index.Rmd

--- 
title: "Practical Computing and Bioinformatics for Conservation and Evolutionary Genomics"
author: "Eric C. Anderson"
date: "`r Sys.Date()`"
documentclass: krantz
bibliography: [references.bib, book.bib]
biblio-style: apalike
link-citations: yes
colorlinks: yes
lot: yes
lof: yes
site: bookdown::bookdown_site
description: "A book example for a Chapman & Hall book."
github-repo: yihui/bookdown-crc
graphics: yes
#cover-image: images/cover.jpg
header-includes: 
  - \usepackage{booktabs}
fig-retina: 2
---

\newcommand{\bitsfa}{{\circ}{\circ}{\circ}{\bullet}}
\newcommand{\bitsfb}{{\circ}{\circ}{\bullet}{\circ}}
\newcommand{\bitsfc}{{\circ}{\bullet}{\circ}{\circ}}
\newcommand{\bitsfd}{{\bullet}{\circ}{\circ}{\circ}}
\newcommand{\bitsopen}{{\circ}{\circ}{\circ}{\circ}}

\newcommand{\bitsa}{\bitsopen~\bitsopen~\bitsfa}
\newcommand{\bitsb}{\bitsopen~\bitsopen~\bitsfb}
\newcommand{\bitsc}{\bitsopen~\bitsopen~\bitsfc}
\newcommand{\bitsd}{\bitsopen~\bitsopen~\bitsfd}

\newcommand{\bitse}{\bitsopen~\bitsfa~\bitsopen}
\newcommand{\bitsf}{\bitsopen~\bitsfb~\bitsopen}
\newcommand{\bitsg}{\bitsopen~\bitsfc~\bitsopen}
\newcommand{\bitsh}{\bitsopen~\bitsfd~\bitsopen}

\newcommand{\bitsi}{\bitsfa~\bitsopen~\bitsopen}
\newcommand{\bitsj}{\bitsfb~\bitsopen~\bitsopen}
\newcommand{\bitsk}{\bitsfc~\bitsopen~\bitsopen}
\newcommand{\bitsl}{\bitsfd~\bitsopen~\bitsopen}
\newcommand{\bitsmany}{\bitsopen~{\circ}{\bullet}{\circ}{\bullet}~{\circ}{\circ}{\bullet}{\bullet}}

```{r setup, include=FALSE}
options(
  htmltools.dir.version = FALSE, formatR.indent = 2, width = 55, digits = 4
)

# install the packages needed by this book; you fill out c(), e.g. c('ggplot2', 'dplyr')
lapply(c('xfun'), function(pkg) {
  if (system.file(package = pkg) == '') install.packages(pkg)
})

library(tidyverse)
```

# Preface {-}

This is a collection of blurbs Eric started writing in the last year to 
help remind himself and others of some useful things to know for bioinformatics.

It was started during an extended government shutdown, when it seemed like writing a book
might be in order.  Fortunately, the shutdown ended eventually.  It is not clear whether a
book will ever come of it, but these notes shall be up on the web indefinitely, so feel free to use
them!


```{r include=FALSE}
# put my knitr options here
options(knitr.graphics.auto_pdf = TRUE)
```