b fn help package rgetstart 14oct18 · workshop: getting started with r. utm 14 oct 2018 .© dr....

Workshop:Getting Startedwith R.UTM14Oct2018.©Dr.NorhaizaAhmad

14 October 2018 Dr. Norhaiza Ahmad

Department of Mathematical SciencesFaculty of Science

Universiti Teknologi Malaysia

http://science.utm.my/norhaiza/

Getting Started with

for newbies

PART B: FUNCTIONS-PACKAGES-HELP!


OutlinePARTB:CoreofR1. Rfunctions(in-built)2. RPackages3. HowtosearchforFunctions/PackagesinR4. HowinstallapackageNOTavailableinyourR5. Howtoload(i.e.open)apackage

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FunctionsinR

• Rcommandsareexecuted byrunningafunction• A functionisaname,whichistypedfollowedbyapair

ofbrackets.Argumentsareaddedinsidethebrackets> sqrt(2)> sin(pi)

• SometimesfunctionsinRhaveextraargument.> sum(2,3,5)> log(10,10)

• Rhasmanyin-builtfunctions.• Thesefunctionscanalsobeprogrammedmanually

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ExamplesofOtherFunctionsinRFUNCTIONS Operationsqrt Squarerootabs Absolutevaluecos tan Trigonometric functions (radians)sinh cosh tanh hyperbolic functionsAsinh acosh atanh inversehyperbolic functionsexp log log10 exponential,naturallogarithm common logarithm

Thesefunctionscanbenestedandcombined tomakemorecomplexexpressions:> sqrt(sin(45*pi/180)) [1]0.8408964

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PackagesinR• RECALL:RFunctionsarecontainedinRPackages

• IfyouwouldliketouseaparticularRfunction,youneedtoknowthenameofthepackageinwhichitliesin.

• Ifyoucannotfindthefunctioninyoursystemè needtoinstall(andopen/load)thepackage.

Package‘stats’

Containsvarious:

• Functions• Datasets• Help

…..

Package‘ggplot2’

Containsvarious:

• Functions• Datasets• Help

Example

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TypesofRPackages• ManyusefulRfunctionsarecontainedinRPackages• TherearemanytypesofRpackagesdesignedfordifferentfunctions:

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• Therearemanymorepackages• NeedtodownloadandinstallthepackagesifyouwanttousetheRfunctions

RPackages

ToManipulateData ToVisualizeData ToModelData ToReport

Results ForSpatialData ForTimeSeries&FinancialData

ForAnalyzingSurveyData

§ zoo§ xts§ quantmod

§ maps§ ggmap§ maotools

§ RShiny§ RMarksown§ xtable

§ car§ mgcv§ nlme§ randomForest§ vcd§ survival§ caret

§ ggplot2§ ggvis§ rgl§ googleVis

§ dplyr§ tidyr§ lubridate

§ survey§ tidyverse


PackagesinR• ApackageisacollectionofRfunctions,datasetsandhelp

documentations.• Differentpackagescaterfordifferentpurposesthatcanbe

reusedbyothersforfree.• TocheckwhichpackagesareavailablelocallyonyourR

session• Typeonyourconsole

>library()

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Demo>library()

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• HowtosearchforparticularRfunctionthatyouwanttouse?

• HowtofindanRpackagethatcandocertaintaskinR?

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Howtosearchforfunction/packagesinR?

Function/Package?

R-help!

https://www.rdocumentation.org/

Googleit!

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UsingHelp!inR• Help:RfunctionnameKNOWN• Help:Rfunction/packagenameNOTKNOWN

Help pagesinRwilltellyouthesourcepackageofthefunction,describe thefunctions,giveyouthesyntaxargument,explanationabouttheargumentsandexample.

Thesefunctionscanbenestedandcombinedtomakemorecomplexexpressions:> sqrt(sin(45*pi/180)) [1]0.8408964

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UseHelp!inRTherearemanyin-builtfunctionsinR,eachwithdifferentindividualarguments.WecanseekhelpinRtolearnmoreaboutthesefunctions.

A)Help:RfunctionnameKNOWN> help(nameOffunction)

> help(log) #help on function log> ?log #help on function log

Attach: see help document for log

Example:FindthehelpdocumentationforanRfunctioncalledlog

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HelpinR(Rfunctions)

UseHelp:Rfunctionsifyouknowthenameofthefunctionsusedandneedmoreinfoaboutit

Help:RfunctionnameKNOWNorattheRibbonselect>Help>Rfunctions(text)

Task:ObtainhelpontheRfunctioncalled“plot”15


Function:plotPackage:graphics

Howtousethefunctionsandwhatareitsarguments

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• ExamplesfortheRfunction• Wecancopyandpastethecodes

onRconsole

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HandyTip• Ifyourhelpdocumentfailstoupload(url failsetc),type

> options(help_type=“text”)

#atextversionofthehelpdocumentwillbedisplayed

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• SupposeyouwanttodoaparticulartaskbuthavenoideawhatisthenameoftheRfunction/Rpackageforthattask.

UseHelp!inR

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SupposeyouwanttodoaparticulartaskbutdonotknowthenameoftheRfunction/RPackageforthetask.

B)Help:Rfunction/packagenameNOTKNOWN> help.start( ) > help.search(“yourquery”)> ??

Example:WhatistheRfunctionforastudent’st-test?

UseHelp!inR

> help.search(“t-test”)

> ??t-test

or

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Alternatively:Searchontheinternetforthenameofthefunction/package


HelpinR(Searchhelp)

• UseSearchHelpifyoudonotknowthefunctionsuseinR

• Showsalistofrelatedfunctions

• Thenusehelp(“nameoffunction”)

Help:RfunctionnameNOTKNOWN

orattheRibbonselect>Help>Rfunctions(text)

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Exampleofhelpsearch

stats:t.test

NameofPackage

Nameoffunction

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OnceyouhaveidentifiedtheRfunction- getfurtherhelpforthefunction(seeslideno.13):> ?t.test

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HowinstallapackageNOTavailableinyourR• SupposethepackageisnotavailableinyourRsession:èitmustbeinstalledlocallyandthenloadup• ThisprocessrequiresinternetsinceRwilldownloadthepackagefromitsrepository.

Eg.CRAN(default)orBioconductoretc (referSlidesPartBonrepositories)

Onceinstalled,youneedtoloadthepackage,tousethefunctions,helpdocumentationetc.inthepackage

Attheribbon,selecttab<Packages>Choose<Installpackage(s)>ChooseanyCRANmirror#pop-upwindowChoosedesiredpackages#pop-upwindow.OK

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Alternatively

> install.packages(“name of package”)



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IMPORTANT:

InordertouseanyRfunction(orthehelpdocumentationforthatRfunction),youneedtoensurethat

(1)therelatedRpackageofthatfunctionhasalreadybeeninstalledlocallyinyourcomputer

(2)Open(i.e.load)thepackage.

Howtoopenapackage(ie.loadapackage)?

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HowtoloadupanRpackage

UseRfunctionlibrary>library(name of package).

Example:toopenapackagecalledstats

Ifanerrormessageappear,thisimpliesthatthepackagerequiredisnotinyourRsession.è Needtoinstallthepackage!

> library(stats)

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NEXT

• PARTC:WorkinginRStudio

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