01-intro.Rmd

# Package List and First Steps{#intro -}


## Getting R{-}

If you have never used or heard of `R` before, 
I suggest you start by reading about [data science in `R`](http://r4ds.had.co.nz/) and [installing RStudio](https://www.rstudio.com/products/rstudio/download/#download).
Only once you have done that can we continue.



## The `rethomics` packages{-}

Rethomics works as a collection of interconnected packages.
Here is a list of all our packages so far (as well as their individual PDF documentation, description and status).


```{r kable, echo=FALSE}
packages <- c("behavr", 
              "ggetho",
              "damr",
              "scopr",
              "sleepr",
              "zeitgebr"
              )
titles <- sapply(packages, 
       function(p){
          if(!p %in% rownames(installed.packages()))
            return("Unavailable")
          packageDescription(p, fields="Title")
          }
  )

package_name <- sprintf("[%s](https://github.com/rethomics/%s)", packages, packages)
doc <- sprintf("[![PDF](assets/pdf_icon.png)](https://github.com/rethomics/%s/raw/master/%s.pdf)", packages, packages)
travis_ci <- sprintf("[![%s Travis-CI Status](https://travis-ci.org/rethomics/%s.svg?branch=master)](https://travis-ci.org/rethomics/%s)", packages,packages,packages)
coverage <- sprintf("[![%s Coverage Status](https://img.shields.io/codecov/c/github/rethomics/%s/master.svg)](https://codecov.io/github/rethomics/%s?branch=master)", packages, packages, packages)


 
cran_img <- sprintf('http://www.r-pkg.org/badges/version/%s',packages)
cran_url <- sprintf('https://cran.r-project.org/package=%s',packages)
cran <- sprintf("[![CRAN](%s)](%s)", cran_img,cran_url)



cran_log_img <- sprintf('https://cranlogs.r-pkg.org/badges/%s',packages)
cran_log_url <- sprintf('https://www.rdocumentation.org/packages/%s',packages)
cran_log <- sprintf("[![CRAN log](%s)](%s)", cran_log_img,cran_log_url)


# `scopr` [![Travis-CI Build Status](https://travis-ci.org/rethomics/scopr.svg?branch=master)](https://travis-ci.org/rethomics/scopr)[![Coverage Status](https://img.shields.io/codecov/c/github/rethomics/scopr/master.svg)](https://codecov.io/github/scopr/behavr?branch=master)

titles <- stringr::str_replace(titles, "\n", " ")

library(knitr)
knitr::kable(data.frame(
              Package = package_name,
              Doc = doc, 
              Description = titles,
              Travis = travis_ci,
              Coverage = coverage,
              CRAN = cran
              #CRAN.log = cran_log
              ),
      row.names = FALSE)
``` 

## Installation{-}

### CRAN{-}
You may have noticed, in the table above, that some packages are on the CRAN (the official `R` package repository).
Therefore, we can use `R`'s default tools to install them.
For instance, `behavr`, can simply be installed with:

```{r, eval=FALSE}
install.packages("behavr")
```


### devtools{-}
For packages that are not on CRAN, or if you want the very latest snapshot of a package, you can use `devtools`.
First, install and load it:

```{r, eval=FALSE}
install.packages("devtools")
library(devtools)
```

You should see a warning message saying something like `"GitHub repo contains submodules, [...]"`, which is fine.
Beyond that, ensure you have *no error messages*. `devtool` is a package that simplifies installation of unofficial packages (for instance hosted on github) like `rethomics` ones. 
To install `behavr`, you would run:

```{r, eval=FALSE}
install_github("rethomics/behavr")
```

In the same way, you could install other `rethomics` packages by changing `"behavr"` for another package name. 
For instance, you could install `ggetho` with `install_github("rethomics/ggetho")`.