R语言vegan包使用教程(18)

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。

4CONSTRAINEDORDINATION

ordispidercommand:

32

2

AC1

1

2 101

2

CA1

>plot(dune.ca,display="sites",type="p")

>with(dune.env,ordiellipse(dune.ca,Management,kind="se",conf=0.95))>with(dune.env,ordispider(dune.ca,Management,col="blue",label=TRUE))>

with(dune.env,ordihull(dune.ca,Management,col="blue",lty=2))

Correspondenceanalysisisaweightedordinationmethod,andvegan

functionsenvfitandordisurfwilldoweighted tting,unlesstheuserspeci esequalweights.

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Constrainedordination

Inunconstrainedordinationwe rst ndthemajorcompositionalvaria-tion,andthenrelatethisvariationtoobservedenvironmentalvariation.

Inconstrainedordinationwedonotwanttodisplayallorevenmostofthecompositionalvariation,butonlythevariationthatcanbeexplainedbytheusedenvironmentalvariables,orconstraints.Constrainedordina-tionisoftenknownas“canonical”ordination,butthisnameismisleading:thereisnothingparticularlycanonicalinthesemethods(seeyourfavoriteDictionaryfortheterm).Thenamewastakenintouse,becausethereisonespecialstatisticalmethod,canonicalcorrelations,buttheseindeedarecanonical:theyarecorrelationsbetweentwomatricesregardedtobesymmetricallydependentoneachother.Theconstrainedordinationisnon-symmetric:wehave“independent”variablesorconstraintsandwehave“dependent”variablesorthecommunity.Constrainedordinationratherisrelatedtomultivariatelinearmodels.

Theveganpackagehasthreeconstrainedordinationmethodswhichallareconstrainedversionsofbasicordinationmethods:

Constrainedanalysisofproximities(cap)infunctioncapscaleisrelatedtometricscaling(cmdscale).Itcanhandleanydissimilaritymeasuresandperformsalinearmapping.

Redundancyanalysis(rda)infunctionrdaisrelatedtoprincipalcomponentsanalysis.ItisbasedonEuclideandistancesandper-formslinearmapping.

Constrainedcorrespondenceanalysis(cca)infunctionccaisre-latedtocorrespondenceanalysis.ItisbasedonChi-squareddis-tancesandperformsweightedlinearmapping.

Wehavealreadyusedfunctionsrdaandccaforunconstrainedordination:theywillperformthebasicunconstrainedmethodasaspecialcaseifconstraintsarenotused.

Allthesethreeveganfunctionsareverysimilar.Thefollowingexam-plesmainlyusecca,butothermethodscanbeusedsimilarly.Actually,theresultsaresimilarlystructured,andtheyinheritpropertiesfromeachother.Forhistoricalreasons,ccaisthebasicmethod,andrdainheritspropertiesfromit.Functioncapscaleinheritsdirectlyfromrda,andthroughthisfromcca.Manyfunctions,arecommonwithallthesemeth-ods,andtherearespeci cfunctionsonlyifthemethoddeviatesfromits

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