R语言vegan包使用教程(16)

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。

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3ENVIRONMENTALINTERPRETATION

alinearrelationshipbetweenordinationandenvironment:directionandstrengthareallyouneedtoknow.Thismaynotalwaysbeappropriate.

Functionordisurf tssurfacesofenvironmentalvariablestoordi-nations.Itusesgeneralizedadditivemodelsinfunctiongamofpackagemgcv.Functiongamusesthinplatesplinesintwodimensions,andauto-maticallyselectsthedegreeofsmoothingbygeneralizedcross-validation.Iftheresponsereallyislinearandvectorsareappropriate,the ttedsur-faceisaplanewhosegradientisparalleltothearrow,andthe ttedcontoursareequallyspacedparallellinesperpendiculartothearrow.

InthefollowingexampleIintroducetwonewRfeatures:

Functionenvfitcanbecalledwithformulainterface.Formulahasaspecialcharactertilde(～),andtheleft-handsidegivestheordinationresults,andtheright-handsideliststheenvironmentalvariables.Inaddition,wemustde nethenameofthedatacon-tainingthe ttedvariables.

ThevariablesindataframesarenotvisibletoRsessionunlessthedataframeisattachedtothesession.Wemaynotwanttomakeallvariablesvisibletothesession,becausetheremaybesynonymousnames,andwemayusewrongvariableswiththesamenameinsomeanalyses.Wecanusefunctionwithwhichmakesthegivendataframevisibleonlytothefollowingcommand.

Nowwearereadyfortheexample.Wemakevector ttingforselectedvariablesandadd ttedsurfacesinthesameplot.

>ef<-envfit(vare.mds~Al+Ca,varechem)>plot(vare.mds,display="sites")>plot(ef)

>tmp<-with(varechem,ordisurf(vare.mds,Al,add=TRUE))

>

with(varechem,ordisurf(vare.mds,Ca,add=TRUE,col="green4"))

Functionordisurfreturnstheresultof ttedgam.Ifwesavethatresult,likewedidinthe rst twithAl,wecanuseitforfurtheranalyses,suchasstatisticaltestingandpredictionofnewvalues.Forinstance,fitted(ef)willgivetheactual ttedvaluesforsites.

3.3Factors

Classcentroidsareanaturalchoiceforfactorvariables,andR2canbeusedasagoodness-of- tstatistic.The“signi cance”canbetestedwithpermutationsjustlikeinvector tting.Variablescanbede nedasfactorsinR,andtheywillbetreatedaccordinglywithoutanyspecialtricks.

Asanexample,weshallinspectdunemeadowdatawhichhasseveralclassvariables.Functionenvfitalsoworkswithfactors:

>data(dune)

>data(dune.env)

>dune.ca<-cca(dune)

>ef<-envfit(dune.ca,dune.env,permutations=999)>

ef

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