R语言vegan包使用教程(10)

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。

2.4Eigenvectormethods9

1

11Cla.phy

10Cla.coc

Poh.nut

Cla.stePin.sylCla.chl

Cla.spCet.isl

Cla.gra1223Vac.vit5

Cla.ran14Pol.pilCet.eriCla.cri

Cla.fimCla.arbSte.sp618Dic.pol21

2

Ich.eriCla.ama13Cla.uncDip.monCla.corCla.defPel.aph24Bet.pubCla.bot

Bar.lycPti.cilC4

7Cal.vulCet.niv1516Vac.uli20Dic.sp

Emp.nig

Led.palVac.myr

1

25

Des.fle

Ple.sch

Hyl.spl28

27

2

10123

PC1

5

.19Bar.lyc2128

10

Bet.pub

0.Pti.cil

Vac.myrHyl.spl

12

27Cla.ste

Cla.phyCla.chl

Cet.islDes.fle

5

Cla.bot

.0Cla.sp

Pin.sylPoh.nutPle.sch3

Emp.nigVac.vitNep.arc

Dic.sp24250

.Pol.jun

0Cla.cer

11

Cla.fim2

Cla.graCla.corPel.aph23A1522C5

Cla.coc

Cla.criCla.def20Cet.eri

Dic.fus

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Dip.monCla.ran

Cla.unc16

Pol.pil0

.Cla.amaCla.arb181Vac.uli

Cal.vul 14

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Ste.sp

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7

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1012

CA1

2ORDINATION:BASICMETHOD

Call:rda(X=varespec,scale=TRUE)InertiaRank

Total44Unconstrained4423Inertiaiscorrelations

Eigenvaluesforunconstrainedaxes:

PC1PC2PC3PC4PC5PC6PC7PC88.904.764.263.732.962.882.732.18

(Showedonly8ofall23unconstrainedeigenvalues)>plot(vare.pca,scaling=3)

Nowinertiaiscorrelation,andthecorrelationofavariablewithitselfisone.Thusthetotalinertiaisequaltothenumberofvariables(species).Therankorthetotalnumberofeigenvectorsisthesameaspreviously.Themaximumpossiblerankisde nedbythedimensionsofthedata:itisonelessthansmallerofnumberofspeciesornumberofsites:

>dim(varespec)[1]2444

Iftherearespeciesorsitessimilartoeachother,rankwillbereducedevenfromthis.

Thepercentageexplainedbythe rstaxisdecreasedfromthepreviouspcaabundant.Thisspeciesisnatural,withsincehighpreviouslyvariances,webutneedednowwetohave“explain”toexplainonlytheallspeciesequally.Weshouldnotlookblindlyatpercentages,buttheresultweget.

Correspondenceanalysisisverysimilartopca:

>vare.ca<-cca(varespec)>vare.ca

Call:cca(X=varespec)

InertiaRank

Total2.08Unconstrained2.0823

Inertiaismeansquaredcontingencycoefficient

Eigenvaluesforunconstrainedaxes:

CA1CA2CA3CA4CA5CA6CA7CA80.52490.35680.23440.19550.17760.12160.11550.0889(Showedonly8ofall23unconstrainedeigenvalues)>plot(vare.ca)

Nowtheinertiaiscalledmeansquaredcontingencycoe cient.Corre-spondenceanalysisisbasedonChi-squareddistance,andtheinertiais

theChi-squaredstatisticofadatamatrixstandardizedtounittotal:

>chisq.test(varespec/sum(varespec))

Pearson'sChi-squaredtest

data:varespec/sum(varespec)

X-squared=2.083,df=989,p-value=1

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