README.Rmd

---
bibliography: vignettes/bibliography.bib
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/",
  echo=TRUE, 
  warning=FALSE, 
  message=FALSE,
  tidy=TRUE
)
```

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  [![R-CMD-check](https://github.com/gtonkinhill/rhierbaps/workflows/R-CMD-check/badge.svg)](https://github.com/gtonkinhill/rhierbaps/actions)
<!-- badges: end -->


# rhierbaps

We have recently developed a faster verion of the BAPs clustering method. It can be found [here](https://github.com/gtonkinhill/fastbaps). 

## Installation
`rhierbaps` is available on CRAN.
```{r, eval=FALSE}
install.packages("rhierbaps")
```

The development version is available on github. It can be installed with `devtools`
```{r, eval = FALSE}
install.packages("devtools")

devtools::install_github("gtonkinhill/rhierbaps")
```

If you would like to also build the vignette with your installation run:

```{r, eval=FALSE}
devtools::install_github("gtonkinhill/rhierbaps", build_vignettes = TRUE)
```

## Quick Start
Run hierBAPS.

```{r, fig.width =8, fig.height=6, fig.align='center'}
# install.packages("rhierbaps")
library(rhierbaps)

fasta.file.name <- system.file("extdata", "seqs.fa", package = "rhierbaps")
snp.matrix <- load_fasta(fasta.file.name)
hb.results <- hierBAPS(snp.matrix, max.depth=2, n.pops=20, quiet = TRUE)
head(hb.results$partition.df)
```

```{r, echo = FALSE}
intro_rmd <- 'vignettes/introduction.Rmd'

raw_rmd <- readLines(intro_rmd)

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

# remove appendix (session info)
appendix <- grep("Session", 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'}
```

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