[Pomp-commits] r632 - in pkg: R inst man

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2012-03-27 17:17:19 +0200 (Tue, 27 Mar 2012)
New Revision: 632

Modified:
   pkg/R/bsmc.R
   pkg/inst/TODO
   pkg/man/bsmc.Rd
Log:
- fix bug in plot method for 'bmscd.pomp'
- parameter posterior means are now stored in the 'params' slot of 'bsmcd.pomp' objects


Modified: pkg/R/bsmc.R
===================================================================
--- pkg/R/bsmc.R	2012-03-27 14:20:08 UTC (rev 631)
+++ pkg/R/bsmc.R	2012-03-27 15:17:19 UTC (rev 632)
@@ -334,6 +334,9 @@
             ##   prior <- partrans(object,prior,dir="forward")
             ## }
 
+            ## replace parameters with point estimate (posterior mean)
+            coef(object,transform=transform) <- apply(params,1,mean)
+
             new(
                 "bsmcd.pomp",
                 object,
@@ -354,10 +357,9 @@
 
 setMethod("$",signature(x="bsmcd.pomp"),function (x,name) slot(x,name))
 
-bsmc.plot <- function (prior, post, est, nbreaks, thin, ...) {
-  if (missing(thin)) thin <- Inf
-  prior <- t(prior[est,sample.int(n=nrow(prior),size=min(thin,nrow(prior)))])
-  post <- t(post[est,sample.int(n=nrow(post),size=min(thin,nrow(post)))])
+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)))])
   all <- rbind(prior,post)
   pairs(
         all,
@@ -372,12 +374,12 @@
         },
         diag.panel=function (x, ...) { ## marginal posterior histogram
           i <- which(x[1]==all[1,])
-          breaks <- hist(c(post[,i],prior[,i]),breaks=nbreaks,plot=FALSE)$breaks
-          y1 <- hist(post[,i],breaks=breaks,plot=FALSE)$counts
+          bks <- hist(c(post[,i],prior[,i]),breaks=breaks,plot=FALSE)$breaks
+          y1 <- hist(post[,i],breaks=bks,plot=FALSE)$counts
           usr <- par('usr')
           op <- par(usr=c(usr[1:2],0,1.5*max(y1)))
           on.exit(par(op))
-          rect(head(breaks,-1),0,tail(breaks,-1),y1,col=rgb(0,0,1,0.5),border=NA,...)
+          rect(head(bks,-1),0,tail(bks,-1),y1,col=rgb(0,0,1,1),border=NA,...)
         }
         )
 }
@@ -385,6 +387,9 @@
 setMethod(
           "plot",
           signature(x="bsmcd.pomp"),
-          function (x, ..., thin, breaks) bsmc.plot(prior=x at prior,post=x at post,est=x at est,
-                                                    nbreaks=breaks,thin=thin,...)
+          function (x, ..., breaks, thin) {
+            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,...)
+          }
           )

Modified: pkg/inst/TODO
===================================================================
--- pkg/inst/TODO	2012-03-27 14:20:08 UTC (rev 631)
+++ pkg/inst/TODO	2012-03-27 15:17:19 UTC (rev 632)
@@ -7,7 +7,7 @@
 * native C routine for vectorfield evaluation inside lsoda
 
 * parameter transformations: put 'transform' option into each estimation routine
-  (bsmc, mif, pmcmc, nlf, *.match)
+  (spect.match)
 
 * unit tests for above
 

Modified: pkg/man/bsmc.Rd
===================================================================
--- pkg/man/bsmc.Rd	2012-03-27 14:20:08 UTC (rev 631)
+++ pkg/man/bsmc.Rd	2012-03-27 15:17:19 UTC (rev 632)
@@ -78,6 +78,7 @@
 }
 \value{
   An object of class \dQuote{bsmcd.pomp}.
+  The \dQuote{params} slot of this object will hold the parameter posterior means.
   The slots of this class include:
   \item{post}{
     A matrix containing draws from the approximate posterior distribution.