R语言vegan包使用教程(13)

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。

2ORDINATION:BASICMETHOD2.6Ordinationgraphics

>data(BCI)

Thisisadi cultdatasetforplotting:ithas225speciesandthereisnowayoflabellingthemallcleanly–unlessweuseverylargeplottingareawithsmalltext.Wemustshowonlyaselectionofthespeciesorsmallpartsoftheplot.Firstanordinationwithdecoranaanditsdefaultplot:

>mod<-decorana(BCI)>plot(mod)

DCA2

++

4

Thereisanadditionalprobleminplottingspeciesordinationwiththesedata:

>names(BCI)[1:5]

[1]"Abarema.macradenium""Acacia.melanoceras"[3]"Acalypha.diversifolia""Acalypha.macrostachya"[5]"Adelia.triloba"

++++++++++

++++++++++++++++++++++++++++++++

+++++++++++++++++++++q+q++++q+q++++++++q+++q+++++q+++qqq++++++q+q++q++qqqq+++++++++qqq+q++++++q+qqqq++q+++++++qq+++++++++++qq++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++

++

+++

++++

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+

+

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Thedatasetusesfullspeciesnames,andthereisnowayof ttingthoseinordinationgraphs.Thereisautilityfunctionmake.cepnamesinvegantoabbreviateLatinnames:

>shnam<-make.cepnames(names(BCI))>shnam[1:5]

[1]"Abarmacr""Acacmela""Acaldive""Acalmacr""Adeltril"

++

Alchlati

DCA2

>pl<-plot(mod,dis="sp")

Allveganordinationplotfunctionsreturninvisiblyanordiplotobjectwhichcontainsinformationonthepointsplotted.Thisinvisibleresultcanbecaughtandusedasinputtoidentify.Thefollowingselectivelylabelssomeextremespeciesasclicked:

>identify(pl,"sp",labels=shnam)

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Theeasiestwaytoselectivelylabelspeciesistouseinteractiveiden-tifyfunction:whenyouclicknexttoapoint,itslabelwillappearonthesideyouclicked.Youcan nishlabellingclickingtherightmousebutton,orwithhandicappedone-buttonmouse,youcanhittheesckey.

4

AbarmacrSocrexor

++Pachquin

++++++++

+Entescho+Nectciss++++++++++++Pachsess+++++++++++++++++Ficuyopo+++++++++++++++++++++++++++Margnobi++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Gustsupe+++++Poularma+++++++++++++++++++++++Ocotwhit++++++++++

+++

Macrrose+++++Tropcauc++++Cavaplat++++Sapibroa+++++++++

++Pourbico

++++

2

Senndari+

+

+Brosguia+

+Quasamar

4

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Thereisan“ordinationtextorpoints”functionorditorpinvegan.Thisfunctionwilllabelanitemonlyifthiscanbedonewithoutover-writingpreviouslabels.Ifanitemcannotbelabelledwithtext,itwillbemarkedasapoint.Itemsareprocessedeitherfromthemargintowardthecentre,orindecreasingorderofpriority.Thefollowinggiveshigherprioritytothemostabundantspecies:

DCA2

CasecommAlchlati

4

>stems<-colSums(BCI)

>plot(mod,dis="sp",type="n")

>sel<-orditorp(mod,dis="sp",lab=shnam,priority=stems,pcol="gray",pch="+")

Wealsocanzoomintosomepartsoftheordinationdiagramsbysettingxlimandylim,andwecanseemoredetails.

Analternativetoorditorpisfunctionordilabelwhichdrawstextonopaquelabelsthatcoverotherlabelsbelowthem.Alllabelscannotbedisplayed,butatleasttheuppermostarereadable.Argumentpriorityworkssimilarlyasinorditorpandcanbeusedtoselectwhichofthelabelsaremostimportanttoshow:

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+

++Socrexor+++Ingacocl+++++

+Entescho+++Cordbico+++++Pachsess++++++Ficuyopo++Cocccoro++++++++++++Unonpitt+++++Talinerv++++++++++++++++Tabeguay++++++++Heisacum+++++++++++++T+++Faraocci+++++++++++++++TFicuinsi+Sapiglan++++++++++++++++++Gustsupe+++++Garcinte+Poularma++++++++++++++++CaseaculSloatern

Ocotwhit++++++T+ripcumi

++Hirttria+MacrroseViromult++++Xylomacr+++Marilaxi++++Drypstan+++

+

4 202

+

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