R语言vegan包使用教程(2)

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。

1INTRODUCTION

5Dissimilaritiesandenvironment

5.1adonis:MultivariateANOVAbasedondissimilarities5.2Homogeneityofgroupsandbetadiversity......5.3Manteltest.......................5.4Protest:Procrustestest................

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6Classi cation

6.1Clusteranalysis........................6.2Displayandinterpretationofclasses............6.3Classi edcommunitytables.................

1Introduction

Thistutorialdemonstratestypicalwork owsinmultivariateordinationanalysisofbiologicalcommunities.Thetutorial rstdiscussesbasicun-constrainedanalysisandenvironmentalinterpretationoftheirresults.Thenitintroducesconstrainedordinationusingconstrainedcorrespon-denceanalysisasanexample:alternativemethodssuchasconstrainedanalysisofproximitiesandredundancyanalysiscanbeused(almost)similarly.Finallythetutorialdescribesanalysisofspecies–environmentrelationswithoutordination,andbrie ytouchesclassi cationofcommu-nities.

Theexamplesinthistutorialaretested:ThisisaSweavedocument.Theoriginalsource lecontainsonlytextandRcommands:theiroutputandgraphicsaregeneratedwhilerunningthesourcethroughSweave.However,youmayneedarecentversionofvegan.Thisdocumentwasgeneretatedusingveganversion2.0-6andRversion2.15.1(2012-06-22).

Themanualcoversordinationmethodsinvegan.Itdoesnotdis-cussmanyothermethodsinvegan.Forinstance,thereareseveralfunc-tionsforanalysisofbiodiversity:diversityindices(diversity,renyi,fisher.alpha),extrapolatedspeciesrichness(specpool,estimateR),speciesaccumulationcurves(specaccum),speciesabundancemodels(rad-fit,fisherfit,prestonfit)etc.NeitherisvegantheonlyRpack-ageforecologicalcommunityordination.BaseRhasstandardstatisticaltools,labdsvcomplementsveganwithsomeadvancedmethodsandpro-videsalternativeversionsofsomemethods,andade4providesanalter-nativeimplementationforthewholegammeofordinationmethods.

Thetutorialexplainsonlythemostimportantmethodsandshowstypicalwork ows.Iseeordinationprimarilyasagraphicaltool,andIdonotshowtoomuchexactnumericalresults.Instead,therearesmallvignettesofplottingresultsinthemarginsclosetotheplacewhereyouseeaplotcommand.Isuggestthatyourepeattheanalysis,trydi erentalternativesandinspecttheresultsmorethoroughlyatyourleisure.Thefunctionsareexplainedonlybrie y,anditisveryusefultocheckthecor-respondinghelppagesforamorethoroughexplanationofmethods.Themethodsalsoareonlybrie yexplained.Itisbesttoconsultatextbookonordinationmethods,ormylectures,for rmertheoreticalbackground.

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