R语言vegan包使用教程(21)

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。

4CONSTRAINEDORDINATIONthereisawholelineofzeros,theobservationmustbelongtotheomittedlevel,orthe rst.Thebasicplotfunctiondisplaysclasscentroidsinsteadofvectorsforfactors.

Inadditiontotheseordinaryfactors,Ralsoknowsorderedfactors.VariableMoistureindune.envisde nedasanorderedfour-levelfactor.Inthiscasethecontrastslookdi erent:

Moisture.LMoisture.QMoisture.C

1-0.67080.5-0.22362-0.2236-0.50.670840.2236-0.5-0.67085

0.67080.50.2236

Rusespolynomialcontrasts:thelineartermLisequaltotreatingMoistureasacontinuousvariable,andthequadraticQandcubicCtermsshownonlinearfeatures.Therewerefourdistinctlevels,andthenumberofcontrastsisoneless,justlikewithordinarycontrasts.Theordinationcon guration,eigenvaluesorrankdonotchangeifthefactorisunorderedorordered,butthepresentationofthefactorintheresultsmaychange:

>a<-cca(dune~Moisture,dune.env)>plot(a)

Nowplotshowsboththecentroidsoffactorlevelsandthecontrasts.

Ifwecouldchangetheorderedfactortoacontinuousvector,onlythelineare ectarrowwouldbeimportant.Iftheresponsetothevariableisnonlinear,thequadratic(andcubic)arrowswouldbelongaswell.

Ihaveexplainedonlythesimplestusageoftheformulainterface.Theformulaisverypowerfulinmodelspeci cation:youcantransformyourcontrastswithintheformula,youcande neinteractions,youcanusepolynomialcontrastsetc.However,modelswithinteractionsorpolyno-mialsmaybedi culttointerpret.

4.2Permutationtests

Thesigni canceofalltermstogethercanbeassessedusingpermutationtests:thedatarepermutedrandomlyandthemodelisre tted.Whenconstrainedinertiainpermutationsisnearlyalwayslowerthanobservedconstrainedinertia,wesaythatconstraintsaresigni cant.

Theeasiestwayofrunningpermutationtestsistousethemockanovafunctioninvegan:

>anova(a)

Permutationtestforccaunderreducedmodel

Model:cca(formula=dune~Moisture,data=dune.env)

DfChisqFN.PermPr(>F)

Model30.632.251990.005**Residual161.49---Signif.codes:0‘***’0.001‘**’0.01‘*’0.05‘.’0.1‘’1

TheModelreferstotheconstrainedcomponent,andResidualtotheunconstrainedcomponentoftheordination,Chisqisthecorresponding

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4.2Permutationtests

12

3

Moisture4

9

1

213

Junbuf132

4

ACSagpro

AlogenCElyrep

810

Moisture2RumaceCirarvPoapraPoatriTrirepJunartMoisture.LBrarut

Agrsto0

LolperLeoautMoisture157AchmilBelperBrohorAirpraTPlalanripraViclatAntodoHypradSalrepMoisture5EmpnigPotpalElepalRanflaChealbCalcus611

161

10

18

Moisture.C1915Moisture.Q2

17

14

20 2 101

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CCA1