[Pomp-commits] r1212 - pkg/pompExamples pkg/pompExamples/vignettes www/vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Jun 17 18:43:30 CEST 2015 

Author: kingaa
Date: 2015-06-17 18:43:30 +0200 (Wed, 17 Jun 2015)
New Revision: 1212

Added:
   www/vignettes/bsflu-mf1.rds
   www/vignettes/bsflu-mf3.rds
   www/vignettes/bsflu-tm1.rds
   www/vignettes/bsflu-tm3.rds
   www/vignettes/bsflu.Rmd
   www/vignettes/bsflu.html
   www/vignettes/parus-mf.rds
   www/vignettes/parus-tm1.rds
   www/vignettes/parus.Rmd
   www/vignettes/parus.html
Removed:
   pkg/pompExamples/vignettes/Makefile
   pkg/pompExamples/vignettes/bsflu-mf1.rds
   pkg/pompExamples/vignettes/bsflu-mf3.rds
   pkg/pompExamples/vignettes/bsflu-tm1.rds
   pkg/pompExamples/vignettes/bsflu-tm3.rds
   pkg/pompExamples/vignettes/bsflu.Rmd
   pkg/pompExamples/vignettes/bsflu.html
   pkg/pompExamples/vignettes/parus-mf.rds
   pkg/pompExamples/vignettes/parus-tm1.rds
   pkg/pompExamples/vignettes/parus.Rmd
   pkg/pompExamples/vignettes/parus.html
Modified:
   pkg/pompExamples/DESCRIPTION
Log:
- remove all vignettes from pompExamples

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/DESCRIPTION	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1,7 +1,7 @@
 Package: pompExamples
 Type: Package
 Title: Additional pomp examples
-Version: 0.27-3
+Version: 0.28-1
 Date: 2015-06-17
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
@@ -17,11 +17,8 @@
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
 Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.65-1)
-Suggests: plyr, reshape2, ggplot2, knitr, markdown
 LinkingTo: pomp
 Additional_repositories: http://r-forge.r-rproject.org
 License: GPL (>= 2)
 LazyData: false
-BuildVignettes: false
-VignetteBuilder: knitr
 Collate: aaa.R pertussis.R

Deleted: pkg/pompExamples/vignettes/Makefile
===================================================================
--- pkg/pompExamples/vignettes/Makefile	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/Makefile	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1,10 +0,0 @@
-RSCRIPT = Rscript --vanilla
-RM = rm -f
-
-vignettes: bsflu.html
-	$(RM) -r figure
-
-%.html: %.Rmd
-	$(RSCRIPT) -e 'knitr::knit("$*.Rmd")'
-	$(RSCRIPT) -e 'markdown::markdownToHTML("$*.md","$*.html")'
-	$(RM) $*.md

Deleted: pkg/pompExamples/vignettes/bsflu-mf1.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-mf1.rds	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/bsflu-mf1.rds	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1 +0,0 @@
-‹      ‹àb```b`fdb`b2™…ó1だm[Y{`|ûo®nÙŽM†óóŽnJó™êý¥5Æwà`€ˆüŸ¨ü·!¬ÛßFyÂùï¿:¤þe``añX84k^bnj1! vD-'?='3Êã„ðôŠS¡,N©%‰0¥™yiz)P{r>:·Áe.ÊȇY[œV”˜Œæ΢ür=˜{xA× $þº£“s‹aŽ†	r¥$–$êÍMòþ ý¹„&~  
\ No newline at end of file

Deleted: pkg/pompExamples/vignettes/bsflu-mf3.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-mf3.rds	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/bsflu-mf3.rds	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1,4 +0,0 @@
-‹      ‹àb```b`fdb`b2™…ó1ãïŠ|ôcÓ`|û]_„¸VÍ…óóŠ¿|>翵ú1ëßþ>߁C€
- ò òŸOòÛòÎPÎÿÕ¹ õ(ˆÏÀÂÀ	¤YósS‹°ã ‚l9ùé9™ÙP'„§Wœ
-`qJ-I„)ÍÌKÓ+HòØ“óѹe.sQF>ÌÚâ´¢Äd4·på—ëÁÜÃ
-¼ ñНœ“Xs4L+%±$Qhln*÷ ¦‚ý®~  
\ No newline at end of file

Deleted: pkg/pompExamples/vignettes/bsflu-tm1.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-tm1.rds	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/bsflu-tm1.rds	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1 +0,0 @@
-‹      ‹àb```b`fdb`b2™…ó1ãØ…UÑFÚ7`| óíóds'MuóŸËKì`mm„ñ8PÕÿy€Ê]è,üþÁM8ÿýWç‚Ôÿ¡,L`ûX84k^bnj1! vD-'?='3Êã„ðôŠS¡,N©%‰0¥™yiz)P{r>:·Áe.ÊȇY[œV”˜Œæ΢ür=˜{xA× $þº£“s‹aŽ†	r¥$–$êÍMòþ î³£¡~  
\ No newline at end of file

Deleted: pkg/pompExamples/vignettes/bsflu-tm3.rds
===================================================================
--- pkg/pompExamples/vignettes/bsflu-tm3.rds	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/bsflu-tm3.rds	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1,4 +0,0 @@
-‹      ‹àb```b`fdb`b2™…ó1ã?Ï—*S,Ua| óí³ß+­v7σó_éþx»TýŒïÀ!€ªþÏTþKÛFÿ©2pþû¯Î©ÿCX˜Àö±0piÖ¼ÄÜÔb C ì8ˆ [N~zNf6”Ç	áé§BXœRKaJ3óÒô
-R <öä|tn‚Ë\”‘³¶8­(1Í-œEùåz0÷ð‚¯HütG'ç$Ã
-äJI,IÔ››
-äý Q&~  
\ No newline at end of file

Deleted: pkg/pompExamples/vignettes/bsflu.Rmd
===================================================================
--- pkg/pompExamples/vignettes/bsflu.Rmd	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/bsflu.Rmd	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1,183 +0,0 @@
-%\VignetteIndexEntry{Boarding-school influenza example}
-%\VignetteEngine{knitr::knitr}
-
-# Boarding-School Flu Outbreak Analysis  
-***Aaron A. King***
-
-```{r setup,include=FALSE}
-require(pomp)
-require(plyr)
-require(reshape2)
-options(stringsAsFactors=FALSE,keep.source=TRUE,encoding="UTF-8")
-
-require(ggplot2)
-theme_set(theme_bw())
-
-require(knitr)
-opts_knit$set(out.format="html")
-opts_chunk$set(
-  progress=TRUE,
-  prompt=FALSE,tidy=FALSE,highlight=TRUE,
-  strip.white=TRUE,
-  warning=FALSE,message=FALSE,error=FALSE,
-  echo=TRUE,cache=FALSE,
-  results='markup',
-  fig.show='asis',
-  fig.height=5,fig.width=10,
-  dpi=100
-  )
-
-require(pompExamples)
-set.seed(862663052L)
-```
-
-First, a little function to cache the results of expensive computations.
-
-```{r bake}
-bake <- function (file, expr) {
-  if (file.exists(file)) {
-    readRDS(file)
-    } else {
-      val <- eval(expr)
-      saveRDS(val,file=file)
-      val
-      }
-  }
-```
-
-## Flu model with exponentially-distributed waiting times
-
-```{r bsflu1,cache=FALSE}
-pompExample(bsflu)
-coef(bsflu)
-```
-```{r plot1}
-simdat <- simulate(bsflu,nsim=10,obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
-ggplot(data=melt(simdat,id=c("sim","time")),
-       mapping=aes(x=time,y=value,group=interaction(variable,sim),
-                   color=variable,size=sim=="data",alpha=sim=="data"))+
-  geom_line()+
-  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
-  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
-```
-
-### Trajectory matching
-
-```{r tm1}
-bake("bsflu-tm1.rds",{
-  traj.match(bsflu,est=c("Beta","inf.pd","rho"),transform=TRUE) -> tm
-  traj.match(tm,method='subplex') -> tm
-  data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
-  }) -> tm1
-```
-```{r tm1-simplot}
-simdat <- simulate(bsflu,params=unlist(tm1),nsim=10,
-                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
-ggplot(data=melt(simdat,id=c("sim","time")),
-       mapping=aes(x=time,y=value,group=interaction(variable,sim),
-                   color=variable,size=sim=="data",alpha=sim=="data"))+
-  geom_line()+
-  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
-  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
-```
-
-### Iterated filtering
-
-```{r mf1}
-bake("bsflu-mf1.rds",{
-  mif(bsflu,rw.sd=c(Beta=0.05,inf.pd=0.05,rho=0.05),
-      cooling.fraction=0.9,var.factor=2,
-      Nmif=50,Np=1000,method='mif2',transform=TRUE) -> mf
-  mif(mf,Nmif=50,cooling.fraction=0.5) -> mf
-  mif(mf,Nmif=50,cooling.fraction=0.1) -> mf
-  ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
-  data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
-  }) -> mf1
-```
-```{r mf1-simplot}
-simdat <- simulate(bsflu,params=unlist(mf1),nsim=10,
-                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
-ggplot(data=melt(simdat,id=c("sim","time")),
-       mapping=aes(x=time,y=value,group=interaction(variable,sim),
-                   color=variable,size=sim=="data",alpha=sim=="data"))+
-  geom_line()+
-  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
-  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
-```
-
-## Model with Erlang(3) confinement period
-
-```{r bsflu3,cache=FALSE}
-pompExample(bsflu3)
-coef(bsflu3)
-```
-```{r plot3}
-simdat <- simulate(bsflu3,nsim=10,obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
-ggplot(data=melt(simdat,id=c("sim","time")),
-       mapping=aes(x=time,y=value,group=interaction(variable,sim),
-                   color=variable,size=sim=="data",alpha=sim=="data"))+
-  geom_line()+
-  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
-  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
-```
-
-### Trajectory matching
-
-```{r tm3}
-bake("bsflu-tm3.rds",{
-  traj.match(bsflu3,est=c("Beta","inf.pd","rho"),transform=TRUE) -> tm
-  traj.match(tm,method='subplex') -> tm
-  data.frame(loglik=logLik(tm),loglik.se=0,as.list(coef(tm)))
-  }) -> tm3
-```
-```{r tm3-simplot}
-simdat <- simulate(bsflu3,params=unlist(tm3),nsim=10,
-                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
-ggplot(data=melt(simdat,id=c("sim","time")),
-       mapping=aes(x=time,y=value,group=interaction(variable,sim),
-                   color=variable,size=sim=="data",alpha=sim=="data"))+
-  geom_line()+
-  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
-  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
-```
-
-### Iterated filtering
-
-```{r mf3}
-bake("bsflu-mf3.rds",{
-  mif(bsflu3,rw.sd=c(Beta=0.05,inf.pd=0.05,rho=0.05),
-      cooling.fraction=0.9,var.factor=2,
-      Nmif=50,Np=1000,method='mif2',transform=TRUE) -> mf
-  mif(mf,Nmif=50,cooling.fraction=0.5) -> mf
-  mif(mf,Nmif=50,cooling.fraction=0.1) -> mf
-  ll <- unname(logmeanexp(raply(5,logLik(pfilter(mf))),se=TRUE))
-  data.frame(loglik=ll[1],loglik.se=ll[2],as.list(coef(mf)))
-  }) -> mf3
-```
-```{r mf3-simplot}
-simdat <- simulate(bsflu3,params=unlist(mf3),nsim=10,
-                   obs=TRUE,as.data.frame=TRUE,include.data=TRUE)
-ggplot(data=melt(simdat,id=c("sim","time")),
-       mapping=aes(x=time,y=value,group=interaction(variable,sim),
-                   color=variable,size=sim=="data",alpha=sim=="data"))+
-  geom_line()+
-  scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0.5))+
-  scale_size_manual(values=c(`TRUE`=2,`FALSE`=1))
-```
-
-## Model comparison
-
-```{r comp}
-tb <- ldply(list(det1=tm1,stoch1=mf1,det3=tm3,stoch3=mf3),.id="model")
-kable(tb)
-```
-
-```{r probes,fig.height=6,fig.width=6}
-plist <- list(probe.acf("confined",lags=c(2),type="cov",transform=sqrt),
-              probe.ccf(c("confined","convalescent"),lags=c(0,3),transform=sqrt),
-              tot=function (x) apply(x,1,sum))
-plot(probe(bsflu,params=unlist(tm1),nsim=500,probes=plist))
-plot(probe(bsflu,params=unlist(mf1),nsim=500,probes=plist))
-plot(probe(bsflu3,params=unlist(tm3),nsim=500,probes=plist))
-plot(probe(bsflu3,params=unlist(mf3),nsim=500,probes=plist))
-```

Deleted: pkg/pompExamples/vignettes/bsflu.html
===================================================================
--- pkg/pompExamples/vignettes/bsflu.html	2015-06-17 16:09:20 UTC (rev 1211)
+++ pkg/pompExamples/vignettes/bsflu.html	2015-06-17 16:43:30 UTC (rev 1212)
@@ -1,290 +0,0 @@
-<!DOCTYPE html>
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-
-<head>
-
-<meta charset="utf-8">
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<meta name="generator" content="pandoc" />
-
-<meta name="author" content />
-
-
-<title></title>
-
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1212

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