R语言vegan包使用教程(5)

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。

2ORDINATION:BASICMETHOD2.FunctionusedBray–Curtisdissimilarities.

3.FunctionrunisoMDSwithseveralrandomstarts,andstoppedei-therafteracertainnumberoftries,orafter ndingtwosimilarcon gurationswithminimumstress.Inanycase,itreturnedthebestsolution.4.Functionrotatedthesolutionsothatthelargestvarianceofsitescoreswillbeonthe rstaxis.5.Functionscaledthesolutionsothatoneunitcorrespondstohalvingofcommunitysimilarityfromthereplicatesimilarity.6.Functionfoundspeciesscoresasweightedaveragesofsitescores,butexpandedthemsothatspeciesandsitescoreshaveequalvari-ances.Thisexpansioncanbeundoneusingshrink=TRUEindis-playcommands.ThehelppageformetaMDSwillgivemoredetails,andpointtoexplanationoffunctionsusedinthefunction.

2.2Communitydissimilarities

Non-metricmultidimensionalscalingisagoodordinationmethodbe-causeitcanuseecologicallymeaningfulwaysofmeasuringcommunitydissimilarities.Agooddissimilaritymeasurehasagoodrankorderrela-tiontodistancealongenvironmentalgradients.Becausenmdsonlyusesrankinformationandmapsranksnon-linearlyontoordinationspace,itcanhandlenon-linearspeciesresponsesofanyshapeande ectivelyandrobustly ndtheunderlyinggradients.

ThemostnaturaldissimilaritymeasureisEuclideandistancewhichisinherentlyusedbyeigenvectormethodsofordination.Itisthedistanceinspeciesspace.Speciesspacemeansthateachspeciesisanaxisorthogonaltoallotherspecies,andsitesarepointsinthismultidimensionalhyper-space.However,Euclideandistanceisbasedonsquareddi erencesandstronglydominatedbysinglelargedi erences.Mostecologicallymean-ingfuldissimilaritiesareofManhattantype,andusedi erencesinsteadofsquareddi erences.Anotherfeatureingooddissimilarityindicesisthattheyareproportional:iftwocommunitiessharenospecies,theyhaveamaximumdissimilarity=1.EuclideanandManhattandissimilaritieswillvaryaccordingtototalabundanceseventhoughtherearenosharedspecies.

PackageveganhasfunctionvegdistwithBray–Curtis,JaccardandKulczy´nskiindices.AlltheseareoftheManhattantypeanduseonly rstorderterms(sumsanddi erences),andallarerelativizedbysiteto-talandreachtheirmaximumvalue(1)whentherearenosharedspeciesbetweentwocomparedcommunities.Functionvegdistisadrop-inre-placementforstandardRfunctiondist,andeitherofthesefunctionscanbeusedinanalysesofdissimilarities.

Therearemanyconfusingaspectsindissimilarityindices.Oneisthatsameindicescanbewrittenwithverydi erentlookingequations:twoalternativeformulationsofManhattandissimilaritiesinthemarginserve

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2.2Communitydissimilarities

djk

=

N(xij xik)2

Euclidean

i=1djk= N|xij xik|Manhattan

i=1

A= Nxij

B=

Nxik

i=1i=1

J=

Nmin(xij,xik)

i=1

djk=A+B 2JManhattan

dA+B 2Jjk=

A+BBraydA+B 2Jjk=

A+B J

Jaccardd1 1 JJ

jk=2A+

B

Kulczy´nski