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Howtoreadthisbook
Thisbookmayserveyoubetterasareferencebookthanatextbook.Itcontainsalargenumberof
technicaldetails,andwedonotexpectyoutoreaditfrombeginningtoend,sinceyoumayeasilyfeel
overwhelmed.Instead,thinkaboutyourbackgroundandwhatyouwanttodofirst,andgototherelevant
chaptersorsections.Forexample:
Ijustwanttofinishmycoursehomework(Chapter2shouldbemorethanenoughforyou).
IknowthisisanRMarkdownbook,butIusePythonmorethanR(GotoSection2.7.1).
Iwanttoembedinteractiveplotsinmyreports,orwantmyreaderstobeablechangemymodel
parametersinteractivelyandseeresultsonthefly(CheckoutSection2.8).
IknowtheoutputformatIwanttouse,andIwanttocustomizeitsappearance(Checkoutthe
documentationofthespecificoutputformatinChapter3orChapter4).Forexample,Iwantto
customizethetemplateformyPowerPointpresentation(GotoSection4.4.1).
Iwanttobuildabusinessdashboardhighlightingsomekeyfiguresandindicators(GotoChapter5).
Iheardabout yolo=TRUEfromafriend,andI’mcuriouswhatthatmeansinthexaringanpackage
(GotoChapter7).
Iwanttobuildapersonalwebsite(GotoChapter10),orwriteabook(GotoChapter12).
IwanttowriteapaperandsubmittotheJournalofStatisticalSoftware(GotoChapter13).
Iwanttobuildaninteractivetutorialwithexercisesformystudentstolearnatopic(GotoChapter14).
I’mfamiliarwithRMarkdownnow,andIwanttogeneratepersonalizedreportsforallmycustomers
usingthesameRMarkdowntemplate(TryparameterizedreportsinChapter15).
IknowsomeJavaScript,andwanttobuildaninterfaceinRtocallaninterestedJavaScriptlibrary
fromR(LearnhowtodevelopHTMLwidgetsinChapter16).
Iwanttobuildfuturereportswithacompanybrandedtemplatethatshowsourlogoandusesour
uniquecolortheme(GotoChapter17).
IfyouarenotfamiliarwithRMarkdown,werecommendthatyoureadatleastChapter2tolearnthe
basics.Alltherestofthechaptersinthisbookcanbereadinanyorderyoudesire.Theyareprettymuch
orthogonaltoeachother.However,tobecomefamiliarwithRMarkdownoutputformats,youmaywantto
thumbthroughtheHTMLdocumentformatinSection3.1,becausemanyotherformatssharethesame
optionsasthisformat.
Estadísticos e-Books & PapersEstadísticos e-Books & Papers

However,theoriginalversionofMarkdowninventedbyJohnGruberwasoftenfoundoverlysimpleandnot

suitabletowritehighlytechnicaldocuments.Forexample,therewasnosyntaxfortables,footnotes,math

expressions,orcitations.Fortunately,JohnMacFarlanecreatedawonderfulpackagenamedPandoc

(http://pandoc.org)toconvertMarkdowndocuments(andmanyothertypesofdocuments)toalarge

varietyofoutputformats.Moreimportantly,theMarkdownsyntaxwassignificantlyenriched.Nowwecan

writemoretypesofelementswithMarkdownwhilestillenjoyingitssimplicity.

Inanutshell,RMarkdownstandsontheshouldersofknitrandPandoc.Theformerexecutesthe

computercodeembeddedinMarkdown,andconvertsRMarkdowntoMarkdown.Thelatterrenders

Markdowntotheoutputformatyouwant(suchasPDF,HTML,Word,andsoon).

Thermarkdownpackage(Allaire,Xie,McPherson,etal.2018)wasfirstcreatedinearly2014.Duringthe

pastfouryears,ithassteadilyevolvedintoarelativelycompleteecosystemforauthoringdocuments,soit

isagoodtimeforustoprovideadefinitiveguidetothisecosystemnow.Atthispoint,therearealarge

numberoftasksthatyoucoulddowithRMarkdown:

CompileasingleRMarkdowndocumenttoareportindifferentformats,suchasPDF,HTML,orWord.

Createnotebooksinwhichyoucandirectlyruncodechunksinteractively.

Makeslidesforpresentations(HTML5,LaTeXBeamer,orPowerPoint).

Producedashboardswithflexible,interactive,andattractivelayouts.

BuildinteractiveapplicationsbasedonShiny.

Writejournalarticles.

Authorbooksofmultiplechapters.

Generatewebsitesandblogs.

ThereisafundamentalassumptionunderneathRMarkdownthatusersshouldbeawareof:weassumeit

sufficesthatonlyalimitednumberoffeaturesaresupportedinMarkdown.By“features”,wemeanthe

typesofelementsyoucancreatewithnativeMarkdown.Thelimitationisagreatfeature,notabug.R

Markdownmaynotbetherightformatforyouifyoufindtheseelementsnotenoughforyourwriting:

paragraphs,(section)headers,blockquotations,codeblocks,(numberedandunnumbered)lists,

horizontalrules,tables,inlineformatting(emphasis,strikeout,superscripts,subscripts,verbatim,and

smallcapstext),LaTeXmathexpressions,equations,links,images,footnotes,citations,theorems,proofs,

andexamples.Webelievethislistofelementssufficeformosttechnicalandnon-technicaldocuments.It

maynotbeimpossibletosupportothertypesofelementsinRMarkdown,butyoumaystarttolosethe

simplicityofMarkdownifyouwishtogothatfar.

Epictetusoncesaid,“Wealthconsistsnotinhavinggreatpossessions,butinhavingfewwants.”Thespirit

isalsoreflectedinMarkdown.Ifyoucancontrolyourpreoccupationwithpursuingtypesettingfeatures,

youshouldbemuchmoreefficientinwritingthecontentandcanbecomeaprolificauthor.Itisentirely

Estadísticos e-Books & PapersEstadísticos e-Books & Papers

possibletosucceedwithsimplicity.JungJae-sungwasalegendarybadmintonplayerwitharemarkably

simpleplayingstyle:hedidnotlooklikeatalentedplayerandwasveryshortcomparedtootherplayers,

somostofthetimeyouwouldjustseehimjumpthreefeetoffthegroundandsmashlikethunderoverand

overagaininthebackcourtuntilhebeatshisopponents.

PleasedonotunderestimatethecustomizabilityofRMarkdownbecauseofthesimplicityofitssyntax.In

particular,Pandoctemplatescanbesurprisinglypowerful,aslongasyouunderstandtheunderlying

technologiessuchasLaTeXandCSS,andarewillingtoinvesttimeintheappearanceofyouroutput

documents(reports,books,presentations,and/orwebsites).Asoneexample,youmaycheckoutthePDF

reportofthe2017EmployerHealthBenefitsSurvey.Itlooksfairlysophisticated,butwasactually

producedviabookdown(Xie2016),whichisanRMarkdownextension.AcustomLaTeXtemplateanda

lotofLaTeXtrickswereusedtogeneratethisreport.Notsurprisingly,thisverybookthatyouarereading

rightnowwasalsowritteninRMarkdown,anditsfullsourceispubliclyavailableintheGitHubrepository

https://github.com/rstudio/rmarkdown-book.

RMarkdowndocumentsareoftenportableinthesensethattheycanbecompiledtomultipletypesof

outputformats.Again,thisismainlyduetothesimplifiedsyntaxoftheauthoringlanguage,Markdown.

Thesimplertheelementsinyourdocumentare,themorelikelythatthedocumentcanbeconvertedto

differentformats.Similarly,ifyouheavilytailorRMarkdowntoaspecificoutputformat(e.g.,LaTeX),you

arelikelytolosetheportability,becausenotallfeaturesinoneformatworkinanotherformat.

Lastbutnotleast,yourcomputingresultswillbemorelikelytobereproducibleifyouuseRMarkdown(or

otherknitr-basedsourcedocuments),comparedtothemanualcut-and-pasteapproach.Thisisbecause

theresultsaredynamicallygeneratedfromcomputersourcecode.Ifanythinggoeswrongorneedstobe

updated,youcansimplyfixorupdatethesourcecode,compilethedocumentagain,andtheresultswill

automaticallyupdated.Youcanenjoyreproducibilityandconvenienceatthesametime.

References

Xie,Yihui.2015.DynamicDocumentswithRandKnitr.2nded.BocaRaton,Florida:Chapman;Hall/CRC.

https://yihui.name/knitr/.

Xie,Yihui.2018d.Knitr:AGeneral-PurposePackageforDynamicReportGenerationinR.

https://yihui.name/knitr/.

Allaire,JJ,YihuiXie,JonathanMcPherson,JavierLuraschi,KevinUshey,AronAtkins,HadleyWickham,

JoeCheng,WinstonChang,andRichardIannone.2018.Rmarkdown:DynamicDocumentsforR.

Xie,Yihui.2016.Bookdown:AuthoringBooksandTechnicalDocumentswithRMarkdown.BocaRaton,

Florida:Chapman;Hall/CRC.https://github.com/rstudio/bookdown.

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