0,0,1,0.01))
+ points(prior[p1,i],prior[p1,j],pch=20,col=rgb(0.85,0.85,0.85,0.1),xlim=range(all[,i]),ylim=range(all[,j]))
+ points(post[p2,i],post[p2,j],pch=20,col=rgb(0,0,1,0.01))
},
diag.panel=function (x, ...) { ## marginal posterior histogram
i <- which(x[1]==all[1,])
- bks <- hist(c(post[,i],prior[,i]),breaks=breaks,plot=FALSE)$breaks
- y1 <- hist(post[,i],breaks=bks,plot=FALSE)$counts
+ d1 <- density(prior[,i])
+ d2 <- density(post[,i])
usr <- par('usr')
- op <- par(usr=c(usr[1:2],0,1.5*max(y1)))
+ op <- par(usr=c(usr[1:2],0,1.5*max(d1$y,d2$y)))
on.exit(par(op))
- rect(head(bks,-1),0,tail(bks,-1),y1,col=rgb(0,0,1,1),border=NA,...)
+ polygon(d1,col=rgb(0.85,0.85,0.85,0.5))
+ polygon(d2,col=rgb(0,0,1,0.5))
}
)
}
@@ -387,9 +395,15 @@
setMethod(
"plot",
signature(x="bsmcd.pomp"),
- function (x, ..., breaks, thin) {
+ function (x, ..., pars, thin) {
+ if (missing(pars)) pars <- names(coef(x,transform=!x at transform))
if (missing(thin)) thin <- Inf
- if (missing(breaks)) breaks <- 30
- bsmc.plot(prior=x at prior,post=x at post,est=x at est,breaks=breaks,thin=thin,...)
+ bsmc.plot(
+ prior=if (x at transform) partrans(x,x at prior,dir="forward") else x at prior,
+ post=if (x at transform) partrans(x,x at post,dir="forward") else x at post,
+ pars=pars,
+ thin=thin,
+ ...
+ )
}
)
Modified: pkg/R/compare-mif.R
===================================================================
--- pkg/R/compare-mif.R 2012-04-04 12:39:27 UTC (rev 643)
+++ pkg/R/compare-mif.R 2012-04-05 19:43:12 UTC (rev 644)
@@ -8,7 +8,7 @@
xx <- z[[1]]
ivpnames <- xx at ivps
estnames <- c(xx at pars,ivpnames)
- parnames <- names(coef(xx))
+ parnames <- names(coef(xx,transform=xx at transform))
unestnames <- parnames[-match(estnames,parnames)]
## plot filter means
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2012-04-04 12:39:27 UTC (rev 643)
+++ pkg/inst/NEWS 2012-04-05 19:43:12 UTC (rev 644)
@@ -2,6 +2,8 @@
0.41-2
o Fix bug in 'bbs' example.
+ o The posterior medians (not means) are now stored in the 'params' slot of the 'bsmcd.pomp' object.
+
0.41-1
o New arguments in 'mif', 'nlf', 'bsmc', 'pmcmc', 'probe-match', and 'traj-match' allow the estimation to be done on a transformed parameter space.
When 'transform=TRUE' in these commands ('transform.params=TRUE' for 'nlf'), estimation is performed on the transformed parameter space.
Modified: pkg/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw 2012-04-04 12:39:27 UTC (rev 643)
+++ pkg/inst/doc/intro_to_pomp.Rnw 2012-04-05 19:43:12 UTC (rev 644)
@@ -1417,7 +1417,7 @@
}
@
Fig.~\ref{fig:bsmc-example-flat-prior} shows the results of this computation.
-Obtain the posterior means of the parameters by doing
+Obtain the posterior medians of the parameters by doing
<<bsmc-example-flat-prior-coef>>=
signif(coef(fit1),digits=2)
@
@@ -1425,14 +1425,14 @@
\begin{figure}
<<bsmc-example-flat-prior-plot,fig=T,pdf=F,png=T,height=6,width=6,echo=F>>=
- plot(fit1,thin=5000)
+ plot(fit1,pars=c("log.r","sigma"),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(fit1,thin=5000)}.
+ The diagonal panels show kernel density estimates of the marginal prior and posterior distributions for each of the parameters.
+ Note that these are shown on the natural scale.
+ This plot was produced by executing \code{plot(fit1,pars=c("r","sigma"),thin=5000)}.
\label{fig:bsmc-example-flat-prior}
}
\end{figure}
Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/manual.pdf
===================================================================
--- pkg/inst/doc/manual.pdf 2012-04-04 12:39:27 UTC (rev 643)
+++ pkg/inst/doc/manual.pdf 2012-04-05 19:43:12 UTC (rev 644)
@@ -1,739 +1,38 @@
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[TRUNCATED]
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