R语言vegan包使用教程(7)

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:BASICMETHODtheyhaveno xedlimit,buttwositeswithnosharedspeciescanvaryindissimilarities,andevenlookmoresimilarthantwositessharingsomespecies.Thiscanbecuredbystandardizingdata.SinceEuclideandis-tancesarebasedonsquareddi erences,anaturaltransformationistostandardizesitestoequalsumofsquares,ortotheirvectornormusingfunctiondecostand:

>dis<-vegdist(decostand(varespec,"norm"),"euclid")

Thisgiveschorddistanceswhichreachamaximumlimitof√

whentherearenosharedspeciesbetweentwosites.AnotherrecommendedalternativeisHellingerdistancewhichisbasedonsquarerootsofsitesstandardizedtounittotal:

>dis<-vegdist(decostand(varespec,"hell"),"euclidean")

Despitestandardization,thesestillareEuclideandistanceswithalltheirgoodproperties,butfortransformeddata.Actually,itisoftenusefultotransformorstandardizedataevenwithotherindices.Ifthereisalargedi erencebetweensmallestnon-zeroabundanceandlargestabundance,wewanttoreducethisdi uallysquareroottransformationissu cienttobalancethedata.Wisconsindoublestandardizationoftenimprovesthegradientdetectionabilityofdissimilarityindices;thiscanbeperformedusingcommandwisconsininvegan.Herewe rstdivideallspeciesbytheirmaxima,andthenstandardizesitestounittotals.Afterthisstandardization,manydissimilarityindicesbecomeidenticalinrankorderingandshouldgiveequalresultsinnmds.

Youarenotrestrictedtouseonlyvegdistindicesinvegan:vegdistreturnssimilardissimilaritystructureasstandardRfunctiondistwhichalsocanbeused,aswellasanyothercompatiblefunctioninanypackage.Somecompatiblefunctionsaredsvdis(labdsvpackage),daisy(clusterpackage),anddistance(analoguepackage),andbetadiversityindicesinbetadiverinvegan.Morever,veganhasfunctiondesigndistwhereyoucande neyourowndissimilarityindicesbywritingitsequationusingeitherthenotationforA,BandJabove,orwithbinarydata,the2×2contingencytablenotationwhereaisthenumberofspeciesfoundonbothcomparedsites,andbandcarenumbersofspeciesfoundonlyinoneofthesites.Thefollowingthreeequationsde nethesameSørensenindexwherethenumberofsharedspeciesisdividedbytheaveragespeciesrichnessofcomparedsites:

>d<-vegdist(varespec,"bray",binary=TRUE)>d<-designdist(varespec,"(A+B-2*J)/(A+B)")

>d<-designdist(varespec,"(b+c)/(2*a+b+c)",abcd=TRUE)

Functionbetadiverde nessomemorebinarydissimilarityindicesinvegan.

Mostpublisheddissimilarityindicescanbeexpressedasdesigndistformulae.However,itismucheasierandsafertousethecannedalter-nativesinexistingfunctions:itisveryeasytomakeerrorsinwritingthedissimilarityequations.

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2.2Communitydissimilarities

Quadraticterms

J=N

=1xijxA= iNikB= i2N=1xiji=1x2ik

Minimumterms

J=N

=1min(xij,xik)A= iN=1xB= iNiji=1xikBinarytermsJ=SharedspeciesA=No.ofspeciesinjB=

No.ofspeciesink

Sitek

presentabsent

Sitej

presentababsent

c

d

J=aA=a+bB=a+c