R语言vegan包使用教程(19)

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。

4CONSTRAINEDORDINATION4.1Modelspeci cation

ancestor.Inveganversion2.0-6thefollowingclassfunctionsarede nedforthesemethods:

cca:add1,alias,anova,as.mlm,bstick,calibrate,coef,deviance,

drop1,eigenvals,extractAIC,fitted,goodness,model.frame,model.matrix,nobs,permutest,plot,points,predict,print,residuals,RsquareAdj,scores,screeplot,simulate,summary,text,tolerance,weights rda:as.mlm,biplot,coef,deviance,fitted,goodness,predict,RsquareAdj,scores,simulate,weights capscale:fitted,print,simulate.

Manyofthesemethodsareinternalfunctionsthatusersrarelyneed.

4.1Modelspeci cation

Therecommendedwayofde ningaconstrainedmodelistousemodelformula.Formulahasaspecialcharacter～,andonitsleft-handsidegivesthenameofthecommunitydata,andright-handgivestheequationforconstraints.Inaddition,youshouldgivethenameofthedatasetwhereto ndtheconstraints.This tsaccaforvarespecconstrainedbysoilAl,KandP:

>a<-cca(varespec~Al+P+K,varechem)>a

Call:cca(formula=varespec~Al+P+K,data=varechem)

InertiaProportionRank

Total2.0831.000Constrained0.6440.3093Unconstrained1.4390.69120

InertiaismeansquaredcontingencycoefficientEigenvaluesforconstrainedaxes:CCA1CCA2CCA30.3620.1700.113

Eigenvaluesforunconstrainedaxes:

CA1CA2CA3CA4CA5CA6CA7CA80.35000.22010.18510.15510.13510.10030.07730.0537(Showedonly8ofall20unconstrainedeigenvalues)

Theoutputissimilarasinunconstrainedordination.Nowthetotalinertiaisdecomposedintoconstrainedandunconstrainedcomponents.Therewerethreeconstraints,andtherankofconstrainedcomponentisthree.Therankofunconstrainedcomponentis20,whenitusedtobe23inthepreviousanalysis.Therankisthesameasthenumberofaxes:youhave3constrainedaxesand20unconstrainedaxes.Insomecases,theranksmaybelowerthanthenumberofconstraints:someoftheconstraintsaredependentoneachother,andtheyarealiasedintheanalysis,andaninformativemessageisprintedwiththeresult.

Itisverycommontocalculatetheproportionofconstrainedinertiafromthetotalinertia.However,totalinertiadoesnothaveaclearmean-ingincca,andthemeaningofthisproportionisjustasobscure.Inrda

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