R语言vegan包使用教程(17)

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。

3ENVIRONMENTALINTERPRETATION***VECTORS

CA1CA2r2Pr(>r)

A10.99820.06060.310.043*---Signif.codes:0‘***’0.001‘**’0.01‘*’0.05‘.’0.1‘’1Pvaluesbasedon999permutations.***FACTORS:Centroids:CA1CA2Moisture1-0.75-0.14Moisture2-0.47-0.22Moisture40.18-0.73Moisture51.110.57ManagementBF-0.73-0.14ManagementHF-0.39-0.30ManagementNM0.651.44ManagementSF0.34-0.68UseHayfield-0.290.65UseHaypastu-0.07-0.56UsePasture0.520.05Manure00.651.44Manure1-0.46-0.17Manure2-0.59-0.36Manure30.52-0.32Manure4

-0.21

-0.88

Goodnessoffit:

r2Pr(>r)

Moisture0.410.005**Management0.440.001***Use0.180.079.Manure0.460.010**---Signif.codes:0‘***’0.001‘**’0.01‘*’0.05‘.’0.1‘’1Pvaluesbasedon999permutations.>plot(dune.ca,display="sites")>plot(ef)

Thenamesoffactorcentroidsareformedbycombiningthenameof

thefactorandthenameofthelevel.Nowtheaxesshowthecentroidsforthelevel,andtheR2valuesareforthewholefactor,justlikethesigni cancetest.Theplotlookscongested,andwemayusetricksof§2.6(p.12)tomakecleanerplots,butobviouslynotallfactorsarenecessaryininterpretation.

Packageveganhasseveralfunctionsforgraphicaldisplayoffactors.Functionordihulldrawsanenclosingconvexhullfortheitemsinaclass,ordispidercombinesitemstotheir(weighted)classcentroid,andordiellipsedrawsellipsesforclassstandarddeviations,standarder-rorsorcon denceareas.TheexampledisplaysalltheseforManagementtypeinthepreviousordinationandautomaticallylabelsthegroupsin

17

3.3Factors

19

3

17

2

ManagementNMManure0

2

AC1

20

UseHayfield18

11

Moisture5

1415A1

ManagementBFUsePasture16

Moisture1ManagementHF5Manure2

7Moisture2Manure1Manure38UseHaypastu

2ManagementSF1

Manure4Moisture449

123

13 1

2 1012

CA1