R语言vegan包使用教程(4)

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。

2.1Non-metricMultidimensionalscaling2ORDINATION:BASICMETHOD

4

5

.014

7

2

.016

13

6

18

22

15

4

2

20

m0

25

i.D023

11

3

24

19

2

12

2

.0 27

28

109

4.0 21

0.6 0.4 0.2

0.00.20.4

Dim1

5

Cla.phy.0Cet.islDic.pol

Cla.ste24

2

11

Cla.chl

Pin.syl12Bar.lyc

Cla.cer

10Poh.nut

Pti.cil

21

9

Cla.bot

Dic.sp

Emp.nig

Vac.vit0

.04Cla.ran19Pol.pilCet.eri6Cla.criCla.unc23Cla.graPel.aphCet.niv

Cal.vul13Cla.corCla.def20Ple.sch28Bet.pub2

S318Cla.fimCla.sp15

Vac.myrLed.pal16DCla.arbCla.coc22M7Pol.jun27

N14

Hyl.spl5Ste.sp

Dip.mon

Dic.fusDes.fle5

Vac.uli

.25

0 Cla.ama

Ich.eri

Nep.arc

0.50.00.51.0

NMDS1

ordinationwithmorenonlinearrelationshipwouldappearworsewiththiscriterion.

Functionsscoresandordiplotinvegancanbeusedtohandletheresultsofnmds:

>ordiplot(vare.mds0,type="t")

Onlysitescoreswereshown,becausedissimilaritiesdidnothaveinfor-mationaboutspecies.

Theiterativesearchisverydi cultinnmds,becauseofnonlinearre-lationshipbetweenordinationandoriginaldissimilarities.Theiterationeasilygetstrappedintolocaloptimuminsteadof ndingtheglobalop-timum.Thereforeitisrecommendedtouseseveralrandomstarts,andselectamongsimilarsolutionswithsmalleststresses.Thismaybete-dious,butveganhasfunctionmetaMDSwhichdoesthis,andmanymorethings.Thetracingoutputislong,andwesuppressitwithtrace=0,butnormallywewanttoseethatsomethinghappens,sincetheanalysiscantakealongtime:

>vare.mds<-metaMDS(varespec,trace=FALSE)>vare.mds

Call:

metaMDS(comm=varespec,trace=FALSE)

globalMultidimensionalScalingusingmonoMDSData:wisconsin(sqrt(varespec))Distance:bray

Dimensions:2Stress:0.1826

Stresstype1,weakties

Twoconvergentsolutionsfoundafter20tries

Scaling:centring,PCrotation,halfchangescaling

Species:expandedscoresbasedon‘wisconsin(sqrt(varespec))’>plot(vare.mds,type="t")

Wedidnotcalculatedissimilaritiesinaseparatestep,butwegavethe

originaldatamatrixasinput.Theresultismorecomplicatedthanpre-viously,andhasquiteafewcomponentsinadditiontothoseinisoMDSre-sults:nobj,nfix,ndim,ndis,ngrp,diss,iidx,jidx,xinit,is-tart,isform,ities,iregn,iscal,maxits,sratmx,strmin,sf-grmn,dist,dhat,points,stress,grstress,iters,icause,call,model,distmethod,distcall,data,distance,converged,tries,engine,species.Thefunctionwrapsrecommendedproceduresintoonecommand.Sowhathappenedhere?

1.Therangeofdatavalueswassolargethatthedataweresquareroottransformed,andthensubmittedtoWisconsindoublestandardiza-tion,orspeciesdividedbytheirmaxima,andstandsstandardizedtoequaltotals.Thesetwostandardizationsoftenimprovethequal-ityofordinations,butweforgottothinkaboutthemintheinitialanalysis.

4