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template.Rmd
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template.Rmd
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---
title: "Template Document"
author: "Aaron A. King"
date: ICTP Spring College 9--20 May 2016
output:
html_document:
toc: yes
toc_depth: 4
bibliography: ../course.bib
csl: ../ecology.csl
---
\newcommand\prob[1]{\mathbb{P}\left[{#1}\right]}
\newcommand\expect[1]{\mathbb{E}\left[{#1}\right]}
\newcommand\var[1]{\mathrm{Var}\left[{#1}\right]}
\newcommand\dist[2]{\mathrm{#1}\left(#2\right)}
\newcommand\dlta[1]{{\Delta}{#1}}
\newcommand\lik{\mathcal{L}}
\newcommand\loglik{\ell}
[Licensed under the Creative Commons Attribution-NonCommercial license](http://creativecommons.org/licenses/by-nc/4.0/).
Please share and remix noncommercially, mentioning its origin.
![CC-BY_NC](../graphics/cc-by-nc.png)
```{r knitr-opts,include=FALSE,purl=FALSE}
library(knitr)
prefix <- "template"
opts_chunk$set(
progress=TRUE,
prompt=FALSE,tidy=FALSE,highlight=TRUE,
strip.white=TRUE,
warning=FALSE,
message=FALSE,
error=FALSE,
echo=TRUE,
cache=TRUE,
cache.extra=rand_seed,
results='markup',
fig.show='asis',
size='small',
fig.lp="fig:",
fig.path=paste0("figure/",prefix,"-"),
cache.path=paste0("cache/",prefix,"-"),
fig.pos="h!",
fig.align='center',
fig.height=4,fig.width=6.83,
dpi=100,
dev='png',
dev.args=list(bg='transparent')
)
options(keep.source=TRUE,encoding="UTF-8")
```
```{r prelims,include=FALSE,purl=TRUE,cache=FALSE}
library(pomp)
options(cores=20,stringsAsFactors=FALSE)
stopifnot(packageVersion("pomp")>="1.4.7")
```
----------------------------
----------------------------
## [Back to course homepage](http://kingaa.github.io/short-course)
## [**R** codes for this document](http://raw.githubusercontent.com/kingaa/short-course/master/mif/mif.R)
----------------------------
## References