From noreply at r-forge.r-project.org  Tue Jan  7 19:04:05 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  7 Jan 2014 19:04:05 +0100 (CET)
Subject: [Pomp-commits] r874 - pkg/pompExamples
Message-ID: <20140107180405.C26D8186A2A@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-07 19:04:04 +0100 (Tue, 07 Jan 2014)
New Revision: 874

Modified:
   pkg/pompExamples/DESCRIPTION
Log:


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2013-12-20 13:06:30 UTC (rev 873)
+++ pkg/pompExamples/DESCRIPTION	2014-01-07 18:04:04 UTC (rev 874)
@@ -1,7 +1,7 @@
 Package: pompExamples
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.21-4
+Version: 0.22-1
 Date: 2013-11-11
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),


From noreply at r-forge.r-project.org  Wed Jan  8 16:35:12 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  8 Jan 2014 16:35:12 +0100 (CET)
Subject: [Pomp-commits] r875 - in pkg/pomp: . inst inst/examples
Message-ID: <20140108153512.6DB4C186925@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-08 16:35:11 +0100 (Wed, 08 Jan 2014)
New Revision: 875

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/examples/gompertz.R
Log:
- fix bug in 'gompertz' example


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2014-01-07 18:04:04 UTC (rev 874)
+++ pkg/pomp/DESCRIPTION	2014-01-08 15:35:11 UTC (rev 875)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-7
-Date: 2013-12-20
+Version: 0.45-8
+Date: 2014-01-08
 Authors at R: c(
 	   person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2014-01-07 18:04:04 UTC (rev 874)
+++ pkg/pomp/inst/NEWS	2014-01-08 15:35:11 UTC (rev 875)
@@ -1,4 +1,7 @@
 NEWS
+0.45-8
+     o	bug fix in 'gompertz' example.
+
 0.45-7
      o	bug fix in 'pmcmc': Metropolis-Hastings ratio was incorrect except for flat priors!
 	

Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R	2014-01-07 18:04:04 UTC (rev 874)
+++ pkg/pomp/inst/examples/gompertz.R	2014-01-08 15:35:11 UTC (rev 875)
@@ -105,7 +105,7 @@
 '
 
 po <- pomp(
-           data=read.csv2(text=dat),
+           data=subset(read.csv2(text=dat),select=-X),
            times="time",
            t0=0,
            params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),


From noreply at r-forge.r-project.org  Wed Jan  8 16:36:38 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  8 Jan 2014 16:36:38 +0100 (CET)
Subject: [Pomp-commits] r876 - www/vignettes
Message-ID: <20140108153638.7EA6118693A@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-08 16:36:38 +0100 (Wed, 08 Jan 2014)
New Revision: 876

Modified:
   www/vignettes/advanced_topics_in_pomp.pdf
   www/vignettes/bsmc-ricker-flat-prior.rda
   www/vignettes/bsmc-ricker-normal-prior.rda
   www/vignettes/complex-sir-def.rda
   www/vignettes/gompertz-multi-mif.rda
   www/vignettes/gompertz-pfilter-guess.rda
   www/vignettes/gompertz-trajmatch.rda
   www/vignettes/intro_to_pomp.R
   www/vignettes/intro_to_pomp.Rnw
   www/vignettes/intro_to_pomp.pdf
   www/vignettes/nlf-block-boot.rda
   www/vignettes/nlf-boot.rda
   www/vignettes/nlf-fit-from-truth.rda
   www/vignettes/nlf-fits.rda
   www/vignettes/nlf-lag-tests.rda
   www/vignettes/nlf-multi-short.rda
   www/vignettes/plugin-C-code.rda
   www/vignettes/plugin-R-code.rda
   www/vignettes/ricker-comparison.rda
   www/vignettes/ricker-first-probe.rda
   www/vignettes/ricker-mif.rda
   www/vignettes/ricker-probe-match.rda
   www/vignettes/ricker-probe.rda
   www/vignettes/sim-sim.rda
   www/vignettes/sir-pomp-def.rda
   www/vignettes/vectorized-C-code.rda
   www/vignettes/vectorized-R-code.rda
Log:
- rebuilt with version 0.45-8


Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/bsmc-ricker-flat-prior.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/bsmc-ricker-normal-prior.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/complex-sir-def.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/gompertz-multi-mif.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/gompertz-pfilter-guess.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/gompertz-trajmatch.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/intro_to_pomp.R
===================================================================
--- www/vignettes/intro_to_pomp.R	2014-01-08 15:35:11 UTC (rev 875)
+++ www/vignettes/intro_to_pomp.R	2014-01-08 15:36:38 UTC (rev 876)
@@ -401,11 +401,10 @@
 ## theta.true <- coef(gompertz)
 ## theta.mif <- apply(sapply(mf,coef),1,mean)
 ## loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-## bl <- mean(loglik.mif)
-## loglik.mif.est <- bl+log(mean(exp(loglik.mif-bl)))
+## loglik.mif.est <- logmeanexp(loglik.mif)
 ## loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
 ## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-## loglik.true.est <- bl+log(mean(exp(loglik.true-bl)))
+## loglik.true.est <- logmeanexp(loglik.true)
 ## loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
 
 
@@ -447,11 +446,10 @@
 theta.true <- coef(gompertz)
 theta.mif <- apply(sapply(mf,coef),1,mean)
 loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-bl <- mean(loglik.mif)
-loglik.mif.est <- bl+log(mean(exp(loglik.mif-bl)))
+loglik.mif.est <- logmeanexp(loglik.mif)
 loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
 loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-loglik.true.est <- bl+log(mean(exp(loglik.true-bl)))
+loglik.true.est <- logmeanexp(loglik.true)
 loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
   toc <- Sys.time()
   etime <- toc-tic
@@ -473,16 +471,15 @@
 
 
 ###################################################
-### code chunk number 41: intro_to_pomp.Rnw:690-691 (eval = FALSE)
+### code chunk number 41: intro_to_pomp.Rnw:689-690 (eval = FALSE)
 ###################################################
 ## theta.true <- coef(gompertz)
 ## theta.mif <- apply(sapply(mf,coef),1,mean)
 ## loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-## bl <- mean(loglik.mif)
-## loglik.mif.est <- bl+log(mean(exp(loglik.mif-bl)))
+## loglik.mif.est <- logmeanexp(loglik.mif)
 ## loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
 ## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-## loglik.true.est <- bl+log(mean(exp(loglik.true-bl)))
+## loglik.true.est <- logmeanexp(loglik.true)
 ## loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
 
 
@@ -935,7 +932,7 @@
 
 
 ###################################################
-### code chunk number 69: intro_to_pomp.Rnw:1125-1126
+### code chunk number 69: intro_to_pomp.Rnw:1124-1125
 ###################################################
 fits
 
@@ -1120,7 +1117,7 @@
 
 
 ###################################################
-### code chunk number 77: intro_to_pomp.Rnw:1271-1272
+### code chunk number 77: intro_to_pomp.Rnw:1270-1271
 ###################################################
 apply(fvals,2,function(x)sd(x)/mean(x))
 
@@ -1133,7 +1130,7 @@
 ##                 transform.params=TRUE,
 ##                 est=c("K","r"),
 ##                 lags=2,
-##                 seed=7639873, 
+##                 seed=7639873L, 
 ##                 method="Nelder-Mead",
 ##                 trace=4,
 ##                 nasymp=5000
@@ -1152,7 +1149,7 @@
                 transform.params=TRUE,
                 est=c("K","r"),
                 lags=2,
-                seed=7639873, 
+                seed=7639873L, 
                 method="Nelder-Mead",
                 trace=4,
                 nasymp=5000
@@ -1162,7 +1159,7 @@
 
 
 ###################################################
-### code chunk number 80: intro_to_pomp.Rnw:1310-1311
+### code chunk number 80: intro_to_pomp.Rnw:1309-1310
 ###################################################
 set.seed(32329L)
 
@@ -1232,7 +1229,7 @@
 
 
 ###################################################
-### code chunk number 83: intro_to_pomp.Rnw:1348-1349
+### code chunk number 83: intro_to_pomp.Rnw:1347-1348
 ###################################################
 apply(pars,2,sd)
 

Modified: www/vignettes/intro_to_pomp.Rnw
===================================================================
--- www/vignettes/intro_to_pomp.Rnw	2014-01-08 15:35:11 UTC (rev 875)
+++ www/vignettes/intro_to_pomp.Rnw	2014-01-08 15:36:38 UTC (rev 876)
@@ -646,11 +646,10 @@
 theta.true <- coef(gompertz)
 theta.mif <- apply(sapply(mf,coef),1,mean)
 loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-bl <- mean(loglik.mif)
-loglik.mif.est <- bl+log(mean(exp(loglik.mif-bl)))
+loglik.mif.est <- logmeanexp(loglik.mif)
 loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
 loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-loglik.true.est <- bl+log(mean(exp(loglik.true-bl)))
+loglik.true.est <- logmeanexp(loglik.true)
 loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
 @ 
 
@@ -1278,7 +1277,7 @@
                 transform.params=TRUE,
                 est=c("K","r"),
                 lags=2,
-                seed=7639873, 
+                seed=7639873L, 
                 method="Nelder-Mead",
                 trace=4,
                 nasymp=5000

Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-block-boot.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-boot.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-fit-from-truth.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-fits.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-lag-tests.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-multi-short.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/plugin-C-code.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/plugin-R-code.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-comparison.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-first-probe.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-mif.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-probe-match.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-probe.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/sim-sim.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/sir-pomp-def.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/vectorized-C-code.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/vectorized-R-code.rda
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Thu Jan  9 17:12:11 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  9 Jan 2014 17:12:11 +0100 (CET)
Subject: [Pomp-commits] r877 - pkg/pomp
Message-ID: <20140109161211.C689C1850F4@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-09 17:12:09 +0100 (Thu, 09 Jan 2014)
New Revision: 877

Modified:
   pkg/pomp/DESCRIPTION
Log:
- remove Author and Maintainer fields


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2014-01-08 15:36:38 UTC (rev 876)
+++ pkg/pomp/DESCRIPTION	2014-01-09 16:12:09 UTC (rev 877)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.45-8
-Date: 2014-01-08
+Date: 2014-01-09
 Authors at R: c(
 	   person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
@@ -17,8 +17,6 @@
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
 	  person(given=c("Simon","N."),family="Wood",role=c("ctb"))
 	  )
-Maintainer: Aaron A. King <kingaa at umich.edu>
-Author: Aaron A. King, Edward L. Ionides, Carles Breto, Stephen P. Ellner, Matthew J. Ferrari, Bruce E. Kendall, Michael Lavine, Dao Nguyen, Daniel C. Reuman, Helen Wearing, Simon N. Wood
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
 Depends: R(>= 2.14.1), stats, graphics, methods, mvtnorm, subplex, deSolve


From noreply at r-forge.r-project.org  Fri Jan 10 20:50:48 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 10 Jan 2014 20:50:48 +0100 (CET)
Subject: [Pomp-commits] r878 - in pkg/pomp: R man
Message-ID: <20140110195049.0E1A7186643@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-10 20:50:48 +0100 (Fri, 10 Jan 2014)
New Revision: 878

Modified:
   pkg/pomp/R/logmeanexp.R
   pkg/pomp/man/logmeanexp.Rd
Log:
- add 'se' argument to 'logmeanexp'


Modified: pkg/pomp/R/logmeanexp.R
===================================================================
--- pkg/pomp/R/logmeanexp.R	2014-01-09 16:12:09 UTC (rev 877)
+++ pkg/pomp/R/logmeanexp.R	2014-01-10 19:50:48 UTC (rev 878)
@@ -1,4 +1,10 @@
-logmeanexp <- function (x) {
+logmeanexp <- function (x, se = FALSE) {
   mx <- max(x)
-  mx+log(mean(exp(x-mx)))
+  mean <- mx+log(mean(exp(x-mx)))
+  if (se) {
+    se <- sd(exp(x-mx))/exp(mean-mx)
+    c(mean,se=se)
+  } else {
+    mean
+  }
 }

Modified: pkg/pomp/man/logmeanexp.Rd
===================================================================
--- pkg/pomp/man/logmeanexp.Rd	2014-01-09 16:12:09 UTC (rev 877)
+++ pkg/pomp/man/logmeanexp.Rd	2014-01-10 19:50:48 UTC (rev 878)
@@ -5,13 +5,15 @@
   \code{logmeanexp} computes the log-mean-exp of a set of numbers.
 }
 \usage{
-logmeanexp(x)
+logmeanexp(x, se = FALSE)
 }
 \arguments{
   \item{x}{numeric}
+  \item{se}{logical; give approximate standard error?}
 }
 \value{
   \code{log(mean(exp(x)))} computed so as to avoid over- or underflow.
+  If \code{se = FALSE}, the approximate standard error is returned as well.
 }
 \author{Aaron A. King \email{kingaa at umich dot edu}}
 \examples{
@@ -20,4 +22,5 @@
   ll <- replicate(n=5,logLik(pfilter(ricker,Np=1000)))
   ## an estimate of the log likelihood:
   logmeanexp(ll)
+  logmeanexp(ll,se=TRUE)
 }


From noreply at r-forge.r-project.org  Fri Jan 10 20:51:11 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 10 Jan 2014 20:51:11 +0100 (CET)
Subject: [Pomp-commits] r879 - in pkg/pomp: . R inst inst/examples man tests
Message-ID: <20140110195111.1752D186646@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-10 20:51:10 +0100 (Fri, 10 Jan 2014)
New Revision: 879

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/example.R
   pkg/pomp/inst/CITATION
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/examples/bbs.R
   pkg/pomp/inst/examples/blowflies.R
   pkg/pomp/inst/examples/dacca.R
   pkg/pomp/inst/examples/euler.sir.R
   pkg/pomp/inst/examples/gillespie.sir.R
   pkg/pomp/inst/examples/gompertz.R
   pkg/pomp/inst/examples/ou2.R
   pkg/pomp/inst/examples/ricker.R
   pkg/pomp/inst/examples/rw2.R
   pkg/pomp/inst/examples/verhulst.R
   pkg/pomp/man/example.Rd
   pkg/pomp/tests/bbs-trajmatch.Rout.save
   pkg/pomp/tests/bbs.Rout.save
   pkg/pomp/tests/blowflies.Rout.save
   pkg/pomp/tests/dacca.Rout.save
   pkg/pomp/tests/dimchecks.Rout.save
   pkg/pomp/tests/fhn.Rout.save
   pkg/pomp/tests/filtfail.Rout.save
   pkg/pomp/tests/gillespie.Rout.save
   pkg/pomp/tests/gompertz.Rout.save
   pkg/pomp/tests/logistic.Rout.save
   pkg/pomp/tests/ou2-bsmc.Rout.save
   pkg/pomp/tests/ou2-forecast.Rout.save
   pkg/pomp/tests/ou2-icfit.Rout.save
   pkg/pomp/tests/ou2-kalman.Rout.save
   pkg/pomp/tests/ou2-mif-fp.Rout.save
   pkg/pomp/tests/ou2-mif.Rout.save
   pkg/pomp/tests/ou2-mif2.Rout.save
   pkg/pomp/tests/ou2-nlf.Rout.save
   pkg/pomp/tests/ou2-pmcmc.Rout.save
   pkg/pomp/tests/ou2-probe.Rout.save
   pkg/pomp/tests/ou2-procmeas.Rout.save
   pkg/pomp/tests/ou2-simulate.Rout.save
   pkg/pomp/tests/ou2-trajmatch.Rout.save
   pkg/pomp/tests/partrans.Rout.save
   pkg/pomp/tests/pfilter.Rout.save
   pkg/pomp/tests/pomppomp.Rout.save
   pkg/pomp/tests/ricker-bsmc.Rout.save
   pkg/pomp/tests/ricker-probe.Rout.save
   pkg/pomp/tests/ricker-spect.Rout.save
   pkg/pomp/tests/ricker.Rout.save
   pkg/pomp/tests/rw2.Rout.save
   pkg/pomp/tests/sir.Rout.save
   pkg/pomp/tests/skeleton.Rout.save
   pkg/pomp/tests/steps.Rout.save
   pkg/pomp/tests/synlik.Rout.save
   pkg/pomp/tests/verhulst.Rout.save
Log:
- add optional 'envir' argument to 'pompExample'


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/DESCRIPTION	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-8
-Date: 2014-01-09
+Version: 0.46-1
+Date: 2014-01-10
 Authors at R: c(
 	   person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),

Modified: pkg/pomp/R/example.R
===================================================================
--- pkg/pomp/R/example.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/R/example.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,16 +1,22 @@
-pompExample <- function (example) {
-  if (missing(example)) {
+pompExample <- function (example, envir = .GlobalEnv) {
+  example <- as.character(substitute(example))
+  if (example=="") {
     avlbl <- list.files(
                         path=system.file("examples",package="pomp"),
                         pattern=".+?R$"
                         )
     avlbl <- gsub("\\.R$","",avlbl)
-    cat("available pomp examples:\n",sQuote(avlbl),"\n")
+    avlbl
   } else {
-    ex <- as.character(substitute(example))
-    file <- system.file(file.path("examples",paste(ex,".R",sep="")),package="pomp")
+    file <- system.file(
+                        file.path("examples",paste(example,".R",sep="")),
+                        package="pomp"
+                        )
     objs <- source(file,local=TRUE)
-    cat("newly created pomp objects:\n",objs$value,"\n")
+    for (i in seq_along(objs$value)) {
+      assign(objs$value[i],get(objs$value[i]),envir=envir)
+    }
+    cat("newly created pomp object(s):\n",objs$value,"\n")
+    invisible(NULL)
   }
-  invisible(NULL)
 }

Modified: pkg/pomp/inst/CITATION
===================================================================
--- pkg/pomp/inst/CITATION	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/CITATION	2014-01-10 19:51:10 UTC (rev 879)
@@ -7,17 +7,19 @@
  	   as.person("Aaron A. King"),
 	   as.person("Edward L. Ionides"),
 	   as.person("Carles Martinez Bret\\'o"),
-   	   as.person("Steve Ellner"), 
-	   as.person("Bruce Kendall"),
-	   as.person("Helen Wearing"),
+   	   as.person("Stephen P. Ellner"), 
 	   as.person("Matthew J. Ferrari"),
+	   as.person("Bruce E. Kendall"),
 	   as.person("Michael Lavine"),
-	   as.person("Daniel C. Reuman")
+	   as.person("Dao Nguyen"),
+	   as.person("Daniel C. Reuman"),
+	   as.person("Helen Wearing"),
+	   as.person("Simon N. Wood")
 	   ),	   
-	 year=2010,
+	 year=2014,
 	 url="http://pomp.r-forge.r-rproject.org",
 	 textVersion=paste(
-			   "Aaron A. King, E. L. Ionides, C. M. Bret\\'o, S. P. Ellner, B. E. Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, and Daniel C. Reuman",
+			   "A. A. King, E. L. Ionides, C. M. Bret\\'o, S. P. Ellner, M. J. Ferrari, B. E. Kendall, M. Lavine, D. Nguyen, D. C. Reuman, H. Wearing, and S. N. Wood",
 			   "pomp: Statistical inference for partially observed Markov processes (R package)",
 			   "http://pomp.r-forge.r-project.org"
 			  )	   

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/NEWS	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,4 +1,9 @@
 NEWS
+0.46-1
+     o	'pompExample' now has an optional argument, 'envir', determining which environment the pomp object will be loaded into.
+
+     o	'logmeanexp' now has an optional argument, 'se', allowing for computation of an approximate standard error.
+
 0.45-8
      o	bug fix in 'gompertz' example.
 

Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/bbs.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -18,67 +18,63 @@
 14;5
 ")
 
-po <- pomp(
-           data=flu,
-           times="day",
-           t0=0,
-           rprocess=euler.sim(
-             step.fun="_sir_euler_simulator",
-             delta.t=1/12,
-             PACKAGE="pomp"
-             ),
-           skeleton.type="vectorfield",
-           skeleton="_sir_ODE",
-           measurement.model=reports~norm(mean=rho*cases,sd=1+sigma*cases),
-           PACKAGE="pomp",
-           obsnames = c("reports"),
-           statenames=c("S","I","R","cases","W"),
-           paramnames=c(
-             "gamma","mu","iota",
-             "beta","beta.sd","pop","rho",
-             "S.0","I.0","R.0"
-             ),
-           zeronames=c("cases"),
-           comp.names=c("S","I","R"),
-           ic.names=c("S.0","I.0","R.0"),
-           nbasis=1L,
-           degree=0L,
-           period=1.0,
-           logvar=c(
-             "beta","gamma","mu","iota","sigma","beta.sd",
-             "S.0","I.0","R.0"
-             ),
-           logitvar="rho",
-           parameter.inv.transform=function (params, logvar, logitvar, ...) {
-             params[logvar] <- log(params[logvar])
-             params[logitvar] <- qlogis(params[logitvar])
-             params
-           },
-           parameter.transform=function (params, logvar, logitvar, ...) {
-             params[logvar] <- exp(params[logvar])
-             params[logitvar] <- plogis(params[logitvar])
-             params
-           },
-           initializer=function(params, t0, comp.names, ic.names, ...) {
-             snames <- c("S","I","R","cases","W")
-             fracs <- params[ic.names]
-             x0 <- numeric(length(snames))
-             names(x0) <- snames
-             x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
-             x0
-           }
-           )
+pomp(
+     data=flu,
+     times="day",
+     t0=0,
+     params=c(
+       gamma=1/3,mu=0.0,iota=0.0,
+       beta=1.4,
+       beta.sd=0,
+       pop=1400,
+       rho=0.9,sigma=3.6,
+       S.0=0.999,I.0=0.001,R.0=0
+       ),
+     rprocess=euler.sim(
+       step.fun="_sir_euler_simulator",
+       delta.t=1/12,
+       PACKAGE="pomp"
+       ),
+     skeleton.type="vectorfield",
+     skeleton="_sir_ODE",
+     measurement.model=reports~norm(mean=rho*cases,sd=1+sigma*cases),
+     PACKAGE="pomp",
+     obsnames = c("reports"),
+     statenames=c("S","I","R","cases","W"),
+     paramnames=c(
+       "gamma","mu","iota",
+       "beta","beta.sd","pop","rho",
+       "S.0","I.0","R.0"
+       ),
+     zeronames=c("cases"),
+     comp.names=c("S","I","R"),
+     ic.names=c("S.0","I.0","R.0"),
+     nbasis=1L,
+     degree=0L,
+     period=1.0,
+     logvar=c(
+       "beta","gamma","mu","iota","sigma","beta.sd",
+       "S.0","I.0","R.0"
+       ),
+     logitvar="rho",
+     parameter.inv.transform=function (params, logvar, logitvar, ...) {
+       params[logvar] <- log(params[logvar])
+       params[logitvar] <- qlogis(params[logitvar])
+       params
+     },
+     parameter.transform=function (params, logvar, logitvar, ...) {
+       params[logvar] <- exp(params[logvar])
+       params[logitvar] <- plogis(params[logitvar])
+       params
+     },
+     initializer=function(params, t0, comp.names, ic.names, ...) {
+       snames <- c("S","I","R","cases","W")
+       fracs <- params[ic.names]
+       x0 <- numeric(length(snames))
+       names(x0) <- snames
+       x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
+       x0
+     }
+     ) -> bbs
 
-coef(po) <- c(
-              gamma=1/3,mu=0.0,iota=0.0,
-              beta=1.4,
-              beta.sd=0,
-              pop=1400,
-              rho=0.9,sigma=3.6,
-              S.0=0.999,I.0=0.001,R.0=0
-              )
-
-bbs <- po
-
-assign("bbs",bbs,envir=.GlobalEnv)
 c("bbs")

Modified: pkg/pomp/inst/examples/blowflies.R
===================================================================
--- pkg/pomp/inst/examples/blowflies.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/blowflies.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -970,7 +970,4 @@
   
 } 
 
-assign("blowflies1",blowflies1,envir=.GlobalEnv)
-assign("blowflies2",blowflies2,envir=.GlobalEnv)
-
 c("blowflies1","blowflies2")

Modified: pkg/pomp/inst/examples/dacca.R
===================================================================
--- pkg/pomp/inst/examples/dacca.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/dacca.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -105,6 +105,7 @@
      data=cholera,
      times='time',
      t0=t0,
+     params=mle,
      nrstage = nrstage,
      rprocess = euler.sim(
        step.fun = "_cholmodel_one",
@@ -153,7 +154,4 @@
      }
      ) -> dacca
 
-coef(dacca) <- mle
-
-assign("dacca",dacca,envir=.GlobalEnv)
 c("dacca")

Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/euler.sir.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -211,56 +211,54 @@
 4;168
 '
 
+pomp(
+     data=read.csv2(text=dat),
+     times="time",
+     t0=0,
+     params=c(
+       gamma=26,mu=0.02,iota=0.01,
+       beta1=400,beta2=480,beta3=320,
+       beta.sd=1e-3,
+       pop=2.1e6,
+       rho=0.6,
+       S.0=26/400,I.0=0.001,R.0=1-26/400
+       ),
+     rprocess=euler.sim(
+       step.fun="_sir_euler_simulator",
+       delta.t=1/52/20,
+       PACKAGE="pomp"
+       ),
+     skeleton.type="vectorfield",
+     skeleton="_sir_ODE",
+     rmeasure="_sir_binom_rmeasure",
+     dmeasure="_sir_binom_dmeasure",
+     PACKAGE="pomp",
+     obsnames = c("reports"),
+     statenames=c("S","I","R","cases","W"),
+     paramnames=c(
+       "gamma","mu","iota",
+       "beta1","beta.sd","pop","rho",
+       "S.0","I.0","R.0"
+       ),
+     zeronames=c("cases"),
+     comp.names=c("S","I","R"),
+     ic.names=c("S.0","I.0","R.0"),
+     parameter.transform="_sir_par_trans",
+     parameter.inv.transform="_sir_par_untrans",
+     nbasis=3L,
+     degree=3L,
+     period=1.0,
+     initializer=function(params, t0, comp.names, ic.names, ...) {
+       snames <- c("S","I","R","cases","W")
+       fracs <- params[ic.names]
+       x0 <- numeric(length(snames))
+       names(x0) <- snames
+       x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
+       x0
+     }
+     ) -> euler.sir
 
-po <- pomp(
-           data=read.csv2(text=dat),
-           times="time",
-           t0=0,
-           params=c(
-             gamma=26,mu=0.02,iota=0.01,
-             beta1=400,beta2=480,beta3=320,
-             beta.sd=1e-3,
-             pop=2.1e6,
-             rho=0.6,
-             S.0=26/400,I.0=0.001,R.0=1-26/400
-             ),
-           rprocess=euler.sim(
-             step.fun="_sir_euler_simulator",
-             delta.t=1/52/20,
-             PACKAGE="pomp"
-             ),
-           skeleton.type="vectorfield",
-           skeleton="_sir_ODE",
-           rmeasure="_sir_binom_rmeasure",
-           dmeasure="_sir_binom_dmeasure",
-           PACKAGE="pomp",
-           obsnames = c("reports"),
-           statenames=c("S","I","R","cases","W"),
-           paramnames=c(
-             "gamma","mu","iota",
-             "beta1","beta.sd","pop","rho",
-             "S.0","I.0","R.0"
-             ),
-           zeronames=c("cases"),
-           comp.names=c("S","I","R"),
-           ic.names=c("S.0","I.0","R.0"),
-           parameter.transform="_sir_par_trans",
-           parameter.inv.transform="_sir_par_untrans",
-           nbasis=3L,
-           degree=3L,
-           period=1.0,
-           initializer=function(params, t0, comp.names, ic.names, ...) {
-             snames <- c("S","I","R","cases","W")
-             fracs <- params[ic.names]
-             x0 <- numeric(length(snames))
-             names(x0) <- snames
-             x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
-             x0
-           }
-           )
-
 ## the following was originally used to generate the data
 ## simulate(po,nsim=1,seed=329343545L) -> euler.sir
 
-assign("euler.sir",po,envir=.GlobalEnv)
 c("euler.sir")

Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/gillespie.sir.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -583,10 +583,9 @@
        x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))
        x0
      }
-     ) -> po
+     ) -> gillespie.sir
 
 ## originally, the data were created via:
 ## simulate(po,nsim=1,seed=1165270654L) -> gillespie.sir
 
-assign("gillespie.sir",po,envir=.GlobalEnv)
 c("gillespie.sir")

Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/gompertz.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -104,31 +104,30 @@
 100;1,28071364632546;1,23495259845453
 '
 
-po <- pomp(
-           data=subset(read.csv2(text=dat),select=-X),
-           times="time",
-           t0=0,
-           params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),
-           rprocess=discrete.time.sim(
-             step.fun="_gompertz_simulator"
-             ),
-           rmeasure="_gompertz_normal_rmeasure",
-           dmeasure="_gompertz_normal_dmeasure",
-           skeleton.type="map",
-           skeleton="_gompertz_skeleton",
-           paramnames=c("r","K","sigma","tau"),
-           statenames=c("X"),
-           obsnames=c("Y"),
-           parameter.transform=function(params,...){
-             exp(params)
-           },
-           parameter.inv.transform=function(params,...){
-             log(params)
-           }
-           )
+pomp(
+     data=subset(read.csv2(text=dat),select=-X),
+     times="time",
+     t0=0,
+     params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),
+     rprocess=discrete.time.sim(
+       step.fun="_gompertz_simulator"
+       ),
+     rmeasure="_gompertz_normal_rmeasure",
+     dmeasure="_gompertz_normal_dmeasure",
+     skeleton.type="map",
+     skeleton="_gompertz_skeleton",
+     paramnames=c("r","K","sigma","tau"),
+     statenames=c("X"),
+     obsnames=c("Y"),
+     parameter.transform=function(params,...){
+       exp(params)
+     },
+     parameter.inv.transform=function(params,...){
+       log(params)
+     }
+     ) -> gompertz
 
 ## the following was used to create the data included
 ## simulate(po,nsim=1,seed=299438676L) -> gompertz
 
-assign("gompertz",po,envir=.GlobalEnv)
 c("gompertz")

Modified: pkg/pomp/inst/examples/ou2.R
===================================================================
--- pkg/pomp/inst/examples/ou2.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/ou2.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -127,7 +127,6 @@
        tau=1, 
        x1.0=-3, x2.0=4
        )
-     ) -> po
+     ) -> ou2
 
-assign("ou2",po,envir=.GlobalEnv)
 c("ou2")

Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/ricker.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -78,7 +78,6 @@
        params
      },
      PACKAGE="pomp"
-     ) -> po
+     ) -> ricker
 
-assign("ricker",po,envir=.GlobalEnv)
 c("ricker")

Modified: pkg/pomp/inst/examples/rw2.R
===================================================================
--- pkg/pomp/inst/examples/rw2.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/rw2.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -133,7 +133,6 @@
        y1 ~ norm(mean=x1,sd=tau),
        y2 ~ norm(mean=x2,sd=tau)
        )
-     ) -> po
+     ) -> rw2
 
-assign("rw2",po,envir=.GlobalEnv)
 c("rw2")

Modified: pkg/pomp/inst/examples/verhulst.R
===================================================================
--- pkg/pomp/inst/examples/verhulst.R	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/verhulst.R	2014-01-10 19:51:10 UTC (rev 879)
@@ -1047,7 +1047,6 @@
        names(f) <- "n"
        f
      }
-     ) -> po
+     ) -> verhulst
 
-assign("verhulst",po,envir=.GlobalEnv)
 c("verhulst")

Modified: pkg/pomp/man/example.Rd
===================================================================
--- pkg/pomp/man/example.Rd	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/man/example.Rd	2014-01-10 19:51:10 UTC (rev 879)
@@ -5,13 +5,16 @@
   \code{pompExample} loads pre-built example \code{pomp} objects.
 }
 \usage{
-pompExample(example)
+pompExample(example, envir = .GlobalEnv)
 }
 \arguments{
   \item{example}{
     example to load given as a name or literal character string.
     Evoked without an argument, \code{pompExample} lists all available examples.
   }
+  \item{envir}{
+    the environment into which the objects should be loaded.
+  }
 }
 \value{
   \code{pompExample} has the side effect of creating one or more \code{pomp} objects in the global workspace.
@@ -23,5 +26,8 @@
   pompExample("gompertz")
 }
 \seealso{
-  \code{\link{blowflies}}, \code{\link{dacca}}, \code{\link{gompertz}}, \code{\link{ou2}}, \code{\link{ricker}}, \code{\link{rw2}}, \code{\link{euler.sir}}, \code{\link{gillespie.sir}}, \code{\link{bbs}}, \code{\link{verhulst}}
+  \code{\link{blowflies}}, \code{\link{dacca}}, \code{\link{gompertz}},
+  \code{\link{ou2}}, \code{\link{ricker}}, \code{\link{rw2}},
+  \code{\link{euler.sir}}, \code{\link{gillespie.sir}},
+  \code{\link{bbs}}, \code{\link{verhulst}}
 }

Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,7 +21,7 @@
 Loading required package: deSolve
 > 
 > pompExample(bbs)
-newly created pomp objects:
+newly created pomp object(s):
  bbs 
 > 
 > guess <- c(
@@ -70,4 +69,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.176   0.032   2.241 
+  2.152   0.044   2.211 

Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/bbs.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,7 +21,7 @@
 Loading required package: deSolve
 > 
 > pompExample(bbs)
-newly created pomp objects:
+newly created pomp object(s):
  bbs 
 > 
 > set.seed(48857734L)
@@ -60,4 +59,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.648   0.048   2.732 
+  2.884   0.060   3.003 

Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/blowflies.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,7 +21,7 @@
 Loading required package: deSolve
 > 
 > pompExample(blowflies)
-newly created pomp objects:
+newly created pomp object(s):
  blowflies1 blowflies2 
 > 
 > init.state(blowflies1)
@@ -72,4 +71,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.124   0.056   1.204 
+  1.232   0.056   1.300 

Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/dacca.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -24,7 +23,7 @@
 > set.seed(1420306530L)
 > 
 > pompExample(dacca)
-newly created pomp objects:
+newly created pomp object(s):
  dacca 
 > 
 > x <- as.data.frame(dacca)
@@ -52,4 +51,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.304   0.044   3.379 
+  3.492   0.048   3.555 

Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/dimchecks.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -24,7 +23,7 @@
 > set.seed(1420306530L)
 > 
 > pompExample(ricker)
-newly created pomp objects:
+newly created pomp object(s):
  ricker 
 > po <- ricker
 > 
@@ -154,7 +153,7 @@
 > stopifnot(identical(g1,g3[,4:6,]))
 > 
 > pompExample(gompertz)
-newly created pomp objects:
+newly created pomp object(s):
  gompertz 
 > p <- parmat(coef(gompertz),5)
 > f1 <- partrans(gompertz,p,"inv")
@@ -164,4 +163,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.452   0.044   0.518 
+  0.480   0.052   0.542 

Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/fhn.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -93,4 +92,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.908   0.060   1.204 
+  1.016   0.040   1.178 

Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/filtfail.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.3 (2013-03-01) -- "Security Blanket"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
 Copyright (C) 2013 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -118,4 +117,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.464   0.044   0.524 
+  0.516   0.048   0.574 

Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/gillespie.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -119,7 +118,7 @@
 105 0.1666667
 > 
 > pompExample(gillespie.sir)
-newly created pomp objects:
+newly created pomp object(s):
  gillespie.sir 
 > 
 > tail(as.data.frame(simulate(gillespie.sir,times=time(gsir),t0=timezero(gsir),seed=1165270654L)))
@@ -133,4 +132,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.392   0.040   2.459 
+  2.496   0.028   2.543 

Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/gompertz.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -23,7 +22,7 @@
 > options(digits=4)
 > 
 > pompExample(gompertz)
-newly created pomp objects:
+newly created pomp object(s):
  gompertz 
 > 
 > po <- gompertz
@@ -135,4 +134,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.488   0.048   1.562 
+  1.544   0.020   1.584 

Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/logistic.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -124,4 +123,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.788   0.056   0.968 
+  0.868   0.056   1.028 

Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -23,7 +22,7 @@
 > 
 > set.seed(398585L)
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > 
 > time(ou2) <- 1:10
@@ -64,7 +63,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 2.994066 secs
+Time difference of 3.214472 secs
 > 
 > print(
 +       cbind(
@@ -100,4 +99,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  4.876   0.048   4.960 
+  5.148   0.104   5.279 

Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-forecast.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -24,7 +23,7 @@
 > set.seed(921625222L)
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > tm <- time(ou2)
 > y <- obs(ou2)
@@ -63,4 +62,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.528   0.044   1.689 
+  1.472   0.028   1.603 

Modified: pkg/pomp/tests/ou2-icfit.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-icfit.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-icfit.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -24,7 +23,7 @@
 > set.seed(921625222L)
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > 
 > ics <- c("x1.0","x2.0")    # names of the initial condition parameters
@@ -109,4 +108,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 16.897   0.048  17.022 
+ 17.689   0.044  17.801 

Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-kalman.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -70,7 +69,7 @@
 + }
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > 
 > # true coefficients
@@ -166,7 +165,7 @@
     117 function evaluations used
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 5.084913 secs
+Time difference of 3.600606 secs
 > tic <- Sys.time()
 > print(loglik.mle <- -kalm.fit1$value,digits=4)
 [1] -477.2
@@ -190,4 +189,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.596   0.044   5.680 
+  4.112   0.064   4.207 

Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,7 +21,7 @@
 Loading required package: deSolve
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > 
 > set.seed(64857673L)
@@ -72,4 +71,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 19.653   0.024  19.956 
+ 19.853   0.076  20.178 

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,5 +1,5 @@
 
-R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
 Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -21,7 +21,7 @@
 Loading required package: deSolve
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > 
 > set.seed(64857673L)
@@ -282,4 +282,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 12.416   0.084  12.654 
+ 12.152   0.060  12.353 

Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-mif2.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.3 (2013-03-01) -- "Security Blanket"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
 Copyright (C) 2013 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,7 +21,7 @@
 Loading required package: deSolve
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
 > 
 > pdf(file="ou2-mif2.pdf")
@@ -130,4 +129,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 49.343   0.076  49.753 
+ 51.519   0.044  51.909 

Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save	2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-nlf.Rout.save	2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -24,7 +23,7 @@
 > set.seed(594861940L)
 > 
 > pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
  ou2 
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 879

From noreply at r-forge.r-project.org  Fri Jan 10 23:43:03 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 10 Jan 2014 23:43:03 +0100 (CET)
Subject: [Pomp-commits] r880 - www/vignettes
Message-ID: <20140110224303.7EF84184BAE@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-10 23:43:03 +0100 (Fri, 10 Jan 2014)
New Revision: 880

Modified:
   www/vignettes/Makefile
   www/vignettes/advanced_topics_in_pomp.R
   www/vignettes/advanced_topics_in_pomp.pdf
   www/vignettes/bsmc-ricker-flat-prior.rda
   www/vignettes/bsmc-ricker-normal-prior.rda
   www/vignettes/complex-sir-def.rda
   www/vignettes/gompertz-multi-mif.rda
   www/vignettes/gompertz-trajmatch.rda
   www/vignettes/intro_to_pomp.R
   www/vignettes/intro_to_pomp.Rnw
   www/vignettes/intro_to_pomp.pdf
   www/vignettes/nlf-fits.rda
   www/vignettes/nlf-lag-tests.rda
   www/vignettes/nlf-multi-short.rda
   www/vignettes/plugin-C-code.rda
   www/vignettes/plugin-R-code.rda
   www/vignettes/ricker-first-probe.rda
   www/vignettes/ricker-mif.rda
   www/vignettes/ricker-probe-match.rda
   www/vignettes/ricker-probe.rda
   www/vignettes/sim-sim.rda
   www/vignettes/sir-pomp-def.rda
   www/vignettes/vectorized-C-code.rda
   www/vignettes/vectorized-R-code.rda
Log:
- update the vignettes


Modified: www/vignettes/Makefile
===================================================================
--- www/vignettes/Makefile	2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/Makefile	2014-01-10 22:43:03 UTC (rev 880)
@@ -9,10 +9,10 @@
 vignettes: advanced_topics_in_pomp.pdf advanced_topics_in_pomp.R intro_to_pomp.pdf intro_to_pomp.R
 
 %.R: %.Rnw
-	$(REXE) CMD Stangle $*
+	$(REXE) CMD Stangle $*.Rnw
 
 %.tex: %.Rnw
-	$(REXE) CMD Sweave $*
+	$(REXE) CMD Sweave $*.Rnw
 
 %.pdf: %.tex
 	$(PDFLATEX) $*

Modified: www/vignettes/advanced_topics_in_pomp.R
===================================================================
--- www/vignettes/advanced_topics_in_pomp.R	2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/advanced_topics_in_pomp.R	2014-01-10 22:43:03 UTC (rev 880)
@@ -1,4 +1,4 @@
-### R code from vignette source 'advanced_topics_in_pomp'
+### R code from vignette source 'advanced_topics_in_pomp.Rnw'
 ### Encoding: UTF-8
 
 ###################################################

Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/bsmc-ricker-flat-prior.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/bsmc-ricker-normal-prior.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/complex-sir-def.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/gompertz-multi-mif.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/gompertz-trajmatch.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/intro_to_pomp.R
===================================================================
--- www/vignettes/intro_to_pomp.R	2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/intro_to_pomp.R	2014-01-10 22:43:03 UTC (rev 880)
@@ -1,4 +1,4 @@
-### R code from vignette source 'intro_to_pomp'
+### R code from vignette source 'intro_to_pomp.Rnw'
 ### Encoding: UTF-8
 
 ###################################################
@@ -401,11 +401,9 @@
 ## theta.true <- coef(gompertz)
 ## theta.mif <- apply(sapply(mf,coef),1,mean)
 ## loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-## loglik.mif.est <- logmeanexp(loglik.mif)
-## loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+## loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
 ## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-## loglik.true.est <- logmeanexp(loglik.true)
-## loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+## loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
 
 
 ###################################################
@@ -446,41 +444,35 @@
 theta.true <- coef(gompertz)
 theta.mif <- apply(sapply(mf,coef),1,mean)
 loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-loglik.mif.est <- logmeanexp(loglik.mif)
-loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
 loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-loglik.true.est <- logmeanexp(loglik.true)
-loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
   toc <- Sys.time()
   etime <- toc-tic
   save(
        mf,estpars,
        theta.mif,theta.true,
        loglik.mif.est,loglik.true.est,
-       loglik.mif.se,loglik.true.se,
        etime,
        file=binary.file,
        compress="xz"
        )
 }
 rbind(
-#      guess=c(signif(theta.guess[estpars],3),loglik=round(loglik.guess,1)),
-      mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est,1),loglik.se=signif(loglik.mif.se,2)),
-      truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est,1),loglik.se=signif(loglik.true.se,2))
+      mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est[1],1),loglik.se=signif(loglik.mif.est[2],2)),
+      truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est[1],1),loglik.se=signif(loglik.true.est[2],2))
       ) -> results.table
 
 
 ###################################################
-### code chunk number 41: intro_to_pomp.Rnw:689-690 (eval = FALSE)
+### code chunk number 41: intro_to_pomp.Rnw:685-686 (eval = FALSE)
 ###################################################
 ## theta.true <- coef(gompertz)
 ## theta.mif <- apply(sapply(mf,coef),1,mean)
 ## loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-## loglik.mif.est <- logmeanexp(loglik.mif)
-## loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+## loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
 ## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-## loglik.true.est <- logmeanexp(loglik.true)
-## loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+## loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
 
 
 ###################################################
@@ -932,7 +924,7 @@
 
 
 ###################################################
-### code chunk number 69: intro_to_pomp.Rnw:1124-1125
+### code chunk number 69: intro_to_pomp.Rnw:1120-1121
 ###################################################
 fits
 
@@ -1117,7 +1109,7 @@
 
 
 ###################################################
-### code chunk number 77: intro_to_pomp.Rnw:1270-1271
+### code chunk number 77: intro_to_pomp.Rnw:1266-1267
 ###################################################
 apply(fvals,2,function(x)sd(x)/mean(x))
 
@@ -1130,7 +1122,7 @@
 ##                 transform.params=TRUE,
 ##                 est=c("K","r"),
 ##                 lags=2,
-##                 seed=7639873L, 
+##                 seed=7639873, 
 ##                 method="Nelder-Mead",
 ##                 trace=4,
 ##                 nasymp=5000
@@ -1149,7 +1141,7 @@
                 transform.params=TRUE,
                 est=c("K","r"),
                 lags=2,
-                seed=7639873L, 
+                seed=7639873, 
                 method="Nelder-Mead",
                 trace=4,
                 nasymp=5000
@@ -1159,7 +1151,7 @@
 
 
 ###################################################
-### code chunk number 80: intro_to_pomp.Rnw:1309-1310
+### code chunk number 80: intro_to_pomp.Rnw:1305-1306
 ###################################################
 set.seed(32329L)
 
@@ -1229,7 +1221,7 @@
 
 
 ###################################################
-### code chunk number 83: intro_to_pomp.Rnw:1347-1348
+### code chunk number 83: intro_to_pomp.Rnw:1343-1344
 ###################################################
 apply(pars,2,sd)
 

Modified: www/vignettes/intro_to_pomp.Rnw
===================================================================
--- www/vignettes/intro_to_pomp.Rnw	2014-01-10 19:51:10 UTC (rev 879)
+++ www/vignettes/intro_to_pomp.Rnw	2014-01-10 22:43:03 UTC (rev 880)
@@ -646,11 +646,9 @@
 theta.true <- coef(gompertz)
 theta.mif <- apply(sapply(mf,coef),1,mean)
 loglik.mif <- replicate(n=10,logLik(pfilter(mf[[1]],params=theta.mif,Np=10000)))
-loglik.mif.est <- logmeanexp(loglik.mif)
-loglik.mif.se <- sd(exp(loglik.mif-bl))/exp(loglik.mif.est-bl)
+loglik.mif.est <- logmeanexp(loglik.mif,se=TRUE)
 loglik.true <- replicate(n=10,logLik(pfilter(gompertz,params=theta.true,Np=10000)))
-loglik.true.est <- logmeanexp(loglik.true)
-loglik.true.se <- sd(exp(loglik.true-bl))/exp(loglik.true.est-bl)
+loglik.true.est <- logmeanexp(loglik.true,se=TRUE)
 @ 
 
 <<gompertz-multi-mif-eval,echo=F,results=hide>>=
@@ -668,16 +666,14 @@
        mf,estpars,
        theta.mif,theta.true,
        loglik.mif.est,loglik.true.est,
-       loglik.mif.se,loglik.true.se,
        etime,
        file=binary.file,
        compress="xz"
        )
 }
 rbind(
-#      guess=c(signif(theta.guess[estpars],3),loglik=round(loglik.guess,1)),
-      mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est,1),loglik.se=signif(loglik.mif.se,2)),
-      truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est,1),loglik.se=signif(loglik.true.se,2))
+      mle=c(signif(theta.mif[estpars],3),loglik=round(loglik.mif.est[1],1),loglik.se=signif(loglik.mif.est[2],2)),
+      truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true.est[1],1),loglik.se=signif(loglik.true.est[2],2))
       ) -> results.table
 @ 
 
@@ -1277,7 +1273,7 @@
                 transform.params=TRUE,
                 est=c("K","r"),
                 lags=2,
-                seed=7639873L, 
+                seed=7639873, 
                 method="Nelder-Mead",
                 trace=4,
                 nasymp=5000

Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-fits.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-lag-tests.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/nlf-multi-short.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/plugin-C-code.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/plugin-R-code.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-first-probe.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-mif.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-probe-match.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/ricker-probe.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/sim-sim.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/sir-pomp-def.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/vectorized-C-code.rda
===================================================================
(Binary files differ)

Modified: www/vignettes/vectorized-R-code.rda
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Sat Jan 11 19:24:48 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 11 Jan 2014 19:24:48 +0100 (CET)
Subject: [Pomp-commits] r881 - in pkg/pompExamples: . R man
Message-ID: <20140111182448.BEF5A186786@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-11 19:24:48 +0100 (Sat, 11 Jan 2014)
New Revision: 881

Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/R/budmoth.R
   pkg/pompExamples/R/pertussis.R
   pkg/pompExamples/man/budmoth.Rd
   pkg/pompExamples/man/pertussis.Rd
Log:
- small change to pertussis.sim and budmoth.sim


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/DESCRIPTION	2014-01-11 18:24:48 UTC (rev 881)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.22-1
-Date: 2013-11-11
+Version: 0.23-1
+Date: 2014-01-10
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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/pompExamples/R/budmoth.R
===================================================================
--- pkg/pompExamples/R/budmoth.R	2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/R/budmoth.R	2014-01-11 18:24:48 UTC (rev 881)
@@ -1,9 +1,10 @@
 budmoth.sim <- function (which) {
   if (missing(which)) {
-    cat("available datasets:",
-        sQuote(c("food","para1","para2","tri")),"\n")
+    datasets <- c("food","para1","para2","tri")
+    cat("available datasets:",sQuote(datasets),"\n")
+    invisible(datasets)
   } else {
-    w <- as.character(substitute(which))
+    which <- as.character(substitute(which))
     simulate(
              pomp(
                   data=data.frame(
@@ -13,32 +14,36 @@
                   time="time",
                   t0=-1,
                   params=switch(
-                    w,
+                    which,
                     tri=c(
-                      alpha=0.5, sig.alpha=0.1, gam=50, lambda=22, sig.lambda=0.25, g=0.08, delta=10,
+                      alpha=0.5, sig.alpha=0.1, gam=50, lambda=22,
+                      sig.lambda=0.25, g=0.08, delta=10,
                       a=1.7, sig.a=0.1, w=0.15, beta0=0, beta1=35, u=0.9,
                       sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
                       Q.0=0.96, N.0=0.02, S.0=0.22
                       ),
                     food=c(
-                      alpha=0.5, sig.alpha=0.1, gam=20, lambda=5, sig.lambda=0.25, g=0.02, delta=10,
+                      alpha=0.5, sig.alpha=0.1, gam=20, lambda=5,
+                      sig.lambda=0.25, g=0.02, delta=10,
                       a=1, sig.a=0.1, w=0, beta0=0, beta1=35, u=0.9,
                       sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
                       Q.0=0.96, N.0=0.02, S.0=0.22
                       ),
                     para1=c(
-                      alpha=0.5, sig.alpha=0.1, gam=50, lambda=22, sig.lambda=0.25, g=0.08, delta=0.5,
+                      alpha=0.5, sig.alpha=0.1, gam=50, lambda=22,
+                      sig.lambda=0.25, g=0.08, delta=0.5,
                       a=1.7, sig.a=0.1, w=0.15, beta0=0, beta1=35, u=0.9,
                       sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
                       Q.0=0.96, N.0=0.02, S.0=0.22
                       ),
                     para2=c(
-                      alpha=0.5, sig.alpha=0.1, gam=50, lambda=10, sig.lambda=5, g=0.08, delta=0.5,
+                      alpha=0.5, sig.alpha=0.1, gam=50, lambda=10,
+                      sig.lambda=5, g=0.08, delta=0.5,
                       a=1.7, sig.a=1, w=0.15, beta0=0, beta1=35, u=0.9,
                       sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
                       Q.0=0.96, N.0=0.02, S.0=0.22
                       ),
-                    stop("unrecognized dataset ",sQuote(w),call.=FALSE)
+                    stop("unrecognized dataset ",sQuote(which),call.=FALSE)
                     ),
                   rprocess=euler.sim(
                     step.fun="budmoth_map",
@@ -75,24 +80,26 @@
                     "g","delta","a","w","sig.a","beta1","sigQobs",
                     "sigNobs", "sigSobs","N.0"
                     ),
-                  parameter.transform=function (params, logitvar, logvar, ...) {
+                  parameter.transform=function (params, logitvar,
+                    logvar, ...) {
                     params[logitvar] <- plogis(params[logitvar])
                     params[logvar] <- exp(params[logvar])
                     params
                   },
-                  parameter.inv.transform=function (params, logitvar, logvar, ...) {
+                  parameter.inv.transform=function (params, logitvar,
+                    logvar, ...) {
                     params[logitvar] <- qlogis(params[logitvar])
                     params[logvar] <- log(params[logvar])
                     params
                   }
                   ),
              seed=switch(
-               w,
+               which,
                tri=1691699385L,
                food=1054866677L,
                para1=1116757478L,
                para2=1361101458L,
-               stop("unrecognized dataset ",sQuote(w),call.=FALSE)
+               stop("unrecognized dataset ",sQuote(which),call.=FALSE)
                )
              )
   }

Modified: pkg/pompExamples/R/pertussis.R
===================================================================
--- pkg/pompExamples/R/pertussis.R	2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/R/pertussis.R	2014-01-11 18:24:48 UTC (rev 881)
@@ -4,11 +4,15 @@
 
 pertussis.sim <- function (which) {
   if (missing(which)) {
-    cat("available datasets:",
-        sQuote(c("SEIR.small","SEIR.big",
-                 "SEIRS.small","SEIRS.big",
-                 "SEIRR.small","SEIRR.big",
-                 "full.small","full.big")),"\n")
+    datasets <- c(
+                  "SEIR.small","SEIR.big",
+                  "SEIRS.small","SEIRS.big",
+                  "SEIRR.small","SEIRR.big",
+                  "full.small","full.big"
+                  )
+
+    cat("available datasets:",sQuote(datasets),"\n")
+    invisible(datasets)
   } else {
     which <- as.character(substitute(which))
     simulate(

Modified: pkg/pompExamples/man/budmoth.Rd
===================================================================
--- pkg/pompExamples/man/budmoth.Rd	2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/man/budmoth.Rd	2014-01-11 18:24:48 UTC (rev 881)
@@ -20,7 +20,7 @@
 plot(budmoth.sim(food))
 plot(budmoth.sim(para1))
 plot(budmoth.sim(para2))
-plot(budmoth.sim(tri))
+plot(budmoth.sim("tri"))
 }
 \seealso{the \dQuote{budmoth-model} vignette}
 \keyword{datasets}

Modified: pkg/pompExamples/man/pertussis.Rd
===================================================================
--- pkg/pompExamples/man/pertussis.Rd	2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/man/pertussis.Rd	2014-01-11 18:24:48 UTC (rev 881)
@@ -18,7 +18,7 @@
 plot(pertussis.sim(SEIR.small))
 plot(pertussis.sim(SEIRS.big))
 plot(pertussis.sim(SEIRR.small))
-plot(pertussis.sim(full.big))
+plot(pertussis.sim("full.big"))
 }
 \seealso{the \dQuote{pertussis-model} vignette}
 \keyword{datasets}


From noreply at r-forge.r-project.org  Tue Jan 14 12:07:52 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 14 Jan 2014 12:07:52 +0100 (CET)
Subject: [Pomp-commits] r882 - pkg/pompExamples
Message-ID: <20140114110752.2A9DC186C5D@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-14 12:07:51 +0100 (Tue, 14 Jan 2014)
New Revision: 882

Modified:
   pkg/pompExamples/DESCRIPTION
Log:


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2014-01-11 18:24:48 UTC (rev 881)
+++ pkg/pompExamples/DESCRIPTION	2014-01-14 11:07:51 UTC (rev 882)
@@ -2,18 +2,18 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.23-1
-Date: 2014-01-10
+Date: 2014-01-14
 Maintainer: Aaron A. King <kingaa at umich.edu>
-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")),
+Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
+	   email="kingaa at umich.edu"),
 	  person(given=c("Carles"),family="Breto",role=c("aut")),
 	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
+	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
+	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
 	  person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),
-	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
-	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
 	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
-	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")))
-Maintainer: Aaron A. King <kingaa at umich.edu>
+	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
+	  person(given=c("Helen"),family="Wearing",role=c("ctb")))
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
 Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.45-4)


From noreply at r-forge.r-project.org  Tue Jan 14 18:48:08 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 14 Jan 2014 18:48:08 +0100 (CET)
Subject: [Pomp-commits] r883 - www
Message-ID: <20140114174808.4C303185764@r-forge.r-project.org>

Author: kingaa
Date: 2014-01-14 18:48:08 +0100 (Tue, 14 Jan 2014)
New Revision: 883

Modified:
   www/index.php
Log:
- add link to bug tracker page


Modified: www/index.php
===================================================================
--- www/index.php	2014-01-14 11:07:51 UTC (rev 882)
+++ www/index.php	2014-01-14 17:48:08 UTC (rev 883)
@@ -3,6 +3,7 @@
 $group_name=ereg_replace('([^\.]*)\..*$','\1',$_SERVER['HTTP_HOST']);
 $themeroot='http://r-forge.r-project.org/themes/rforge/';
 $rforgepkgs = "http://r-forge.r-project.org/R/?group_id=214";
+$tracker = "http://r-forge.r-project.org/tracker/?group_id=214";
 $cranpage = "http://cran.at.r-project.org/web/packages/pomp/";
 $crancontents = file_get_contents($cranpage);
 preg_match("/<tr><td valign=top>Version:<\/td>\\n<td>(.+?)<\/td>/",$crancontents,$matches);
@@ -54,6 +55,7 @@
 <li><a href="http://lists.r-forge.r-project.org/pipermail/pomp-announce/"><i>pomp-announce</i> mailing list archives</a></li>
 <li><a target="_blank" href="http://cran.at.r-project.org/web/packages/pomp/NEWS">Package NEWS file</a></li>
 <li><a href="./index.php?nav=vignettes">Tutorial vignettes</a></li>
+<li><a href="<?php echo $tracker;?>">Bug reports, feature &amp; support requests</a></li>
 <li><a href="./index.php?nav=bib">References to the literature</a></li>
 <li><a href="./index.php?nav=authors">Authors' homepages</a></li>
 </ul>