YASSINE MOUSAIF - R: Notes For Professionals

R
Notes for Professionals

Section 103.2: Removing features with high numbers of NA................................................................................ 378

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Please send feedback and corrections to web@petercv.com You might wish to install RStudio after you have installed R. RStudio is a development environment for R thatsimplifies many programming tasks.
Windows only:

Visual Studio (starting from version 2015 Update 3) now features a development environment for R called R Tools,that includes a live interpreter, IntelliSense, and a debugging module. If you choose this method, you won't have toinstall R as specified in the following section.

For Windows

1.Go to the CRAN website, click on download R for Windows, and download the latest version of R.
2.Right-click the installer file and RUN as administrator.
3.Select the operational language for installation.
4.Follow the instructions for installation.

For OSX / macOS
Alternative 1
(0. Ensure XQuartz is installed )

1.Go to the CRAN website and download the latest version of R.
2.Open the disk image and run the installer.
3.Follow the instructions for installation.

This will install both R and the R-MacGUI. It will put the GUI in the /Applications/ Folder as R.app where it can eitherbe double-clicked or dragged to the Doc. When a new version is released, the (re)-installation process will overwriteR.app but prior major versions of R will be maintained. The actual R code will be in the
/Library/Frameworks/R.Framework/Versions/ directory. Using R within RStudio is also possible and would be usingthe same R code with a different GUI.

Alternative 2
1.Install homebrew (the missing package manager for macOS) by following the instructions on https://brew.sh/2.brew install R
Those choosing the second method should be aware that the maintainer of the Mac fork advises against it, and willnot respond to questions about difficulties on the R-SIG-Mac Mailing List.
For Debian, Ubuntu and derivatives
You can get the version of R corresponding to your distro via apt-get. However, this version will frequently be quitefar behind the most recent version available on CRAN. You can add CRAN to your list of recognized "sources".
sudo apt-get install r-base
You can get a more recent version directly from CRAN by adding CRAN to your sources list. Follow the directionsfrom CRAN for more details. Note in particular the need to also execute this so that you can useinstall.packages(). Linux packages are usually distributed as source files and need compilation:sudo apt-get install r-base-dev

For Red Hat and Fedorasudo dnf install R
For Archlinux

R is directly available in the Extra package repo.
sudo pacman -S rMore info on using R under Archlinux can be found on the ArchWiki R page. "Hello World!"
Also, check out the detailed discussion of how, when, whether and why to print a string. You can use function help() or ? to access documentations and search for help in R. For even more generalsearches, you can use help.search() or ??.
#For help on the help function of R
help()

#For help on the paste function
help(paste)#OR
help("paste") #OR
?paste#OR
?"paste"

Visit https://www.r-project.org/help.html for additional information The interactive mode
The most basic way to use R is the interactive mode. You type commands and immediately get the result from R.
Using R as a calculator
Start R by typing R at the command prompt of your operating system or by executing RGui on Windows. Below youcan see a screenshot of an interactive R session on Linux:
This is RGui on Windows, the most basic working environment for R under Windows:
After the > sign, expressions can be typed in. Once an expression is typed, the result is shown by R. In thescreenshot above, R is used as a calculator: Type
1+1
to immediately see the result, 2. The leading [1] indicates that R returns a vector. In this case, the vector containsonly one number (2).
The first plot
R can be used to generate plots. The following example uses the data set PlantGrowth, which comes as an exampledata set along with R
Type int the following all lines into the R prompt which do not start with ##. Lines starting with ## are meant todocument the result which R will return.

data(PlantGrowth)
str(PlantGrowth)
## 'data.frame': 30 obs. of 2 variables:
## $ weight: num 4.17 5.58 5.18 6.11 4.5 4.61 5.17 4.53 5.33 5.14 ...## $ group : Factor w/ 3 levels "ctrl","trt1",..: 1 1 1 1 1 1 1 1 1 1 ...anova(lm(weight ~ group, data = PlantGrowth))
## Analysis of Variance Table
##
## Response: weight
## Df Sum Sq Mean Sq F value Pr(>F)
## group 2 3.7663 1.8832 4.8461 0.01591 *
## Residuals 27 10.4921 0.3886
## -
## Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1boxplot(weight ~ group, data = PlantGrowth, ylab = "Dry weight")

The following plot is created:

data(PlantGrowth) loads the example data set PlantGrowth, which is records of dry masses of plants which weresubject to two different treatment conditions or no treatment at all (control group). The data set is made availableunder the name PlantGrowth. Such a name is also called a Variable.

To load your own data, the following two documentation pages might be helpful:
Reading and writing tabular data in plain-text files (CSV, TSV, etc.)
I/O for foreign tables (Excel, SAS, SPSS, Stata)

str(PlantGrowth) shows information about the data set which was loaded. The output indicates that PlantGrowthis a data.frame, which is R's name for a table. The data.frame contains of two columns and 30 rows. In this case,each row corresponds to one plant. Details of the two columns are shown in the lines starting with $: The firstcolumn is called weight and contains numbers (num, the dry weight of the respective plant). The second column,group, contains the treatment that the plant was subjected to. This is categorial data, which is called

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