Table Of ContentStatistical Modeling With R
Statistical Modeling
With R
A dual frequentist and Bayesian
approach for life scientists
PABLO INCHAUSTI
CentroUniversitarioRegionaldelEste,UniversidaddelaRepública,Uruguay
GreatClarendonStreet,Oxford,OX26DP,
UnitedKingdom
OxfordUniversityPressisadepartmentoftheUniversityofOxford.
ItfurtherstheUniversity’sobjectiveofexcellenceinresearch,scholarship,
andeducationbypublishingworldwide.Oxfordisaregisteredtrademarkof
OxfordUniversityPressintheUKandincertainothercountries
©PabloInchausti2023
Themoralrightsoftheauthorhavebeenasserted
Impression:1
Allrightsreserved.Nopartofthispublicationmaybereproduced,storedin
aretrievalsystem,ortransmitted,inanyformorbyanymeans,withoutthe
priorpermissioninwritingofOxfordUniversityPress,orasexpresslypermitted
bylaw,bylicenceorundertermsagreedwiththeappropriatereprographics
rightsorganization.Enquiriesconcerningreproductionoutsidethescopeofthe
aboveshouldbesenttotheRightsDepartment,OxfordUniversityPress,atthe
addressabove
Youmustnotcirculatethisworkinanyotherform
andyoumustimposethissameconditiononanyacquirer
PublishedintheUnitedStatesofAmericabyOxfordUniversityPress
198MadisonAvenue,NewYork,NY10016,UnitedStatesofAmerica
BritishLibraryCataloguinginPublicationData
Dataavailable
LibraryofCongressControlNumber:2022937827
ISBN978–0–19–285901–3(hbk)
ISBN978–0–19–285902–0(pbk)
DOI:10.1093/oso/9780192859013.001.0001
Printedandboundby
CPIGroup(UK)Ltd,Croydon,CR04YY
Coverimage:JohnLund/GettyImages.
LinkstothirdpartywebsitesareprovidedbyOxfordingoodfaithand
forinformationonly.Oxforddisclaimsanyresponsibilityforthematerials
containedinanythirdpartywebsitereferencedinthiswork.
ForJoana,
becausetwoissomuchmorethanone...
Preface
Aprefaceistheclosestanauthormayhavetothe“letterofmarque”usedbyEuropean
governmentsintheseventeenthcenturytoauthorizepiracywiththesovereign’stacitcon-
sent.Anauthorcanwritejustaboutanythingintheprefacewiththeresignedpermission
oftheeditor.
Havingfinishedthebook,Iherebygivemyselfpermissiontowriteinthefirstperson
singular.Ihavespentmanythousandsofhoursendlesslywritingandrewritingthisbook
overthelast24months.Ithasbeenachallenge,apleasure,athrill,andaburdenatthe
sametime.
Atthispoint,Ihavethefollowingunsettlingmixtureoffeelings:
* Reliefandjoy:Finallyitisover.
* Prideandaccomplishment:Ihavedoneit!Ihavedoneit!Ihavedoneit!
* Uncertainty:Wasitworththeeffort?Willitbewell/badlyreceived?
* Insecurity:DidIdouble-checkeverything?Doesithaveanyembarrassingerrors?
Itisnowtimeforthebooktosinkorswimonitsownatthehandsofitsreaders.
A long time ago, my undergraduate adviser sent me to fetch some rainfall data from
theVenezuelanMinistryoftheEnvironment.Ireluctantlywent,gotlostinsidetheugly
building, failed to gather the data, but stumbled by chance into a nearly empty and
shabby Ministry bookstore. There I found a gem: the original 1975 Spanish edition of
the book Areografía: estrategias geográficas de las especies by Eduardo Rapoport. He was a
clever and original Argentinian ecologist who anticipated what later became known as
macroecology. The Pergamon Press translation (Areography: The Geographic Strategies of
Species) missed the preface of the Spanish original, easily the best preface of a scientific
bookIhaveeverread.IreadRapoport’sprefaceatthebookstore,andrightawayIbought
the book using all the money I had, including the return bus fare. I walked the 4.5 km
home,readingthebookbetweentrafficlights.Recognizingtheabsenceofrulesforwhat
the preface of a scientific book should contain, Rapoport aimed to bring a humanized
depictionofhisCV,sothat“sciencebookswouldleavehomeandbetakentothedentist
waiting room,” and you knew what to say if you ever meet the author. Following the
masterEduardoRapoport,hereismyattempt.
Things that I love
* The dazzling imaginations of Gabriel García Márquez, Julio Cortázar, and Alejo Car-
pentier,thedignityofPrimoLevi,thewisdomofUmbertoEco,thehumanityofItalo
Calvino,TheMagusbyJohnFowles.
* ThemusicandshiningsmileofLouisArmstrong,thesaxophoneofJohnColtrane(his
mission:“amasterpiecebymidnight”),andArtTatumplayingthepiano;theBeatles,
Eric Clapton, Sting, and Mark Knopfler; the blues of Taj Mahal, Keb’Mo, and Buddy
viii PREFACE
Guy; the stirring voices of Annie Lennox, Ute Lemper, and Madeleine Peyroux; the
lyricsofLeonardCohenandBobDylan.
* Twoscientificheroes:John(JBS)HaldaneandRichardFeynman.
* AlltheMontyPythonfilmsandtheoriginalBBCseries.
* AllPicasso,exceptthepinkperiod;GustavKlimtandVincentvanGogh.
* Let’sshareafullUruguayanbarbecue,includingmollejas(thymus),kidneys,andsweet
blood sausages. It would be glorious to enjoy some French goat cheese, a fresh green
saladwithendivesandcherrytomatoes,redwineofcourse,andamangoorpassionfruit
moussetobringmysoulclosertoearthlyparadise.
* And,aboveall,let’stalk,exchangingstories,books,andanecdotes.Thefoldersofmy
memory hold countless megabytes of historical, literary, and scientific information,
someofwhichmayeveninterestorentertainyouforawhile.AndIcanswiftlychange
myopiniononanyissueunderthesunasmanytimesasyoucanmanagetoconvince
mewithgoodarguments,sensibleevidence,andamodicumofstraightreasoning.
Things I hate
* Socialinjusticeinanyshapeorform.
* Thestupidityofthemilitaryandallitscheerleaders.
* Social,racial,andsexualdiscriminationunderanydisguiseorshade.
* Alltotalitarianideologiesandformsofthought.
* Thestiffness,conservatism,intolerance,andbackwardnessofthetraditionalCatholic
Churchandofmanyrecentlycreatedprotestantchurches.
* Pineappleonpizza:ahorrendousmixthatspoilstwogreatthings.
My story
My own biography is pretty ordinary. I will recall just a few events that might perhaps
inspireotherstobelieveinthemselves.IwasborninUruguay,asmallcountrythatlies
sandwichedbetweenArgentinaandBrazilatthebottomleftoftheworldmap.Afterstart-
ing public primary school there, I followed my father to Venezuela. I started university
wishingtobecomeanelectricalengineer,butfinallymanagedtograduateinbiologyat
thetardyageof26.
I desperately wanted to study more and become a scientist. With my then partner,
we managed to get admitted to the State University of New York at Stony Brook (now
StonyBrookUniversity)bysheerluck.InSeptember1992,wegatheredallourmoneyand
belongings,gotsomefamilyloans,andtraveledtoNewYork.Welandedthereperfectly
unawareofeverything,includinghowtogettotheuniversityfromtheairport.Wehad
PREFACE ix
expectedtopaythefirstyearofuniversityfees,bettingthatourgoodbackgroundwould
allow us to obtain good grades that might lead to some financial support. But it turned
outthatwedidnothavetopayanyuniversityfeesatall!
Andevenbetter,onedaybeforethestartofmyfirstsemester,anothergraduatestudent
chosetotakecareofherillgrandmotheranddeclinedherteachingassistantposition.I
was offered it, and of course took it: $750 a month minus taxes amounted to touching
heaven. The next day I went to teach some very basic biology to 25 puzzled American
students.DuringmyfourthdayinanEnglish-speakingcountry,Ibarelyunderstood40%
of what the students said. But I had an inspired idea that saved me. I shamelessly told
them of a hearing disability that required them to speak slowly and very loudly for me
tounderstandthem.Andtheydidittosuchanextentthatmystrangedisabilitymirac-
ulouslydisappearedafterafewweeks.WequicklyboughtaTVtohelptrainmywooden
ears. At first, the only program that I could understand was the (British) Prime Minis-
ter’sQuestionsthatwasbroadcastonCSPANverylateatnightjustforthe(dis)pleasure
ofinsomniacs.Thisverytheatrical,ceremonial,andmostlypointlessweeklyexerciseof
British politics was my door to understanding spoken English, and the starting of an
anglophiliathatonlyBrexitrecentlyanddefinitelymanagedtocure.
AtStonyBrook,ImetLevGinzburgbychancewhileeatingsandwichesattheDepart-
ment of Ecology and Evolution. This very intelligent and witty Russian mathematician
becamemyPhDsupervisor.Atfirst,itwasnearlyimpossibletounderstandwhatthisman
wastalkingsoquicklyabout.Iusedtosharea6m2officeinfrontofhis.Лeвoftencalled
meintohisofficeusingmundaneexcusestospendmanyhourstalkingandteachingme
onaone-to-onebasisasifIwasamedievalapprentice.Theseinteractionsovertheyears
shapedmeintoascientist,andaffectedmybrainmorethananythingsincegastrulation.
Thewiderangeoftopicsoftheseconversationsincludedmathematics,ecology,classical
physics,dynamicalsystems,riskanalysis,philosophyofscience,thelatestbookswewere
reading, and who knows what else ... I still vividly recall two entire Friday afternoons
that Лeв devoted to teaching me the puzzling basics of quantum mechanics (including
the Schrödinger wave equation) using a small green blackboard and white chalk. It was
anindescribablepleasuretohavereceivedsuchagiftofhumanknowledgefromyou,мoй
дopoгoйдpугинacтaвник.
Igraduatedin1998,andmyItalianpassport(lifelessonfortheyoung:youcannever
havetoomanypassports;acquireasmanyaspossiblesincesomemayopenunexpected
doors)gotmeanEUfellowshipforapostdocwithJohnLawtonatImperialCollege,UK.
IlatermovedtoFrancewhereIlivedandworkedfornineyears.Othermovesfollowing
anon-traditionalandhardlystraightpathtookmebacktoUruguay,whereIlivenow.
I will not bother the reader with further details of my academic past. There is hardly
anymeritinvolvedinit.Likeyou,Ihave23pairsofchromosomesineverycell,bloodthe
samecolorasyours,andagenomethatdiffersfromyoursandfromMandela’s,Einstein’s,
Himmler’s,andStalin’sbyaboutsixmillionDNAbases(~0.06%,anirrelevantdifference
sinceonlyabout2%ofourDNAistranslatedintoproteins).Therefore,restassuredthat
there is nothing special, unique, or even good about me. You can easily do better than
meifyouwish.
Just trust me on this one. Most people who succeed in life are those that seriously
applytheirheartandmindandenergylongenoughtopursuetheirdreamswithstubborn
determination.Iamconvincedthatlife(ortheuniverse,orthegods)rewardspersistence
andsingle-mindednessoverapparentleapsofinspiredgenius.However,forthatyoufirst
need to hold dreams and ambitions for yourself. Nobody can teach you to dream and
