[Pomp-commits] r1213 - www/vignettes

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

Author: kingaa
Date: 2015-06-17 19:25:51 +0200 (Wed, 17 Jun 2015)
New Revision: 1213

Modified:
   www/vignettes/bsflu.Rmd
   www/vignettes/bsflu.html
   www/vignettes/parus.Rmd
   www/vignettes/parus.html
Log:
- update parus and bsflu vignettes

Modified: www/vignettes/bsflu.Rmd
===================================================================
--- www/vignettes/bsflu.Rmd	2015-06-17 16:43:30 UTC (rev 1212)
+++ www/vignettes/bsflu.Rmd	2015-06-17 17:25:51 UTC (rev 1213)
@@ -1,18 +1,40 @@
-%\VignetteIndexEntry{Boarding-school influenza example}
-%\VignetteEngine{knitr::knitr}
+---
+title: "Boarding-School Flu Outbreak Analysis"
+author: "Aaron A. King"
+output:
+  html_document:
+    theme: flatly
+    toc: yes
+bibliography: pomp.bib
+csl: ecology.csl
+---
 
-# Boarding-School Flu Outbreak Analysis  
-***Aaron A. King***
+Licensed under the [Creative Commons attribution-noncommercial license](http://creativecommons.org/licenses/by-nc/3.0).
+Please share and remix noncommercially, mentioning its origin.  
+![CC-BY_NC](../graphics/cc-by-nc.png)
 
+This document was produced using `pomp` version `r packageVersion("pomp")` and `pompExamples` version `r packageVersion("pompExamples")`.
+
 ```{r setup,include=FALSE}
 require(pomp)
+stopifnot(packageVersion("pomp")>="0.65-1")
+
+options(
+  keep.source=TRUE,
+  stringsAsFactors=FALSE,
+  encoding="UTF-8",
+  scipen=5
+  )
+
 require(plyr)
 require(reshape2)
-options(stringsAsFactors=FALSE,keep.source=TRUE,encoding="UTF-8")
 
 require(ggplot2)
 theme_set(theme_bw())
 
+set.seed(862663052L)
+```
+```{r knitr-options,include=FALSE,purl=FALSE}
 require(knitr)
 opts_knit$set(out.format="html")
 opts_chunk$set(
@@ -26,9 +48,6 @@
   fig.height=5,fig.width=10,
   dpi=100
   )
-
-require(pompExamples)
-set.seed(862663052L)
 ```
 
 First, a little function to cache the results of expensive computations.
@@ -48,6 +67,7 @@
 ## Flu model with exponentially-distributed waiting times
 
 ```{r bsflu1,cache=FALSE}
+require(pompExamples)
 pompExample(bsflu)
 coef(bsflu)
 ```

Modified: www/vignettes/bsflu.html
===================================================================
--- www/vignettes/bsflu.html	2015-06-17 16:43:30 UTC (rev 1212)
+++ www/vignettes/bsflu.html	2015-06-17 17:25:51 UTC (rev 1213)
@@ -8,14 +8,14 @@
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
 
-<meta name="author" content />
+<meta name="author" content="Aaron A. King" />
 
 
-<title></title>
+<title>Boarding-School Flu Outbreak Analysis</title>
 
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1213