An introduction to R

An introduction to R

S. Manzi & A. Salmon

South West Peninsula Collaboration for Leadership in Applied Health Researchand Care (PenCLAHRC)

University of Exeter

January 2019

An introduction to R

Outline

1 Aims and topics of the trainingAims of the trainingTraining topics – IntroductionTraining topics – Core R functionalityTraining topics – Data visualisation and statistics

2 IntroductionInstalling R and R studio

Windows installationLinux installation

The power and limitations of RFamiliarisation with the R studio environmentSetting the working directoryPackages for the extension of R functionalityR conventions

An introduction to R

Aims and topics of the training

Outline

1 Aims and topics of the trainingAims of the trainingTraining topics – IntroductionTraining topics – Core R functionalityTraining topics – Data visualisation and statistics

2 IntroductionInstalling R and R studio

Windows installationLinux installation

The power and limitations of RFamiliarisation with the R studio environmentSetting the working directoryPackages for the extension of R functionalityR conventions

An introduction to R

Aims and topics of the training

Aims of the training

Aims of this training

To familarise you withpurpose and use of R and Rstudio

To provide you with anunderstanding of the basicdata structures andfunctionality of R

To provide you with theskills to produce datavisualisations in R

To introduce the use ofpackages for extending thefunctionality of R

An introduction to R

Aims and topics of the training

Training topics – Introduction

Training topics – Introduction

Introduction

Installation of R and RstudioThe power and limitationsof RFamiliarisation with the Rstudio environmentPackages for theextension of RfunctionalityThe R language

An introduction to R

Aims and topics of the training

Training topics – Core R functionality

Training topics – Core R functionality

Core R functionality and skillsSequence generation and replicationVariable types and conversionData structures and conversionVector arithmaticIdentifying unique valuesArray sizesString concatenation and splittingConditional logic and functionsReading from and writing to filesSubscripting and subsettingMerging and appending dataSorting dataDate and time data handlingTablulationLoops and the apply based functionsUser defined functions

An introduction to R

Aims and topics of the training

Training topics – Data visualisation and statistics

Data visualisation and statistics

Plotting

Scatter and line graphsHistogramsBar chartsStatistical process controlcharts

Statistics

Descriptive statisticsT-testsLinear regression

An introduction to R

Introduction

Outline

1 Aims and topics of the trainingAims of the trainingTraining topics – IntroductionTraining topics – Core R functionalityTraining topics – Data visualisation and statistics

2 IntroductionInstalling R and R studio

Windows installationLinux installation

The power and limitations of RFamiliarisation with the R studio environmentSetting the working directoryPackages for the extension of R functionalityR conventions

An introduction to R

Introduction

Installing R and R studio

Windows installation – base R

Go to the R project websitehttps:

//www.r-project.org/

Click on ’download R’ in theget started section

R uses a hosting structurecalled CRAN(Comprehensive R ArchiveNetwork). Scroll down thelist and select your localCRAN mirror. This willmost likely be Bristol

An introduction to R

Introduction

Installing R and R studio

Windows installation – base R

Select ’Download R for Windows’

Click on the ’base’ link as we wantto install base R.

Click on ’Download R 3.5.2 forWindows

Your download should begin

Launch the .exe installer and followthe on screen instructions

An introduction to R

Introduction

Installing R and R studio

Windows installation – R Studio

Go to the R Studiodownload pagehttps://www.rstudio.com/

products/rstudio/

download/

Select the Windows installer

Your download should begin

Launch the .exe installer andfollow the on screeninstructions

An introduction to R

Introduction

Installing R and R studio

Linux installation - R and R Studio

The R base is available through the Ubuntu software center oryou can install it from the command line using sudo apt installrbase

RStudio can be installed in a couple of different ways but theeasiest (thanks Mike) seems to be:

Download the R studio installer from https:

//download1.rstudio.org/rstudio-1.1.463-amd64.deb

Go to your downloads folder and open a terminal there thentype sudo dpkg -i rstudio...(use tab complete to get the full filename)To complete the installation some dependencies need to beinstalled. Use sudo apt install -fR Studio should now be installed

An introduction to R

Introduction

The power and limitations of R

S as the basis for R

Developed as part of theGNU project – free andopen source

The R language is based onthe S language developed byJohn Chambers in 1976while at Bell Laboratoriesspecifically for statisticalcomputing

An introduction to R

Introduction

The power and limitations of R

The development of R

R was created by Ross Ihakaand Robert Gentleman atthe University of Auckland

R was named partly afterthe first names of the twocreators and partly as a playon the name of S.

The project began in 1992,the first version was releasedin 1995 and a stable betaversion was released in 2000

An introduction to R

Introduction

The power and limitations of R

The power of R

Designed for vector and matrixarithmatic enabling faster calaculationover larger matrices than possible withobject orientated languages such asC++, Java and Python

Designed as a script based languagerather than object orientated althoughdoes allow meta-programming forobject like tasks

Supports parallel processing andmultithreading

Can implement other languages e.g.C, C++, Fortran, Python and LaTex

An introduction to R

Introduction

Familiarisation with the R studio environment

The R console

R consolewindow -directly inputcommands intoR, view inputsand outputs

An introduction to R

Introduction

Familiarisation with the R studio environment

R Scripting window

Script window- write and runan R script

An introduction to R

Introduction

Familiarisation with the R studio environment

The variable explorer

Variable explorer -lists activevariables/objects

An introduction to R

Introduction

Familiarisation with the R studio environment

The plot window

Plot window -displays andretains all plots

An introduction to R

Introduction

Setting the working directory

Setting your working directory in R Studio

Navigate to the tools dropdown on the top tool bar inR Studio

Select global options whichopen a new window

The first option you will seeis the working directorysetting

Browse or manually enterthe location of your Rworking directory

An introduction to R

Introduction

Setting the working directory

Setting your working directory in an R script

Normally you will want to place your R scripts in specificsub-folders of your working directory to keep things organised

The command to set the working directory manually in ascript is setwd(’folder location’)

When reading or writing anything to and from sub-folders ofyour working directory you need to add the sub-folder name(s)in the standard drive location format e.g.’/subfolder/subsubfolder/subsubsubfolder’

An introduction to R

Introduction

Packages for the extension of R functionality

Installing and using packages

R makes use of packages toextend its base functionality

Packages need to beinstalled for eachdistribution of R that yourun

Packages are installed in Rstudio by going to the toolsdrop down on the top toolbar, selecting installpackages, searching for therequired package andselecting install

An introduction to R

Introduction

Packages for the extension of R functionality

Installing and using packages

Packages can also beinstalled from the Rcommand line using thecommand install.packages()function

Packages need to beinitialised in an R script.This is done by conventionat the start of the scriptusing library(package name)

An introduction to R

Introduction

R conventions

R does not require the use of correct indentations for the codeto run however, convention dictates that standard indents areused

The # (hash) symbol is used to insert comments into the code

R uses specific assignment operators

< − is assign the output from the right to the left= is the same as ¡- but it is poor practice to use this operatorin this way< − is assign the output from the left to the right<< − is assign the out from the right to the global/parentvariable on the left− >> is assign the out from the left to the global/parentvariable on the right