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Chapter12: Graphicalprocedures
75
itwillbeoverwritten. Thisis s the caseevenifthefilewasonly createdearlier inthesameR
session.
ManyusagesofPostScriptoutputwillbetoincorporatethefigureinanotherdocument.This
worksbestwhenencapsulated PostScriptisproduced: : Ralwaysproducesconformant t output,
butonlymarkstheoutputassuchwhentheonefile=FALSEargumentissupplied.Thisunusual
notationstemsfromS-compatibility:itreallymeansthattheoutputwillbeasinglepage(which
ispartoftheEPSFspecification).Thustoproduceaplotforinclusionusesomethinglike
> postscript("plot1.eps", , horizontal=FALSE, onefile=FALSE,
height=8, width=6, , pointsize=10)
12.6.2 Multiplegraphicsdevices
InadvanceduseofRitisoftenusefultohaveseveralgraphicsdevicesinuseatthesametime.
Ofcourseonlyonegraphicsdevicecanacceptgraphicscommandsatanyonetime,andthisis
knownasthecurrentdevice. Whenmultipledevicesareopen,theyformanumberedsequence
withnamesgivingthekindofdeviceatanyposition.
The maincommands used for operating withmultipledevices, andtheirmeanings areas
follows:
X11()
[UNIX]
windows()
win.printer()
win.metafile()
[Windows]
quartz() [OSX]
postscript()
pdf()
png()
jpeg()
tiff()
bitmap()
...
Eachnewcalltoadevicedriverfunctionopensanewgraphicsdevice,thusextending
by onethedevicelist. . This s devicebecomesthecurrentdevice,towhichgraphics
outputwillbesent.
dev.list()
Returnsthenumberandnameofallactivedevices.Thedeviceatposition1onthe
listisalwaysthenulldevice whichdoesnotacceptgraphicscommandsatall.
dev.next()
dev.prev()
Returns thenumberandname ofthe graphics devicenext to,orprevious tothe
currentdevice,respectively.
dev.set(which=k)
Canbeusedtochangethecurrentgraphicsdevicetotheoneatpositionkofthe
devicelist. Returnsthenumberandlabelofthedevice.
dev.off(k)
Terminatethegraphicsdeviceatpointkofthedevicelist. Forsomedevices,suchas
postscriptdevices,thiswilleitherprintthefileimmediatelyorcorrectlycomplete
thefileforlaterprinting,dependingonhowthedevicewasinitiated.
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Chapter12: Graphicalprocedures
76
dev.copy(device,...,which=k)
dev.print(device,...,which=k)
Makeacopyofthedevicek.Heredeviceisadevicefunction,suchaspostscript,
withextraarguments,ifneeded,specifiedby ‘...’. . dev.printis s similar,butthe
copieddeviceisimmediatelyclosed,sothatendactions,suchasprintinghardcopies,
areimmediatelyperformed.
graphics.off()
Terminateallgraphicsdevicesonthelist,exceptthenulldevice.
12.7 Dynamicgraphics
R does s not have e builtin n capabilities for dynamic or r interactive e graphics, e.g. . rotating point
cloudsorto“brushing”(interactivelyhighlighting)points.However,extensivedynamicgraphics
facilitiesareavailableinthesystemGGobibySwayne,CookandBujaavailablefrom
http://www.ggobi.org/
and thesecanbe accessed fromR R via the package rggobi(https://CRAN.R-project.org/
package=rggobi),describedathttp://www.ggobi.org/rggobi.
Also,packagergl(https://CRAN.R-project.org/package=rgl)provideswaystointeract
with3Dplots,forexampleofsurfaces.
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77
13 Packages
AllR functions s anddatasets are e stored inpackages. . Only y whena package is loadedare its
contentsavailable. Thisisdonebothforefficiency(thefulllistwouldtakemorememoryand
wouldtakelonger tosearchthanasubset),andtoaidpackagedevelopers,whoareprotected
fromnameclasheswithothercode. TheprocessofdevelopingpackagesisdescribedinSection
“CreatingRpackages”inWritingRExtensions.Here,wewilldescribethemfromauser’spoint
ofview.
Toseewhichpackagesareinstalledatyoursite,issuethecommand
> library()
withnoarguments. Toloadaparticularpackage(e.g.,the e boot(https://CRAN.R-project.
org/package=boot)packagecontainingfunctionsfromDavison&Hinkley(1997)),useacom-
mandlike
> library(boot)
UsersconnectedtotheInternetcanusetheinstall.packages()andupdate.packages()
functions(availablethroughthePackagesmenuintheWindowsandOSXGUIs,seeSection
“Installingpackages”inRInstallationandAdministration)toinstallandupdatepackages.
Toseewhichpackagesarecurrentlyloaded,use
> search()
todisplaythesearchlist.Somepackagesmaybeloadedbutnotavailableonthesearchlist(see
Section13.3[Namespaces],page78): thesewillbeincludedinthelistgivenby
> loadedNamespaces()
Toseealistofallavailablehelptopicsinaninstalledpackage,use
> help.start()
to start the
HTML
help system, and thennavigate to the package listing in the Reference
section.
13.1 Standardpackages
Thestandard(or base)packagesareconsideredpartof the Rsourcecode. . Theycontainthe
basicfunctions thatallowR towork,andthedatasetsandstandardstatisticalandgraphical
functionsthataredescribedinthismanual. Theyshouldbeautomatically y availableinanyR
installation. SeeSection“Rpackages”inRFAQ,foracompletelist.
13.2 Contributedpackagesand
CRAN
Therearethousands ofcontributedpackages for R,writtenby manydifferentauthors. . Some
ofthesepackagesimplementspecializedstatisticalmethods,othersgiveaccesstodataorhard-
ware,andothersaredesignedtocomplementtextbooks. Some(therecommendedpackages)are
distributed witheverybinarydistributionofR.Mostare available for r downloadfrom
CRAN
(https://CRAN.R-project.org/anditsmirrors)andotherrepositoriessuchasBioconductor
(https://www.bioconductor.org/). andOmegahat t (http://www.omegahat.net/). . The
R FAQ containsalistofCRANpackagescurrent atthetimeofrelease,butthecollectionof
availablepackageschangesveryfrequently.
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Chapter13: Packages
78
13.3 Namespaces
Allpackageshavenamespaces,andhavesinceR2.14.0.Namespacesdothreethings:theyallow
thepackagewritertohidefunctionsanddatathataremeantonlyforinternaluse,theyprevent
functionsfrombreakingwhenauser(orotherpackagewriter)picksanamethatclasheswith
oneinthepackage,andtheyprovideawaytorefertoanobjectwithinaparticularpackage.
Forexample,t()isthetransposefunctioninR,butusersmightdefinetheirownfunction
namedt. Namespacespreventtheuser’sdefinitionfromtakingprecedence,andbreakingevery
functionthattriestotransposeamatrix.
Therearetwooperatorsthatwork withnamespaces. . Thedouble-colonoperator::selects
definitions froma particular namespace. . In n the example above, the transpose function will
alwaysbeavailableasbase::t,becauseitisdefinedinthebasepackage. Onlyfunctionsthat
areexportedfromthepackagecanberetrievedinthisway.
The triple-colon operator ::: : may y be seen in n a few places s in n R R code: : it t acts like the
double-colonoperator but also allows access to hidden n objects. . Users s aremore likely to use
thegetAnywhere()function,whichsearchesmultiplepackages.
Packagesareofteninter-dependent,andloadingonemaycauseotherstobeautomatically
loaded. Thecolonoperatorsdescribedabovewillalsocauseautomaticloadingoftheassociated
package. Whenpackageswithnamespacesareloadedautomaticallytheyarenotaddedtothe
searchlist.
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79
14 OSfacilities
RhasquiteextensivefacilitiestoaccesstheOSunderwhichitisrunning: thisallowsittobe
usedasascriptinglanguageandthat ability is muchusedby R itself,for example toinstall
packages.
BecauseR’sownscriptsneedtoworkacrossallplatforms,considerableefforthasgoneinto
makethescriptingfacilitiesasplatform-independentasisfeasible.
14.1 Filesanddirectories
Therearemanyfunctionstomanipulatefilesanddirectories. Herearepointerstosomeofthe
morecommonlyusedones.
To create an (empty) file e or r directory, , use file.create e or r create.dir. . (These e are the
analoguesofthePOSIXutilitiestouchandmkdir.) Fortemporaryfilesanddirectoriesinthe
Rsessiondirectoryseetempfile.
Files canbe removedby either file.remove or unlink: : the e latter canremove directory
trees.
Fordirectorylistingsuselist.files(alsoavailableasdir)orlist.dirs.Thesecanselect
filesusingaregularexpression:toselectbywildcardsuseSys.glob.
Manytypesofinformationonafilepath(includingforexampleifitisafileordirectory)can
befoundbyfile.info.
Thereareseveralwaystofindoutifafile‘exists’(afilecanexistonthefilesystemandnot
bevisibletothecurrentuser).Therearefunctionsfile.exists,file.accessandfile_test
withvariousversionsofthistest:file_testisaversionofthePOSIXtestcommandforthose
familiarwithshellscripting.
Functionfile.copyistheRanalogueofthePOSIXcommandcp.
Choosingfilescanbedoneinteractivelybyfile.choose: theWindowsport t hasthemore
versatilefunctionschoose.filesandchoose.dirandtherearesimilarfunctionsinthetcltk
package: tk_choose.filesandtk_choose.dir.
Functionsfile.showandfile.editwilldisplayandeditoneormorefilesinawayappro-
priatetotheRport,usingthefacilitiesofaconsole(suchasRGuionWindowsorR.apponOS
X)ifoneisinuse.
Thereissomesupportforlinksinthefilesystem:seefunctionsfile.linkandSys.readlink.
14.2 Filepaths
Withafewexceptions,RreliesontheunderlyingOSfunctionstomanipulatefilepaths. Some
aspectsofthisareallowedtodependontheOS,anddo,evendowntotheversionoftheOS.
TherearePOSIXstandardsforhowOSesshouldinterpretfilepathsandmanyRusersassume
POSIXcompliance: butWindowsdoesnotclaimtobecompliantandotherOSesmaybeless
thancompletelycompliant.
Thefollowingaresomeissueswhichhavebeenencounteredwithfilepaths.
 POSIXfilesystemsarecase-sensitive,sofoo.pngandFoo.PNGaredifferentfiles. . However,
thedefaultsonWindowsandOSXaretobecase-insensitive,andFATfilesystems(com-
monlyusedonremovablestorage)arenotnormallycase-sensitive(andallfilepathsmaybe
mappedtolowercase).
 AlmostalltheWindows’OSservicessupporttheuseofslashorbackslashasthefilepath
separator,andRconvertstheknownexceptionstotheformrequiredbyWindows.
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Chapter14: OSfacilities
80
 ThebehaviouroffilepathswithatrailingslashisOS-dependent. . Suchpathsarenotvalid
on Windows and should not be expected to work. . POSIX-2008 8 requires such paths to
matchonlydirectories,butearlierversionsallowedthemtoalsomatchfiles. Sotheyare
bestavoided.
 Multipleslashesinfilepathssuchas/abc//defarevalidonPOSIXfilesystemsandtreated
as if f there e was only one e slash. . They y are e usually y accepted d by Windows’ OS functions.
However,leadingdoubleslashesmayhaveadifferentmeaning.
 Windows’
UNC
filepaths
(such
as
\\server\dir1\dir2\file
and
\\?\UNC\server\dir1\dir2\file) are e not t supported, , but t they y may y work k in
someRfunctions.POSIXfilesystemsareallowedtotreataleadingdoubleslashspecially.
 Windowsallowsfilepathscontainingdrivesandrelativetothecurrentdirectoryonadrive,
e.g.d:foo/barreferstod:/a/b/c/foo/barifthecurrentdirectoryondrived:is/a/b/c.
Itisintendedthatthesework,buttheuseofabsolutepathsissafer.
Functionsbasenameanddirname select parts ofafilepath: : therecommendedway y to as-
sembleafilepathfromcomponentsisfile.path.Functionpathexpanddoes‘tildeexpansion’,
substitutingvaluesforhomedirectories(thecurrentuser’s,andperhapsthoseofotherusers).
On filesystems s with h links, a single file can n be e referred d to o by many y filepaths. . Function
normalizePathwillfindacanonicalfilepath.
Windowshastheconceptsofshort(‘8.3’)andlongfilenames:normalizePathwillreturnan
absolutepathusinglongfilenamesandshortPathNamewillreturnaversionusingshortnames.
Thelatterdoesnotcontainspacesandusesbackslashastheseparator,soissometimesuseful
forexportingnamesfromR.
File permissions s are e a related topic.
R has support for the POSIX concepts s of
read/write/execute permission for owner/group/allbut this may beonly partially supported
onthefilesystem(soforexampleonWindowsonlyread-onlyfiles(fortheaccountrunningthe
R session) are recognized. . Access s Control l Lists s (ACLs) areemployed d onseveral filesystems,
butdonothaveanagreedstandardandRhasnofacilitiestocontrolthem. UseSys.chmodto
changepermissions.
14.3 Systemcommands
Functions system andsystem2 are usedtoinvokea systemcommandand d optionally y collect
itsoutput. system2isalittlemoregeneralbutitsmainadvantageisthatitiseasiertowrite
cross-platformcodeusingit.
system behaves differently onWindowsfromotherOSes (because the APIC callof that
name does). . Elsewhereitinvokes s ashelltorunthe command: : theWindows s portofRhasa
functionshelltodothat.
TofindoutiftheOSincludesacommand,useSys.which,whichattemptstodothis ina
cross-platformway(unfortunatelyitisnotastandardOSservice).
FunctionshQuotewillquotefilepathsasneededforcommandsinthecurrentOS.
14.4 CompressionandArchives
RecentversionsofRhaveextensivefacilitiestoreadandwritecompressedfiles,oftentranspar-
ently. ReadingoffilesinRistoaveylargeextentdonebyconnections,andthefilefunction
whichisusedtoopenaconnectiontoafile(oraURL)andisabletoidentifythecompression
usedfromthe‘magic’headerofthefile.
The type e of compression which has s been supported for longest is s gzip compression, , and
thatremainsagoodgeneralcompromise.FilescompressedbytheearlierUnixcompressutility
canalsoberead,butthesearebecomingrare. Twoother r forms ofcompression,thoseofthe
Chapter14: OSfacilities
81
bzip2andxzutilities arealsoavailable. . Thesegenerally y achievehigherrates ofcompression
(dependingonthefile,muchhigher)attheexpenseofslowerdecompressionandmuchslower
compression.
Thereis someconfusionbetweenxzandlzma compression(seehttps://en.wikipedia.
org/wiki/Xzandhttps://en.wikipedia.org/wiki/LZMA): Rcanreadfiles s compressedby
mostversionsofeither.
Filearchivesaresinglefileswhichcontainacollectionoffiles,themostcommononesbeing
‘tarballs’andzipfilesasusedtodistributeRpackages.Rcanlistandunpackboth(seefunctions
untarandunzip)andcreateboth(forzipwiththehelpofanexternalprogram).
82
AppendixA Asamplesession
Thefollowingsessionis intendedtointroducetoyou u somefeatures s ofthe Renvironment by
using them. . Many y features s of f the system will be e unfamiliar r and d puzzling at first, but this
puzzlementwillsoondisappear.
StartRappropriatelyforyourplatform(seeAppendix B[InvokingR],page 85).
TheRprogrambegins,withabanner.
(WithinRcode,thepromptonthelefthandsidewillnotbeshowntoavoidcon-
fusion.)
help.start()
Start the
HTML
interface toon-linehelp(using awebbrowser r available e at your
machine).Youshouldbrieflyexplorethefeaturesofthisfacilitywiththemouse.
Iconifythehelpwindowandmoveontothenextpart.
x<-rnorm(50)
y<-rnorm(x)
Generatetwopseudo-randomnormalvectorsofx-andy-coordinates.
plot(x,y)
Plotthepointsintheplane. Agraphicswindowwillappearautomatically.
ls()
SeewhichRobjectsarenowintheRworkspace.
rm(x,y)
Removeobjectsnolongerneeded.(Cleanup).
x<-1:20 Makex=(1;2;:::;20).
w<-1+sqrt(x)/2
A‘weight’vectorofstandarddeviations.
dummy<-data.frame(x=x,y=x+rnorm(x)*w)
dummy
Makeadataframeoftwocolumns,xandy,andlookatit.
fm<-lm(y~x,data=dummy)
summary(fm)
Fit asimple linearregressionandlook at the analysis. . Withy y totheleft ofthe
tilde,wearemodellingydependentonx.
fm1<-lm(y~x,data=dummy,weight=1/w^2)
summary(fm1)
Sinceweknowthestandarddeviations,wecandoaweightedregression.
attach(dummy)
Makethecolumnsinthedataframevisibleasvariables.
lrf<-lowess(x,y)
Makeanonparametriclocalregressionfunction.
plot(x,y)
Standardpointplot.
lines(x,lrf$y)
Addinthelocalregression.
abline(0,1,lty=3)
Thetrueregressionline: (intercept0,slope1).
abline(coef(fm))
Unweightedregressionline.
AppendixA:Asamplesession
83
abline(coef(fm1),col="red")
Weightedregressionline.
detach() Removedataframefromthesearchpath.
plot(fitted(fm),resid(fm),
xlab="Fittedvalues",
ylab="Residuals",
main="ResidualsvsFitted")
Astandardregressiondiagnosticplottocheckforheteroscedasticity. Canyousee
it?
qqnorm(resid(fm),main="ResidualsRankitPlot")
Anormalscoresplottocheckforskewness,kurtosisandoutliers. (Notveryuseful
here.)
rm(fm,fm1,lrf,x,dummy)
Cleanupagain.
ThenextsectionwilllookatdatafromtheclassicalexperimentofMichelsontomeasurethe
speedoflight. Thisdatasetis s availableinthe morleyobject,butwewillreadittoillustrate
theread.tablefunction.
filepath<-system.file("data","morley.tab",package="datasets")
filepath Getthepathtothedatafile.
file.show(filepath)
Optional. Lookatthefile.
mm<-read.table(filepath)
mm
ReadintheMichelsondataasadataframe,andlookatit. Therearefiveexper-
iments(columnExpt) andeachhas20runs (columnRun) andslis therecorded
speedoflight,suitablycoded.
mm$Expt<-factor(mm$Expt)
mm$Run<-factor(mm$Run)
ChangeExptandRunintofactors.
attach(mm)
Makethedataframevisibleatposition3(thedefault).
plot(Expt,Speed,main="SpeedofLightData",xlab="ExperimentNo.")
Comparethefiveexperimentswithsimpleboxplots.
fm<-aov(Speed~Run+Expt,data=mm)
summary(fm)
Analyzeasarandomizedblock,with‘runs’and‘experiments’asfactors.
fm0<-update(fm,.~.-Run)
anova(fm0,fm)
Fitthesub-modelomitting‘runs’,andcompareusingaformalanalysisofvariance.
detach()
rm(fm,fm0)
Cleanupbeforemovingon.
Wenowlookatsomemoregraphicalfeatures: contourandimageplots.
x<-seq(-pi,pi,len=50)
y<-x
xisavectorof50equallyspacedvaluesin x.yisthesame.
84
f<-outer(x,y,function(x,y)cos(y)/(1+x^2))
f is s asquarematrix,withrows andcolumns indexedby x andyrespectively,of
valuesofthefunctioncos(y)=(1+x
2
).
oldpar<-par(no.readonly=TRUE)
par(pty="s")
Savetheplottingparametersandsettheplottingregionto“square”.
contour(x,y,f)
contour(x,y,f,nlevels=15,add=TRUE)
Makeacontourmapoff;addinmorelinesformoredetail.
fa<-(f-t(f))/2
faisthe“asymmetricpart”off. (t()istranspose).
contour(x,y,fa,nlevels=15)
Makeacontourplot,...
par(oldpar)
...andrestoretheoldgraphicsparameters.
image(x,y,f)
image(x,y,fa)
Makesomehighdensityimageplots,(ofwhichyoucangethardcopiesifyouwish),
...
objects();rm(x,y,f,fa)
...andcleanupbeforemovingon.
Rcandocomplexarithmetic,also.
th<-seq(-pi,pi,len=100)
z<-exp(1i*th)
1iisusedforthecomplexnumberi.
par(pty="s")
plot(z,type="l")
Plottingcomplexarguments meansplotimaginaryversusrealparts. . This s should
beacircle.
w<-rnorm(100)+rnorm(100)*1i
Supposewewanttosamplepointswithintheunitcircle.Onemethodwouldbeto
takecomplexnumberswithstandardnormalrealandimaginaryparts ...
w<-ifelse(Mod(w)>1,1/w,w)
...andtomapanyoutsidethecircleontotheirreciprocal.
plot(w,xlim=c(-1,1),ylim=c(-1,1),pch="+",xlab="x",ylab="y")
lines(z) Allpointsareinsidetheunitcircle,butthedistributionisnotuniform.
w<-sqrt(runif(100))*exp(2*pi*runif(100)*1i)
plot(w,xlim=c(-1,1),ylim=c(-1,1),pch="+",xlab="x",ylab="y")
lines(z) Thesecondmethodusestheuniformdistribution.Thepointsshouldnowlookmore
evenlyspacedoverthedisc.
rm(th,w,z)
Cleanupagain.
q()
QuittheRprogram. YouwillbeaskedifyouwanttosavetheRworkspace,and
foranexploratorysessionlikethis,youprobablydonotwanttosaveit.
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