R语言vegan包使用教程(11)

时间：2025-07-13

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:BASICMETHOD2.5Detrendedcorrespondenceanalysis

YoushouldnotpayanyattentiontoP-valueswhicharecertainlymis-leading,butnoticethatthereportedX-squaredisequaltotheinertiaabove.

Correspondenceanalysisisaweightedaveragingmethod.Inthegraphabovespeciesscoreswereweightedaveragesofsitescores.Withdi erentscalingofresults,wecoulddisplaythesitescoresasweightedaveragesofspeciesscores:

>plot(vare.ca,scaling=1)

Wealreadysawanexampleofscaling=3orsymmetricscalinginpca.Theothertwointegersmeanthateitherspeciesareweightedaveragesofsites(2)orsitesareweightedaveragesofspecies(1).Whenwetakeweightedaverages,therangeofaveragesshrinksfromtheoriginalval-ues.Theshrinkagefactorisequaltotheeigenvalueofca,whichhasatheoreticalmaximumof1.

2.5Detrendedcorrespondenceanalysis

Correspondenceanalysisisamuchbetterandmorerobustmethodfor

communityordinationthanprincipalcomponentsanalysis.However,withlongecologicalgradientsitsu ersfromsomedrawbacksor“faults”whichwerecorrectedindetrendedcorrespondenceanalysis(dca):

Singlelonggradientsappearascurvesorarcsinordination(arce ect):thesolutionistodetrendthelateraxesbymakingtheirmeansequalalongsegmentsofpreviousaxes.

Sitesarepackedmorecloselyatgradientextremesthanatthecen-tre:thesolutionistorescaletheaxestoequalvariancesofspeciesscores.

Rarespeciesseemtohaveanundulyhighin uenceontheresults:thesolutionisstodownweightrarespecies.

AllthesethreeseparatetricksareincorporatedinfunctiondecoranawhichisafaithfulportofMarkHill’soriginalprogrammewiththesamename.Theusageissimple:

>vare.dca<-decorana(varespec)>vare.dca

Call:

decorana(veg=varespec)

Detrendedcorrespondenceanalysiswith26segments.Rescalingofaxeswith4iterations.DCA1DCA2DCA3DCA4

Eigenvalues0.5240.3250.20010.1918Decoranavalues0.5250.1570.09670.0608Axislengths2.8162.2051.54651.6486>plot(vare.dca,display="sites")

Bar.lyc2Bet.pub

Hyl.spl

Pti.cil