R语言vegan包使用教程(14)

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

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

4

22

ACD02 4 6 4 20246

DCA1

>ordilabel(mod,dis="sp",lab=shnam,priority=stems)

Finally,thereisfunctionordipointlabelwhichusesbothpointsand

labelstothesepoints.Thepointsarein xedpositions,butthelabelsareiterativelylocatedtominimizetheiroverlap.TheBarroColoradoIslanddatasethasmuchtoomanynamesfortheordipointlabelfunction,butitcanbeusefulinmanycases.

Inadditiontotheseautomaticfunctions,functionorditkplotallowseditingofplots.Ithaspointsin xedpositionswithlabelsthatcanbedraggedtobetterplaceswithamouse.Thefunctionusesdi erentgraphicaltoolset(Tcl/Tk)thanordinaryRgraphics,buttheresultscanbepassedtostandardRplotfunctionsforeditingordirectlysavedasgraphics les.Moreover,theordipointlabelouputcanbeeditedusingorditkplot.

Functionsidentify,orditorp,ordilabelandordipointlabelmayprovideaquickandeasywaytoinspectordinationresults.Oftenweneedabettercontrolofgraphics,andjudicuouslyselectthelabelledspecies.Inthatcasewecan rstdrawanemptyplot(withtype="n"),andthenuseselectargumentinordinationtextandpointsfunctions.Theselectargumentcanbeanumericvectorthatliststheindicesofselecteditems.Suchindicesaredisplayedfromidentifyfunctionswhichcanbeusedtohelpinselectingtheitems.Alternatively,selectcanbealogicalvectorwhichisTRUEtoselecteditems.Suchalistwasproducedinvisiblyfromorditorp.Youcannotseeinvisibleresultsdirectlyfromthemethod,butyoucancatchtheresultlikewedidaboveinthe rstorditorpcall,andusethisvectorasabasisforfullycontrolledgraphics.Inthiscasethe rstitemswere:

>sel[1:14]

AbarmacrAcacmelaAcaldiveAcalmacrAdeltrilAegipanaAlchcost

FALSEFALSEFALSEFALSEFALSEFALSEFALSEAlchlatiAlibedulAllopsilAlseblacAmaicoryAnacexceAndiiner

TRUEFALSEFALSEFALSETRUETRUEFALSE

3Environmentalinterpretation

Itisoftenpossibleto“explain”ordinationusingecologicalknowledgeonstudiedsites,uallyitispreferabletouseexternalenvironmentalvariablestointer-prettheordination.Therearemanywaysofoverlayingenvironmentalinformationontoordinationdiagrams.Oneofthesimplestistochangethesizeofplottingcharactersaccordingtoanenvironmentalvariables(argumentcexinplotfunctions).Theveganpackagehassomeusefulfunctionsfor ttingenvironmentalvariables.

3.1Vector tting

Themostcommonlyusedmethodofinterpretationisto tenvironmentalvectorsontoordination.The ttedvectorsarearrowswiththeinterpre-tation:

14