Introduction to R and Version Control

# Introduction to R and Version Control
### Susy Echeverría-Londoño and Drew Kerkhoff

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# Get started with version control
<img src="./Figs/Octocat.png" style="width: 50%"/>

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# Let's recap

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# Version control

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# Workflow

![BES](./Figs/version_control.png)

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# Set up repository

1. Go to your [Gihub](https://github.com/) account
2. Go to the repositories tab and press New
3. Name your new repository
4. Copy the web url https://github.com/username/repository.git

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# Workflow

![BES](./Figs/version_control.png)

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# Set up remote

![](./Figs/projects_new.png)

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# Set up remote

![](Figs/RStudio-clone-git-project.gif)

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# Create files or add files

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# First commit

![](./Figs/rstudio-commit1.png)

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# First commit

![](./Figs/rstudio-commit2.png)

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# Check changes

![](./Figs/rstudio-history.png)

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# Now push!

![](./Figs/push_github.png)

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# Set up Git

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# Cloning a repository

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# Cloning a repository
1. Go to your Github acccount
2. Copy the url of the repository you want to clone

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# Cloning a repository

![](Figs/RStudio-clone-git-project.gif)

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# Get started with R

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# Comments and sections in R

```r
# LIBS -----------------------------
# Some notes
library(tidyverse)
library(lubridate)

# DATA -----------------------------
# Some notes
dat1<-read.csv("file2.csv")
```

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# Working directory

Common way but not reproducible

```r
# Working directory -----------------------------
setwd("~/Git_Repos/Ecoinformatics_practicals/Ecoinformatics/01_intro_reproducibility/")
```
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# Working directory
Avoid absolute path

```r
# Absolute path -----------------------------
"C:/project_root_folder/data/species_dat.csv"

# Relative path -----------------------------
"data/species_dat.csv"
```
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# RStudio projects

![](./Figs/projects_new.png)

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# Exercise

1. Create a new folder called "data"

2.  Move "file2.csv" into the folder

3.  Read the file using the  [read.csv](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html)  function using:
  - Absolute path
  - Relative path
  
--

4. Commit your changes

```r
# Absolute path -----------------------------
"C:/project_root_folder/data/species_dat.csv"

# Relative path -----------------------------
"data/species_dat.csv"
```
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# Packages in R

*Collection of functions, data and compiled code, with a well-defined format, designed to perform a particular task of interest*

Library: directory where the packages are stored

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## Installing a package
#### Directly from CRAN-like repositories

```r
install.packages("tidyverse")
```

```r
install.packages(c("ggplot2","tibble","tidyr","readr","purr","dplyr"), dependencies=TRUE)
```
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## Installing a package
### Web-based Git version control repository "Github"

- [devtools](https://cran.r-project.org/web/packages/devtools/index.html) R package
- "username/repo"

```r
install.packages("devtools")

# Read library
library(devtools)

install_github("tidyverse/tidyr")
```
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## Getting help in R

- `?the-function-name`
- `?read.csv`

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## Check your data

```r
dat1<-read.csv("file2.csv")

head(dat1)

tail(dat1)

str(dat1)
```

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## Exercise
1. Read the "file2.csv" file using the `read.table` function
2. Check the data using the `head` function
3. Open your "file2.csv" in a text editor (I recommend to install Atom)

--
4. What are the main differences between `read.table` and `read.csv`?
5. Try to open the file again using `read.table` function with the correct arguments.

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## Tidyverse packages

![](./Figs/tidyverse.png)

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# Tidyverse cheat sheets

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# tidyR::gather

![](./Figs/tidyR.png)

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# dplyr::mutate

![](./Figs/mutatedply.png)

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# ggplot2

![](./Figs/ggplot_1.png)

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# ggplot2

![](./Figs/ggplot_2.png)

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# ggplot2

![](./Figs/ggplot_3.png)

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# Folder sctructure

![](./Figs/pipeline1.png)