[Pomp-commits] r865 - in pkg/pompExamples: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 5 18:22:33 CET 2013
Author: kingaa
Date: 2013-11-05 18:22:33 +0100 (Tue, 05 Nov 2013)
New Revision: 865
Added:
pkg/pompExamples/vignettes/
Removed:
pkg/pompExamples/inst/LICENSE
pkg/pompExamples/inst/doc/
Modified:
pkg/pompExamples/.Rbuildignore
pkg/pompExamples/DESCRIPTION
pkg/pompExamples/NAMESPACE
pkg/pompExamples/vignettes/budmoth-model.Rnw
pkg/pompExamples/vignettes/budmoth-model.pdf
pkg/pompExamples/vignettes/pertussis-model.Rnw
pkg/pompExamples/vignettes/pertussis-model.pdf
Log:
- changes to bring 'pompExamples' up to date with the package building and checking process
- vignettes are now rebuilt
Modified: pkg/pompExamples/.Rbuildignore
===================================================================
--- pkg/pompExamples/.Rbuildignore 2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/.Rbuildignore 2013-11-05 17:22:33 UTC (rev 865)
@@ -1,6 +1,3 @@
-inst/doc/Makefile
+vignettes/Makefile
inst/data-R/Makefile
-inst/doc/(.+?)\.bst$
-inst/doc/(.+?)\.R$
-inst/doc/(.+?)\.png$
-inst/doc/(.+?)\.pbs$
+vignettes/(.+?)\.pbs$
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/DESCRIPTION 2013-11-05 17:22:33 UTC (rev 865)
@@ -1,23 +1,24 @@
Package: pompExamples
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.21-3
-Date: 2013-06-11
+Version: 0.21-4
+Date: 2013-11-05
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")),
person(given=c("Carles"),family="Breto",role=c("aut")),
person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
+ 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("Bruce","E."),family="Kendall",role=c("ctb")),
person(given=c("Michael"),family="Lavine",role=c("ctb")),
- person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
- person(given=c("Helen"),family="Wearing",role=c("ctb")))
+ person(given=c("Daniel","C."),family="Reuman",role=c("ctb")))
+Maintainer: Aaron A. King <kingaa at umich.edu>
URL: http://pomp.r-forge.r-project.org
Description: More 'pomp' examples.
-Depends: R(>= 3.0.0), stats, methods, graphics, pomp(>= 0.45-4)
+Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.45-4)
+Suggests: Rmpi,mpifarm,plyr,reshape2,ggplot2,xtable
License: GPL (>= 2)
-LazyLoad: true
LazyData: false
-BuildVignettes: no
+BuildVignettes: true
Collate: version.R budmoth.R pertussis.R
Modified: pkg/pompExamples/NAMESPACE
===================================================================
--- pkg/pompExamples/NAMESPACE 2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/NAMESPACE 2013-11-05 17:22:33 UTC (rev 865)
@@ -1,3 +1,3 @@
useDynLib(pompExamples)
-importFrom(pomp)
+import(pomp)
export(pertussis.sim,budmoth.sim)
Deleted: pkg/pompExamples/inst/LICENSE
===================================================================
--- pkg/pompExamples/inst/LICENSE 2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/inst/LICENSE 2013-11-05 17:22:33 UTC (rev 865)
@@ -1,16 +0,0 @@
-The POMP package: Inference for partially-observed Markov processes
-
-This package is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or (at
-your option) any later version.
-
-This package is distributed in the hope that it will be useful, but
-WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 675 Mass Ave., Cambridge, MA 02139 USA.
-
Modified: pkg/pompExamples/vignettes/budmoth-model.Rnw
===================================================================
--- pkg/pompExamples/inst/doc/budmoth-model.Rnw 2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/vignettes/budmoth-model.Rnw 2013-11-05 17:22:33 UTC (rev 865)
@@ -24,7 +24,7 @@
\newcommand\logit{{\mathrm{logit}}}
\newcommand\expit{{\mathrm{expit}}}
-\SweaveOpts{echo=T,results=verbatim,print=F,eps=F,pdf=F,png=T,keep.source=T,split=T,prefix=T,prefix.string=budmoth-model,resolution=150}
+\SweaveOpts{echo=T,results=verbatim,print=F,eps=F,pdf=F,png=T,keep.source=T,split=F,prefix=T,prefix.string=budmoth-model,resolution=150}
\title{Larch Budmoth State-Space Model}
\author{AAK, ELI, SPE, KBN}
@@ -159,7 +159,7 @@
<<data-plot,fig=T,height=6,width=8,pdf=T,png=F,echo=F>>=
require(pompExamples)
require(plyr)
-require(reshape)
+require(reshape2)
require(ggplot2)
data(budmoth.sim)
x <- ldply(budmoth.sim,as.data.frame)
@@ -429,9 +429,11 @@
<<slices-plot,fig=T,png=T,pdf=F,echo=F,height=7,width=7>>=
require(ggplot2)
require(plyr)
-require(reshape)
-x <- melt(slices,id.vars=c(".id","dataset","slice","loglik","nfail","etime"))
-x$.id <- NULL
+require(reshape2)
+slices$.id <- NULL
+slices$etime <- NULL
+slices$nfail <- NULL
+x <- melt(slices,id.vars=c("dataset","slice","loglik"))
x$slice <- factor(x$slice,levels=levels(x$variable))
x <- subset(x,slice==variable)
x <- ddply(x,~dataset+slice,subset,loglik>max(loglik)-50)
Modified: pkg/pompExamples/vignettes/budmoth-model.pdf
===================================================================
(Binary files differ)
Modified: pkg/pompExamples/vignettes/pertussis-model.Rnw
===================================================================
--- pkg/pompExamples/inst/doc/pertussis-model.Rnw 2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/vignettes/pertussis-model.Rnw 2013-11-05 17:22:33 UTC (rev 865)
@@ -370,7 +370,7 @@
<<dataplots,fig=T,echo=F,png=T,pdf=F,height=8,width=6>>=
require(ggplot2)
require(plyr)
-require(reshape)
+require(reshape2)
require(pompExamples)
data(pertussis.sim)
x <- ldply(pertussis.sim,as.data.frame)
Modified: pkg/pompExamples/vignettes/pertussis-model.pdf
===================================================================
(Binary files differ)
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