[Pomp-commits] r1060 - pkg/pompExamples/vignettes

Wed Jan 28 14:33:26 CET 2015

Author: kingaa
Date: 2015-01-28 14:33:25 +0100 (Wed, 28 Jan 2015)
New Revision: 1060

Modified:
   pkg/pompExamples/vignettes/bsflu.Rmd
   pkg/pompExamples/vignettes/bsflu.html
   pkg/pompExamples/vignettes/parus.Rmd
   pkg/pompExamples/vignettes/parus.html
Log:
- replace 'juliaChild' with 'bake'

Modified: pkg/pompExamples/vignettes/bsflu.Rmd
===================================================================

--- pkg/pompExamples/vignettes/bsflu.Rmd	2015-01-28 12:34:07 UTC (rev 1059)
+++ pkg/pompExamples/vignettes/bsflu.Rmd	2015-01-28 13:33:25 UTC (rev 1060)
@@ -33,8 +33,8 @@
 
 First, a little function to cache the results of expensive computations.
 
-```{r juliaChild}
-juliaChild <- function (file, expr) {
+```{r bake}
+bake <- function (file, expr) {
   if (file.exists(file)) {
     readRDS(file)
     } else {
@@ -64,11 +64,11 @@
 ### Trajectory matching
 
 ```{r tm1}
-juliaChild("bsflu-tm1.rds",{
+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
+  }) -> tm1
 ```
 ```{r tm1-simplot}
 simdat <- simulate(bsflu,params=unlist(tm1),nsim=10,
@@ -84,7 +84,7 @@
 ### Iterated filtering
 
 ```{r mf1}
-juliaChild("bsflu-mf1.rds",{
+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
@@ -92,7 +92,7 @@
   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
+  }) -> mf1
 ```
 ```{r mf1-simplot}
 simdat <- simulate(bsflu,params=unlist(mf1),nsim=10,
@@ -124,11 +124,11 @@
 ### Trajectory matching
 
 ```{r tm3}
-juliaChild("bsflu-tm3.rds",{
+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
+  }) -> tm3
 ```
 ```{r tm3-simplot}
 simdat <- simulate(bsflu3,params=unlist(tm3),nsim=10,
@@ -144,7 +144,7 @@
 ### Iterated filtering
 
 ```{r mf3}
-juliaChild("bsflu-mf3.rds",{
+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
@@ -152,7 +152,7 @@
   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
+  }) -> mf3
 ```
 ```{r mf3-simplot}
 simdat <- simulate(bsflu3,params=unlist(mf3),nsim=10,

Modified: pkg/pompExamples/vignettes/bsflu.html
===================================================================
--- pkg/pompExamples/vignettes/bsflu.html	2015-01-28 12:34:07 UTC (rev 1059)
+++ pkg/pompExamples/vignettes/bsflu.html	2015-01-28 13:33:25 UTC (rev 1060)
@@ -1,213 +1,72 @@
 <!DOCTYPE html>
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
 
-<title>Boarding-School Flu Outbreak Analysis</title>
+<html xmlns="http://www.w3.org/1999/xhtml">
 
-<script type="text/javascript">
-window.onload = function() {
-  var imgs = document.getElementsByTagName('img'), i, img;
-  for (i = 0; i < imgs.length; i++) {
-    img = imgs[i];
-    // center an image if it is the only element of its parent
-    if (img.parentElement.childElementCount === 1)
-      img.parentElement.style.textAlign = 'center';
-  }
-};
-</script>
+<head>
 
-<!-- Styles for R syntax highlighter -->
-<style type="text/css">
-   pre .operator,
-   pre .paren {
-     color: rgb(104, 118, 135)
-   }
+<meta charset="utf-8">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="pandoc" />
 
-   pre .literal {
-     color: #990073
-   }
+<meta name="author" content />
 
-   pre .number {
-     color: #099;
-   }
 
-   pre .comment {
-     color: #998;
-     font-style: italic
-   }
+<title></title>
 
-   pre .keyword {
-     color: #900;
-     font-weight: bold
-   }
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1060
