ETC1010:DataModellingandComputingWeekofintroduction:RmarkdownProfessorDiCook&Dr. NicholasTierneyEBS,MonashU.2019-08-02

Whatisthissong?

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Recap3/62

Tra�cLightSystem

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RedPostit

--

IneedahandSlowdown

GreenPostit

--

IamuptospeedIhavecompletedthething

Tra�cLightSystem

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Ressentials:Ashortlist(fornow)Functionsare(mostoften)verbs,followedbywhattheywillbeappliedtoinparentheses:

do_this(to_this)do_that(to_this,to_that,with_those)

Columns(variables)indataframesareaccessedwith$:

dataframe$var_name

Packagesareinstalledwiththeinstall.packagesfunctionandloadedwiththelibraryfunction,oncepersession:

install.packages("package_name")library(package_name)

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Today:Outline

WhywecareaboutReproducibilityR+markdown=RmarkdownControlingoutputandinputofrmarkdownExercisesoncreatingrmarkdownreportsonthehumbleplatypusFormupassignmentgroupsQuizReleaseassignment(latertoday)

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Weareinatightspotwithreproducibility

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Only6outof53landmarkresultscouldbereproduced

--Amgen,2014*

*HeardviaGarretGrolemund'sgreattalk

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Anestimated75%-90%ofpreclinicalresultscannotbereproduced

--Begley,2015*

*HeardviaGarretGrolemund'sgreattalk

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Estimatedannualcostofirreproducibilityforbiomedicalindustry=28BillionUSD

--Freedman,2015*

*HeardviaGarretGrolemund'sgreattalk

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Sowhatcanwedoaboutit?

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Reproducibilitychecklist

Near-termgoals:

Arethetablesand�guresreproduciblefromthecodeanddata?Doesthecodeactuallydowhatyouthinkitdoes?Inadditiontowhatwasdone,isitclearwhyitwasdone?(e.g.,howwereparametersettingschosen?)

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Reproducibilitychecklist

Long-termgoals:

Canthecodebeusedforotherdata?Canyouextendthecodetodootherthings?

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Literateprogrammingisapartialsolution

Literateprogrammingshinessomelightonthisdarkareaofscience.

AnideafromDonaldKnuthwhereyoucombineyourtextwithyourcodeoutputtocreateadocument.

Ablendofyourliterature(text),andyourprogramming(code),tocreatesomethingyoucanreadfromtoptobottom.

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So

Imagineareport:

Introduction,methods,results,discussion,andconclusion,

andallthebitsofcodethatmakeeachsection.

Withrmarkdown,youcanseeallthepiecesofyourdataanalysisll t th

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ll t th

Markdownasanewplayertolegibility

In2004,JohnGruber,ofdaring�reballcreatedmarkdown,asimplewaytocreatetextthatrenderedintoaHTMLwebpage.

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-bulletlist-bulletlist-bulletlist bulletlist

bulletlistbulletlist

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1.numberedlist2.numberedlist3.numberedlist

__bold__,**bold**,_italic_,*italic*

>quoteofsomethingprofound

1.numberedlist2.numberedlist3.numberedlist

bold,bold,italic,italic

quoteofsomethingprofound

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Withverylittlemarkingup,wecancreaterichtext,thatactuallyresemblesthetextthatwewanttosee.

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LearntousemarkdownInyoursmallgroups,spend�veminutesworkingthroughmarkdowntutorial.com

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Rmarkdownhelpscompletethesolutiontothereproducibilityproblem

Q:Howdowetakemarkdown+Rcode="literateprogrammingenvironment"

A:Rmarkdown

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Rmarkdown...

Providesanenvironmentwhereyoucanwriteyourcompleteanalysis,andmarriesyourtext,andcodetogetherintoarichdocument.

Youwriteyourcodeascodechunks,putyourtextaroundthat,andthenheypresto,youhaveadocumentyoucanreproduce.

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Reminder:You'vealreadyusedrmarkdown!

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HowwillweuseRMarkdown?

Everyassignment+project/isanRMarkdowndocumentYou'llalwayshaveatemplateRMarkdowndocumenttostartwithTheamountofsca�oldinginthetemplatewilldecreaseoverthesemesterTheselecturenotesarecreatedusingRMarkdown(!)

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Theanatomyofanrmarkdowndocument

Therearethreepartstoanrmarkdowndocument.

Metadata(YAML)Text(markdownformatting)Code(codeformatting)

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Metadata:YAML(YAMLAin'tMarkupLanguage)

Themetadataofthedocumenttellsyouhowitisformed-whatthetitleis,whatdatetoput,andothercontrolinformation.

Ifyou'refamiliarwith ,thisisksimilartohowyouspecifydocumenttype,styles,fonts,options,etcinthefrontmatter/preamble.

LT XAE

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Metadata:YAML

RmarkdowndocumentsuseYAMLtoprovidethemetadata.Itlookslikethis:

---title:"Anexampledocument"author:"NicholasTierney"output:html_document---

Itstartsanendswiththreedashes---,andhas�eldslikethe 35/62

f ll d

1.bulletlist2.bulletlist3.bulletlist

1.bulletlist2.bulletlist3.bulletlist

Text

Ismarkdown,aswediscussedintheearliersection,

Itprovidesasimplewaytomarkuptext

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Code

Werefertocodeinanrmarkdowndocumentintwoways:

1.Codechunks,and2.Inlinecode.

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Code:Codechunks

Codechunksaremarkedbythreebackticksandcurlybraceswithrinsidethem:

```{rchunk-name}#acodechunk```

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abacktickisaspecialcharacteryoumightnothaveseenbefore,itistypicallylocatedunderthetildekey(~).OnUSA/Australiakeyboards,isundertheescapekey:

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Code:Inlinecode

Sometimesyouwanttorunthecodeinsideasentence.Thisiscalledrunningthecode"inline".

Youmightwanttorunthecodeinlinetonamethenumberofvariablesorrowsinadatasetinasentencelike:

ThereareXXXobservationsintheairqualitydataset,andXXXvariables.

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Code:Inlinecode

Youcancallcode"inline"likeso:

Thereare`rnrow(airquality)`observationsintheairqualitydataset,and`rncol(airquality)`variables.

Whichgivesyouthefollowingsentence

Thereare153observationsintheairqualitydataset,and6i bl

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i bl

Code:Inlinecode

What'sgreataboutthisisthatifyourdatachangesupstream,thenyoudon'tneedtoworkoutwhereyoumentionedyourdata,youjustupdatethedocument.

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YourTurn:Putittogether

Gotorstudio.cloudand

openthedocument"01-oz-atlas.Rmd"knitthedocumentChangethedatasectionatthetoptobefromadi�erentstateinsteadof"NewSouthWales"knitthedocumentagain

Howdothetextand�guresinthedocumentchange? 05:0043/62

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Code:Chunknames

Straightafterthe```{ryoucanuseatextstringtonamethechunk:

```{rread-crime-data}

```{rread-crime-data}crime<-read_csv("data/crime-data.csv")```

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Code:ChunkNames

Namingcodechunkshasthreeadvantages:

1.Navigatetospeci�cchunksusingthedrop-downcodenavigatorinthebottom-leftofthescripteditor.

2.Graphicsproducedbychunksnowhaveusefulnames.3.Youcansetupnetworksofcachedchunkstoavoidre-performing

expensivecomputationsoneveryrun.

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Code:Chunknames

Everychunkshouldideallyhaveaname.Namingthingsishard,butfollowtheserulesandyou'llbe�ne:

1.Onewordthatdescribestheaction(e.g.,"read")2.Onewordthatdescribesthethinginsidethecode(e.g,

"gapminder")3.Separatewordswith"-"(e.g.,read-gapminder)

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Code:Chunkoptions

Youcancontrolhowthecodeisoutputbychangingthecodechunkoptionswhichfollowthetitle.

```{rread-gapminder,eval=FALSE,echo=TRUE}gap<-read_csv("gapminder.csv")```

Whatdoyouthinkthisdoes?

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Code:ChunkoptionsThecodechunkoptionsyouneedtoknowaboutrightnoware:

cache:TRUE/FALSE.Doyouwanttosavetheoutputofthechunksoitdoesn'thavetorunnexttime?eval:TRUE/FALSEDoyouwanttoevaluatethecode?echo:TRUE/FALSEDoyouwanttoprintthecode?include:TRUE/FALSEDoyouwanttoincludecodeoutputinthe�naloutputdocument?SettingtoFALSEmeansnothingisputintotheoutputdocument,butthecodeisstillrun.

Youcanreadmoreabouttheoptionsattheo�cialdocumentation:https://yihui.name/knitr/options/#code-evaluation 50/62

Yourturn

gotorstudio.cloud,opendocument01-oz-atlas.Rmdandchangethedocumentsothatthecodeoutputishidden,butthegraphicsareshown.(Hint:Google"rstudiormarkdowncheatsheet"forsometips!)Re-Knitthedocument.TakealookattheRMarkdownGallery.

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Globaloptions:Setandforget

Youcansetthedefaultchunkbehaviouronceatthetopofthe.Rmd�leusingachunklike:

knitr::opts_chunk$set(echo=FALSE,cache=TRUE)

thenyouwillonlyneedtoaddchunkoptionswhenyouhavethei l th t 'd lik t b h di� tl

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i l th t 'd lik t b h di� tl

Yourturn

Gotoyour01-oz-atlas.Rmddocumentonrstudio.cloudandchangetheglobalsettingsatthetopofthermarkdowndocumenttoecho=FALSE,andcache=TRUEUpdatetheothercodechunksbyremovingthecodechunkoptions.

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DEMO

Themanydi�erentoutputsofrmarkdown

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Yourturn:Di�erenttypesofdocuments

1.ChangetheoutputofyourcurrentRMarkdown�letoproduceaWorddocument.Nowtrytoproducepdf-thismaynotwork!That'sOK,wedo'ntneeditrightnow.

2.CreateanewdocumentthatwillproduceaslideshowFile>NewRMarkdown>Presentation

3.Createa�exdashboarddocument-seethisoptionintheFile>NewRMarkdown>Fromtemplate

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YourTurn:Makingthegroups

Wearegoingtosetupthegroupsfordoingassignmentwork.

1.Chooseaquotefromthebag.2.Findtheotherpeopleintheclasswiththesamequoteasyou3.Grabyourgearandclaimatabletoworktogetherat.

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YourTurn:Askyourteammatesthesequestions:

1.Whatisonefoodyou'dneverwanttotasteagain?2.Ifyouwereacomicstripcharacter,whowouldyoubeandwhy?

LASTLY,comeupwithanameforyourteamandtellthistoatutor,alongwiththenamesofmembersoftheteam.

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YourTurn

Gotorstudio.cloudtooz-atlas-final.RmdReadthroughthedocumentandaddtextwherepromptedtolearnmoreabouttheAustraliannativeplatypus!

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Recap:

ThereisaReproducibilityCrisisrmarkdown=YAML+text+codermarkdownhasmanydi�erentoutputtypesPlatypusareinteresting!Assignmentwillbeannouncedlatertoday

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Learningmore:

RMarkdowncheatsheetandMarkdownQuickReference(Help->MarkdownQuickReference)handy,we'llrefertoitoftenasthecourseprogresses

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Labquiz

TakethequizfortodayfromED.

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Shareandsharealike

ThisworkislicensedunderaCreativeCommonsAttribution-NonCommercial-ShareAlike4.0InternationalLicense.

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