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RStudio.Rmd
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---
title: "RStudio IDE"
author: "by Stuart Hertzog"
date: "March–May 2018"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
[<img src="images/RStudio-Logo-Blue-Gradient.png" style="float: left; margin-right: 1em; margin-bottom: 0.25em;" width=200>](https://www.rstudio.com/products/rstudio)**is a free, open-source, professionally-designed IDE for programming in R** (and other languages including Python and associated Python packages).
[RStudio](https://en.wikipedia.org/wiki/RStudio) is available in two free versions:
* [RStudio Desktop](https://www.rstudio.com/products/rstudio/#Desktop), run locally as a desktop application. and
* [RStudio Server](https://www.rstudio.com/products/rstudio/#Server), which runs on a networked or remote Linux server.
[RStudio Server Pro](https://www.rstudio.com/products/rstudio-server-pro/) is a full-service, paid edition for business and government use.
**The advantages of using RStudio include**:
* Free and open source for non-commercial use
* Easy to install on Windows, Mac, and Linux
* Well-designed, multi-pane GUI interface
* Paid, full-service, professional versions
* Git and Subversion versioning support
* Can import data from online sources
* Outputs to HTML, PDF, Word files
* Built-in R package management
* Keyboard shortcuts display
* Active community support
* Tab key code completion
* Ongoing development
* Well-documented
* Code folding
* It's So Cool
* So is R!
From the [ RStudio web Site](https://www.rstudio.com/products/rstudio/features/):
**An IDE that was built just for R**
* Syntax highlighting, code completion, and smart indentation
* Execute R code directly from the source editor
* Quickly jump to function definitions
**Bring your workflow together**
* Integrated R help and documentation
* Easily manage multiple working directories using projects
* Workspace browser and data viewer
**Powerful authoring & Debugging**
* Interactive debugger to diagnose and fix errors quickly
* Extensive package development tools
* Authoring with Sweave and R Markdown
## The RStudio Interface
**The RStudio Console interface is flexible, rich, and capable**:
* Tabs in each pane display different aspects of the current project
* Panes can share a column or be raised to fill an entire column
* File and Viewer panes can be zoomed into a larger new window
* Toolbars in each tab allow direct control of content elements
* Console comands are integrated into the running OS and files
* Console display can be changed by selecting a different theme
* Code syntax colors can be changed with another editor theme
## RStudio Projects
<img src="images/RStudio_project_dropdown.png" style="float: left; margin: 0 1em 0.25em 0;" width=200>
RStudio advises that **all data files and packages** belonging to a project be contained in a dedicated directory as an **RStudio Project** with an executable **`.Rproj` file**.
**Project management is built into RStudio**. Start a new Project either from the _File -> New Project_ main menu, or from the drop-down **Project menu** at the top right of the RStudio window (left).
_New Project..._ opens a dialogue window that enables a Project to be created in a _New_ or _Existing_ directory, or from a _Version Control Repository_.
If an existing Project has unsaved changes, you will be asked to save them.
_Open Project..._ brings up a File dialogue to locate an existing project directory and double-click its `.Rproj` file.
_Open Project in New Session..._ allows you to create a new Project in a new R session without closing the existing Project R session.
_Close Project_ will close the running R session and after saving any changes.
**Existing RStudio Projects** are listed below these to facilitate switching between active projects. Entries are created when a project is started by RStudio. This list can be emptied by selecting _Clear Project List_.
**Project Options** lets you set options specific only to the running Project.
## Package Management In RStudio
**Package management is an integral part of the RStudio interface**. The _Packages_ tab in the Files/Viewer pane shows all locally-installed and system packages.
**Clicking the checkbox to the left of each package listing** will load a package's library into memory and make its functions available. The corresponding installation command will appear immediately in the Console plus any warning messages.
**Packages with checkmarks have already been loaded**. Unclicking a loaded package will unload it unless it is required by RMarkdown, in which case a warning message will inform you of that restriction and the package will remain loaded.
**There are two ways of installing packages** in the RStudio interface:
* Using the **_Install Packages_ GUI**
* Entering commands in the **Console**.
The progress of any compilation or installation will be displayed in the Console.
### The Install Packages GUI
<img src="images/RStudio_install_package.png" style="float: left; margin-right: 1em; margin-bottom: 0.25em;" width=200>
**Clicking _Install_ on the Packages tab toolbar** opens an _Install Packages_ dialogue (left) that gives the choice of installing a package directly from CRAN or from a local package archive.
**Multiple packages can be installed** by separating the package names with commas. This installs and makes the packages available for use.
**The _Install to Library_ drop-down menu** allows you to chose the Library where you want the package installed. The _default location_ is selected: this is usually acceptable.
**The location of the R installation on your system** can be found by entering `R.home(component = "home")` in the Console. Other component values for the paths to specific directories of the current R installation are `"bin"`, `"doc"`, `"etc"`, `"include"`, `library`, `"modules"` and `"share"`.
**Clicking the _Install dependencies_ checkbox** will also download and install any other packages required for the requested package(s). This is recommended.
**NOTE: This option will not work when installing from a local archive**. In this case the dependencies must be installed first, or the installation will fail.
###Installing From The Console
**Packages can be installed and loaded from the Console**. The command sequence is:
`install.packages("PackageName")`
`library(PackageName)`
The delimiters `" "` or `' '` must be used to install a package.
Most R packages are hosted on CRAN, but some are only available on [GitHub](https://github.com) or [Bitbucket]( https://bitbucket.org). To install from these locations, the `devtools` package first must be installed, as [described above](#installing-packages-from-github).
### Project Package Management
**RStudio projects are built with different versions of `R`** using the then-current versions of any installed packages. As both `R` and `R packages` are constantly being updated, this can cause problems when developing packages or `RMarkdown` documents.
**There are four solutions to project package management**:
* Installing the [`packrat`](https://rstudio.github.io/packrat/) package to write package versions in a `packrat.lock` text file and store the packages in a project `packrat` directory;
* Using [MRAN](https://mran.microsoft.com/timemachine) (Microsoft R Application Network) to determine dependencies based on the “snapshot” of CRAN that Microsoft has stored on a given day;
* Installing the [`checkpoint`](https://cran.r-project.org/web/packages/checkpoint/vignettes/checkpoint.html) package to choose package versions based on a given day in MRAN history.
For more information, see [Package Management for Reproducible R Code](https://rviews.rstudio.com/2018/01/18/package-management-for-reproducible-r-code/)
### Installing And Using `packrat`
**Packrat stores all added packages in its own directory library**, rather than relying on the user R library that is shared across all R sessions.
The advantages of this are:
* **Isolation**: Installing a new or updated package for one project does not break other projects, and vice versa;
* **Portability**: Enables moving projects from one computer to another, even across different platforms. (NOTE: this requires installation for each OS as the compiled libraries are not always identical);
* **Reproducibility**: Ensures the correct package versions are assembled where and whenever the project is installed.
**`packrat` is integrated into the RStudio environment** so it is easy to install and initiate. The _Packages_ tab in the _Files/Viewer_ window has a `packrat` item menu. Clicking on this brings up the **Packrat Options** window:
<a name="packrat_options"></a>
**It's advisable to select the _Automatically snapshot local changes_ option.**
**Clicking `OK` will download, install, and initiate`packrat`** in exactly the same way the same as issuing the commands from the Console:
> install.packages("packrat")
packrat::init()
**There also is an option in the _New Project_ window** to create a new project with `packrat` pre-installed and initiated.
<img src="images/RStudio_packrat_menu.png" style="float: left; margin-right: 1em; margin-bottom: 0.25em;" width=200>
**Once `packrat` is up and running** the _Packrat_ link will become a drop-down menu (left), containing the following options:
_Check Library Status..._ -- shows if any packages require updating
_Clean Unused Packages_ -- removes unneccessary packages. If you want to keep a package from appearing in the Unused list, just add a `library(PackageName)` call to any .R file in your Project directory.
_Export Project Bundle_ -- creates a zipped bundle of your Project in the `packrat` directory, for transport to another system. The bundle contains application code, a manifest file, an html file, and a `packrat` folder with a `packrat.lock` file.
_Packrat Options..._ -- brings up the options window. ([See above](#packrat_options))
**For more information see**
* [Packrat](https://rstudio.github.io/packrat/)
* [Packrat Commands](https://rstudio.github.io/packrat/commands.html)
* [Packrat by example](https://rstudio.github.io/packrat/walkthrough.html)
* [Using Packrat with RStudio](https://rstudio.github.io/packrat/rstudio.html)
* [Bundle Downloads](https://support.rstudio.com/hc/en-us/articles/115003639788-Bundle-Downloads)
## Using Python In RStudio
### <img src="images/reticulated_python.png" class="small-left">[reticulate](https://rstudio.github.io/reticulate/index.html)
Until recently it has not been possible to easily use Python in RStudio. The newly-developed [reticulate](https://rstudio.github.io/reticulate/index.html) package provides a **comprehensive set of tools for interoperability between Python and R** within RStudio.
**[reticulate](https://rstudio.github.io/reticulate/index.html) includes facilities for**:
* **Calling Python from R** in a variety of ways including R Markdown, sourcing Python scripts, importing Python modules, and using Python interactively within an R session.
* **Translation between R and Python objects** (for example, between R and Pandas data frames, or between R matrices and NumPy arrays).
* **Flexible binding to different versions of Python** including virtual environments and Conda environments.
**[reticulate](https://rstudio.github.io/reticulate/index.html) embeds a Python session within your R session**, enabling seamless, high-performance interoperability. If you are a Python developer, or an R developer who uses Python for some of your work, or a member of data science team that uses both languages, [reticulate](https://rstudio.github.io/reticulate/index.html) can dramatically streamline your workflow.
<p class="bottom-navbar"><span class="bottom-navbar-contents"><span class="glyphicon glyphicon-arrow-left"> </span> [<span class="bottom-navbar-link">Part 1 - R For Data Science</span>](R_Data_Science.html) | [<span class="bottom-navbar-link">Part 1 - RStudio Ecosystem</span>](RStudio_Ecosystem.html) <span class="glyphicon glyphicon-arrow-right"></span></span></p>