R语言vegan包使用教程(6)

R语言中的外在软件包“Vegan”是专门用于群落生态学分析的工具。Vegan能够提供所有基本的排序方法,同时具有生成精美排序图的功能,版本更新很快。我们认为Vegan包完全可以取代CANOCO,成为今后排序分析的首选统计工具。

2.2Communitydissimilarities2ORDINATION:BASICMETHOD

forA=BforA=B

dAB=0dAB>0dAB=dBAdAB≤dAx+dxB

asanexample.Anothercomplicationisnaming.Functionvegdistusescolloquialnameswhichmaynotbestrictlycorrect.ThedefaultindexinveganiscalledBray(orBray–Curtis),butitprobablyshouldbecalledSteinhausindex.Ontheotherhand,itscorrectnamewassupposedtobeCzekanowskiindexsomeyearsago(butnowthisisregardedasanotherindex),anditisalsoknownasSørensenindex(butusuallymisspelt).Strictlyspeaking,Jaccardindexisbinary,andthequantitativevariantinveganshouldbecalledRuˇziˇckaindex.However,vegan ndseitherquantitativeorbinaryvariantofanyindexunderthesamename.

Thesethreebasicindicesareregardedasgoodindetectinggradi-ents.Inaddition,vegdistfunctionhasindicesthatshouldsatisfyothercriteria.Morisita,Horn–Morisita,Raup–Cric,BinomialandMountfordindicesshouldbeabletocomparesamplingunitsofdi erentsizes.Eu-clidean,CanberraandGowerindicesshouldhavebettertheoreticalprop-erties.

FunctionmetaMDSusedBray-Curtisdissimilarityasdefault,whichusuallyisagoodchoice.Jaccard(Ruˇziˇcka)indexhasidenticalrankorder,buthasbettermetricproperties,andprobablyshouldbepreferred.Functionrankindexinvegancanbeusedtostudywhichoftheindicesbestseparatescommunitiesalongknowngradientsusingrankcorrelationasdefault.Thefollowingexampleusesallenvironmentalvariablesindatasetvarechem,butstandardizesthesetounitvariance:

>data(varechem)

>rankindex(scale(varechem),varespec,c("euc","man","bray","jac","kul"))eucmanbrayjackul0.23960.27350.28380.28380.2840

arenon-linearlyrelated,buttheyhaveidenticalrankorders,andtheirrankcorrelationsareidentical.Ingeneral,thethreerecommendedindicesarefairlyequal.

Itookaverypracticalapproachonindicesemphasizingtheirabilitytorecoverunderlyingenvironmentalgradients.Manytextbooksempha-sizemetricpropertiesofindices.Theseareimportantinsomemethods,butnotinnmdswhichonlyusesrankorderinformation.Themetricpropertiessimplysaythat

1.iftwositesareidentical,theirdistanceiszero,

2.iftwositesaredi erent,theirdistanceislargerthanzero,3.distancesaresymmetric,and

4.theshortestdistancebetweentwositesisaline,andyoucannotimprovebygoingthroughothersites.Theseallsoundverynaturalconditions,buttheyarenotful lledbyalldissimilarities.Actually,onlyEuclideandistances–andprobablyJaccardindex–ful llallconditionsamongthedissimilaritiesdiscussedhere,andaremetrics.Manyotherdissimilaritiesful llthree rstconditionsandaresemimetrics.

Thereisaschoolthatsaysthatweshouldusemetricindices,andmostnaturally,Euclideandistances.Oneoftheirdrawbackswasthat

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