template.Rmd

---
title: "Template Document"
subtitle: 'ICTP Workshop on Mathematical Models of Climate Variability, Environmental Change and Infectious Diseases'
author: "Aaron A. King"
date: '8--19 May 2017'
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\cov[1]{\mathrm{Cov}\left[{#1}\right]}
\newcommand\dist[2]{\mathrm{#1}\left(#2\right)}
\newcommand\dlta[1]{{\Delta}{#1}}
\newcommand{\dd}[1]{\mathrm{d}{#1}}
\newcommand{\transpose}{\mathrm{T}}
\newcommand\lik{\mathcal{L}}
\newcommand\loglik{\ell}
\newcommand{\scinot}[2]{#1{\times}10^{#2}}
\newcommand{\pd}[3][]{\frac{\partial^{#1}{#2}}{\partial{#3}^{#1}}}
\newcommand{\deriv}[3][]{\frac{\mathrm{d}^{#1}{#2}}{\mathrm{d}{#3}^{#1}}}

[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)
stop("set the prefix")
## prefix <- "SETME"
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")
```

----------------------------

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## [Back to course homepage](../)
## [**R** codes for this document](http://raw.githubusercontent.com/kingaa/clim-dis/master/mif/mif.R)

----------------------------

## References