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Robert Fletcher Marie-Josée Fortin Spatial Ecology and Conservation Modeling Applications with R Spatial Ecology and Conservation Modeling (cid:129) Robert Fletcher Marie-Josée Fortin Spatial Ecology and Conservation Modeling Applications with R RobertFletcher Marie-JoséeFortin DepartmentofWildlifeEcology DepartmentofEcologyandEvolutionary andConservation Biology UniversityofFlorida UniversityofToronto Gainesville,FL,USA Toronto,ON,Canada ISBN978-3-030-01988-4 ISBN978-3-030-01989-1 (eBook) https://doi.org/10.1007/978-3-030-01989-1 LibraryofCongressControlNumber:2018965604 ©SpringerNatureSwitzerlandAG2018 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. 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ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland To Christine, Hayden, and Ava: You inspire me everyday —Robert Fletcher To Ian —Marie-Josée Fortin Preface Allquestionsinecologyandproblemsinconservationplayoutinspace.Thissimple facthasgeneratedalong-standinginterestfromscientistsandpractitioners,anditis nowwellknownthatexplicitlyaccountingforspaceinecology,orspatialecology, is necessary for accurately answering ecological questions and providing useful conservationsolutions. Onlyinthepastfewdecades,however,hasspatialecologyreallymatured.With advances in data collection across both broad and fine spatial scales, data are now widelyavailablethatarespatiallyexplicit.Atthesametime,thegrowthinwaysto analyze,model,andinterpretspatialdatahasalsoincreasedsubstantiallyinthepast two decades. The synergism of data availability and new models and methods for interpreting spatial data has led to rapid advancements in our understanding of spatialecologyandthewayinwhichspatialconceptsareappliedtoconservation. Why Do We Need a New Book on Spatial Ecology and Conservation? Severalbookshavebeenpublishedovertheyearsthatarerelevanttospatialecology and conservation (see Chap. 1). Some of these books have focused on spatial ecology explicitly while others have been on related topics, such as landscape ecology and metapopulation ecology. In addition, there have been several books publishedonspatialanalysis,andsomefocusspecificallyonecologicaldata.There have also been books that emphasize spatial theory in ecology. These books have beenveryhelpfultotheecologicalcommunity. Despite these efforts, a book on spatial ecology that provides a general,applied overview and allows readers to go “under-the-hood” to interpret concepts and models with real data has remained absent. Our book attempts to fill this gap by providing an introduction to relevant concepts and modeling techniques used by vii viii Preface applied ecologists and conservation biologists to address ecological and conserva- tionproblems.Weprovidethisintroductionbyusingempiricalexamplestoillustrate notjustwhatspatialecologyis,buthowitisimplemented.Ourbookcoversseveral topics, and in doing so, it illustrates to readers many of the commonalities among topicstoaddresstheproblemofspace. Who Should Read this Book? Thisbookisintendedtoprovideagentleintroductiontotheconceptsandmodeling involvedinthefieldofspatialecologyandconservation.Thetargetaudienceofthe book includes students and professionals. Scientists and conservation practitioners whoseektounderstandecologyandconservationshouldbenefitfromtheoverviews provided. This is not a book written for experts in spatial ecology and modeling. There are several advanced books written for experts, and our intent is not to re-create those books. Rather, students and professionals who would like to find outwhatspatialecologyisaboutandhowitisappliedtoconservationproblemsare thetargetaudience. Readers should have a general familiarity with statistics and models. Such knowledgeisessentialforfurtherextendingquantitativetechniquestotheproblem ofspace.Wedonotexpectallreaderstobeespeciallyquantitative.Throughoutthis book, we provide examples of spatial concepts, models, and analyses using the programR.ReadersdonotneedtobeproficientinR,however,tousethisbook.We provide an Appendix that covers some foundational topics for the use of R that should provide readers enough information on R to interpret the examples in thisbook. The material from this book has been developed from graduate courses that the authors teach. We have used this material both for lecture development and lab development, where students work through the examples provided in the book. We expectthatthisbookcouldprovideausefulcomplementtocoursesonspatialecology, landscape ecology, species distributions, spatial analysis for non-statisticians, and appliedconservation. Organization of the Book The goal of this book is to provide an overview of several (but not all) issues in spatialecologyandconservation.Ourbookwaswrittenasanintroductiontothese topicswithanemphasisonlearning-by-doing,whereweillustratethesetopicswith realdataandtheapplicationofspatialmodelingtothesetopics.Foreachapplication, key R code is provided as an illustration of the aspects needed to understand the essenceofeachtopicanditspotentialrelevancetoconservationapplications. Preface ix The first part of the book (Quantifying Spatial Pattern in Ecological Data) focuses primarily on spatial pattern analysis and modeling of relevance to ecology and conservation. Issues such as the problem of scale, spatial dependence, land- coverpatternandchangequantification,aswellasspatialpredictionareintroduced andillustratedusingcasestudies. The second part of the book (Ecological Responses to Spatial Pattern and Conservation) focuses on spatial ecological disciplines and topics, ranging from species distributions and resource selection, movement and connectivity, to metapopulation and metacommunity dynamics. Again, an overview of these ecological processes and resulting spatial patterns are presented and case studies are usedtodepicthowtoanalyzethemspatially. For each chapter, we first provide a concise overview of the relevant terms and concepts. We focus on practical issues and concepts, only briefly providing the relevant spatial ecological theory and concepts needed to understand the spatial analysespresented.Keytermsthatarerequiredforunderstandingthemajorconcepts are highlighted in italics and defined in tables and text. The latter portion of each chapterdepictstheseconceptsandattemptstodemystifythemviaworkedexamples usingrealdataandRcode.Weendeachchapterwitha“NextStepsandAdvanced Issues”sectionthatdirectsreaders tofurtherapproachesandissues ofrelevance to eachtopic. Throughout the book, R code is provided as well as the interpretation of modeloutputs.WeuseRforseveralreasons:(1)Risanopen-sourceenvironment that works on Windows, Mac OS X, and Linux; (2) the R environment is flexible enoughtoofferstatistical,visualization,andsimpleprogramminglanguagefeatures; and (3) a series of R packageshave been developed by scientists, including ecologists, offering moreadvanced analyticalmethods toanalyzespatialecologicaldata thanothersoftware.ThemajordrawbackofRisthatthereisasteeplearningcurveto master data manipulation within the R environment. This is why our book aims to knockdown thislearning roadblockbyproviding notonlytherelevant Rcodebut alsoitsinterpretation.ByprovidingkeyfoundationsinR,wehopethatstudentsand researcherswillbeabletoadapttheRcodetoanalyzetheirowndata.Ingeneral,we take a practical approach to programming in R: in many cases, the code provided couldbemademoreefficientandelegant,butweusecodetoprovidewhatwehope arethemostintuitivewaystogofromanideaormodeltotheactualcodingofit.We provideanAppendixthatprovidessomenecessarybackgroundonusingRforthose readers that are not familiar with this software. All data and R code can be downloaded at the first author’s website (http://www.fletcherlab.com under “Prod- ucts”)andattheUniversityofFlorida’sInstitutionalRepository(http://ufdc.ufl.edu/ ufirg). Thisbookcouldbeusedinavarietyofways.Forreadersinterestedprimarilyin concepts,thefirstportionofeachchapterwillprovideaconciseoverviewonterms andconceptsneededforunderstandingspatialecologyandconservation.Forthose readerswhowanttousespatialecologyintheirownwork,theexampleswillprovide insight to the applications of terms, concepts, and modeling approaches. For those x Preface unfamiliarwithR,readersshouldfirstgothroughmaterialsintheAppendixpriorto workingthroughthemaintext. We hope that this book will be a useful guide for learning spatial ecology and solvingappliedproblemsfacingbiodiversitythroughouttheworld. Gainesville,FL,USA RobertFletcher Toronto,ON,Canada Marie-JoséeFortin August2018 Acknowledgments Ourresearchhasbeensupportedbyseveralagenciesovertheyears,andmuchofthis research has been directly or indirectly incorporated into the development of this book. Fletcher thanks the National Science Foundation (DEB-1343144, DEB-1655555), the US Department of Agriculture (USDA-NIFA Initiative Grant No. 2012-67009-20090), the US Army Corps of Engineers, the Florida Fish and WildlifeConservationCommission,andtheUniversityofFloridaforsupport.Most ofthedatausedinthebookcomefromthisresearch.WealsothankRichardHutto fortheuseofthelandbirddata(Chaps.6,7,and11),DaveOrnatoandtheFlorida Fish and Wildlife Conservation Commission for collecting data on panthers (Chap. 8), and Raymond Tremblay and Elvia Melendez-Ackerman for data on orchids(Chap.10). Fletcher is grateful for all of the support and feedback he received from his lab and students in his graduate courses over the years. Many students and colleagues encouragedtheproductionofthisbook,anditwouldnothavematerializedwithout theirencouragement. Fletcheralsothanks many collaborators andmentors, includ- ingJimAustin,MatthewBetts,BillClark,BrentDanielson,NickHaddad,Richard Hutto, Rolf Koford, Tom Martin, Bob McCleery, John Orrock, and Katie Sieving. Fletcher also thanks his family for encouraging him to pursue the development of thisbookandhisfatherforhissupportovertheyears. Fortin thanks NSERC Discovery Grant Program and a Canada Research Chair inSpatialEcologyforfinancialsupportandtheDepartmentofEcologyandEvolu- tionaryBiologyoftheUniversityofTorontofortheirsupport.Fortinalsothanksher sonforhissupport. We thank several people for reviewing chapters of this book. Special thanks to Dan Thornton, Kirk Moloney, Kevin McGarigal, Matthew Betts, Chris Rota, Brian Reichert, Ben Baiser, Chevonne Reynolds, Rob Ahrens, Divya Vasudev, EllenRobertson,JessicaHightower,BradUdell,JulianResasco,andNoahBurrell. Theirattentiontodetailandusefulsuggestionsimprovedeachchapterconsiderably. xi