R语言vegan包使用教程(12)

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。

2.6Ordinationgraphics21

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2ORDINATION:BASICMETHOD

Functiondecorana ndsonlyfouraxes.Eigenvaluesarede nedasshrinkagevaluesinweightedaverages,similarlyasinccaabove.The“Decoranavalues”arethenumbersthattheoriginalprogrammereturnsas“eigenvalues”—Ihavenoideaoftheirpossiblemeaning,andtheyshouldnotbeused.Mostoftenpeoplecommentonaxislengths,whichsometimesarecalled“gradientlengths”.Theetymologyisobscure:thesearenotgradients,butordinationaxes.Itisoftensaidthatiftheaxislengthisshorterthantwounits,thedataarelinear,andpcashouldbeused.Thisisonlyfolkloreandnotbasedonresearchwhichshowsthatcaisatleastasgoodaspcawithshortgradients,andusuallybetter.

Thecurrentdatasetishomogeneous,andthee ectsofdcaarenotverylarge.Inheterogeneousdatawithacleararce ectthechangesoftenaremoredramatic.Rescalingmayhavelargerin uencethandetrendinginmanycases.

Thedefaultanalysisiswithoutdownweightingofrarespecies:seehelppagesfortheneededarguments.Actually,downweightisanindependentfunctionthatcanbeusedwithccaaswell.

Thereisaschoolofthoughtthatregardsdcaasthemethodofchoiceinunconstrainedordination.However,itseemstobeafragileandvaguebackoftricksthatisbetteravoided.

2.6Ordinationgraphics

Wehavealreadyseenmanyordinationdiagramsinthistutorialwithonefeatureincommon:theyareclutteredandlabelsaredi culttoread.Ordinationdiagramsaredi culttodrawcleanlybecausewemustputalargenumberoflabelsinasmallplot,andoftenitisimpossibletodrawcleanplotswithallitemslabelled.Inthischapterwelookatproducingcleanerplots.Forthiswemustlookattheanatomyofplottingfunctionsinveganandseehowtogainabettercontrolofdefaultfunctions.

Ordinationfunctionsinveganhavetheirdedicatedplotfunctionswhichprovidesasimpleplot.Forinstance,theresultofdecoranaisdisplayedbyfunctionplot.decoranawhichbehindthescenesiscalledbyourplotfunction.Alternatively,wecanusefunctionordiplotwhichalsoworkswithmanynon-veganordinationfunctions,butusespointsinsteadoftextasdefault.Theplot.decoranafunction(orordiplot)actuallyworksinthreestages:

1.Itdrawsanemptyplotwithlabelledaxes,butwithnosymbolsforsitesorspecies.2.Itusesfunctionstextorpointstoaddspeciestotheemptyframe.Iftheuserdoesnotaskspeci cally,thefunctionwillusetextinsmalldatasetsandpointsinlargedatasets.3.Itaddsthesitessimilarly.

Forbettercontroloftheplotswemustrepeatthesestagesbyhand:drawanemptyplotandthenaddsitesand/orspeciesasdesired.

Inthischapterwestudyadi cultcase:plottingtheBarroColoradoIslandordinations.

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