R语言vegan包使用教程(3)

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:BASICMETHOD

2

Ordination:basicmethod

2.1

Non-metricMultidimensionalscaling

Non-metricmultidimensionalscalingcanbeperformedusingisoMDSfunc-tionintheMASSpackage.Thisfunctionneedsdissimilaritiesasinput.Functionvegdistinvegancontainsdissimilaritieswhicharefoundgoodincommunityecology.ThedefaultisBray-Curtisdissimilarity,nowadaysoftenknownasSteinhausdissimilarity,orinFinlandasSørensenindex.Thebasicstepsare:

>library(vegan)>library(MASS)>data(varespec)

>vare.dis<-vegdist(varespec)>

vare.mds0<-isoMDS(vare.dis)

initialvalue18.026495iter5value10.095483finalvalue10.020469converged

Thedefaultisto ndtwodimensionsandusemetricscaling(cmdscale)asthestartingsolution.Thesolutionisiterative,ascanbeseenfromthetracinginformation(thiscanbesuppressedsettingtrace=F).

TheresultsofisoMDSisalist(itemspoints,stress)forthecon- gurationandthestress.StressSisastatisticofgoodnessof t,anditisafunctionofandnon-linearmonotonetransformationofobserved

dissimilaritiesθ(d)andordinationdistancesd

.nationNmdsspacemapsandobserveditcanhandlecommunitynonlineardissimilaritiesspeciesresponsesnonlinearlyofanyontoshape.ordi-WecaninspectthemappingusingfunctionShepardinMASSpackage,orasimplewrapperstressplotinvegan:

>stressplot(vare.mds0,vare.dis)

FunctionstressplotdrawsaShepardplotwhereordinationdistancesareplottedagainstcommunitydissimilarities,andthe tisshownasamonotonestepline.Inaddition,stressplotshowstwocorrelationlikestatisticsofgoodnessof t.ThecorrelationbasedonstressisR2=1 S2.The“ t-basedR2”isordinationdistancesd

thecorrelationbetweenthe ttedvaluesθ(d)and

,orbetweenthesteplineandthepoints.Thisshouldbelinearevenwhenthe tisstronglycurvedandisoftenknownasthe“linear t”.ThesetwocorrelationsarebothbasedontheresidualsintheShepardplot,buttheydi erintheirnullmodels.Inlinear t,thenullmodelisthatallordinationdistancesareequal,andthe tisa athorizontalline.Thissoundssensible,butyouneedN 1dimensionsforthenullmodelofNpoints,andthisnullmodelisgeometricallyimpossi-bleintheordinationspace.Thebasicstressusesthenullmodelwhereallobservationsareputinthesamepoint,whichisgeometricallypossible.Finallyawordofwarning:yousometimesseethatpeopleusecorrelationbetweencommunitydissimilaritiesandordinationdistances.Thisisdan-gerousandmisleadingsincenmdsisanonlinearmethod:animproved

3

S= i=j[θ(dij) d ij]2i=jd2

ij

Non metric fit, R2 = 0.99 q

.Linear fit, R2 = 0.943

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Observed Dissimilarity