README.Rmd

---
output: 
  github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "inst/vignette-supp/",
  tidy = TRUE
)
```

[![Travis-CI Build Status](https://travis-ci.org/sa-lee/starmie.svg?branch=master)](https://travis-ci.org/sa-lee/starmie)
[![](http://cranlogs.r-pkg.org/badges/grand-total/starmie?color=brightgreen)](http://cran.rstudio.com/web/packages/starmie/index.html)

# Quick Start
Construct a barplot for your STRUCTURE/ADMIXTURE output using `starmie` in a few
lines of code!
```{r, fig.width =8, fig.height=6, fig.align='center'}
# install.packages("starmie")
library(starmie)
str_output <- system.file("extdata/microsat_testfiles/",  "locprior_K5.out_f", package = "starmie")
k5_data <- loadStructure(str_output)
k5_data
plotBar(k5_data, facet = FALSE)
```

```{r, echo = FALSE}

intro_rmd <- 'vignettes/using-starmie.Rmd'

raw_rmd <- readLines(intro_rmd)

# remove yaml 
yaml_lines <- grep("---", raw_rmd)

# remove appendix (session info)
appendix <- grep("Appendix", raw_rmd)

compressed_rmd <- raw_rmd[c(-seq(yaml_lines[1], yaml_lines[2], by = 1), 
                            -seq(appendix, length(raw_rmd)))]
writeLines(compressed_rmd, "child.Rmd")
```

```{r, child = 'child.Rmd'}
```

# Installation
`starmie` is available as an R package on CRAN
```{r, eval = FALSE}
install.packages("starmie")
```

The development version of `starmie` can be installed with `devtools`
```{r, eval = FALSE}
install.packages("devtools")

devtools::install_github("sa-lee/starmie")
```
If you would like to also build the vignette with your installation run:

```{r, eval=FALSE}
devtools::install_github("sa-lee/starmie", build_vignettes = TRUE)
```


```{r cleanup, echo=FALSE, include=FALSE}
if (file.exists("child.Rmd")) {
  file.remove("child.Rmd")
}
```