R软件与生物多态性分析概述.pptVIP

用R语言进行生物多样性分析 王绪高 中国科学院沈阳应用生态所 Diversity Sample Single sampling ~ square sample.ran.squ=function(data, side, plotdim=c(1000,500)) { xlo=runif(1,min=0,max=plotdim[1]-side) ylo=runif(1,min=0,max=plotdim[2]-side) xhi=xlo+side yhi=ylo+side randsample=subset(data, gx=xlogxxhigy=ylogyyhi) no.ind=length(randsample$sp) no.spp=length(unique(randsample$sp)) return(c(side^2/1e4,no.ind,no.spp)) } Sample Single sampling ~ rectangular sample.ran.rect=function(data, side.x, side.y, plotdim=c(1000,500)) { xlo=runif(1,min=0,max=plotdim[1]-side.x) ylo=runif(1,min=0,max=plotdim[2]-side.y) xhi=xlo+side.x yhi=ylo+side.y randsample=subset(data, gx=xlogxxhigy=ylogyyhi) no.ind=length(randsample$sp) no.spp=length(unique(randsample$sp)) return(c(side.x*side.y/1e4,no.ind,no.spp)) } Sample Single sampling ~ circle sample.ran.circle=function(data, radius, plotdim=c(1000,500),graph=T) { xlo=runif(1,min=radius,max=plotdim[1]-radius) ylo=runif(1,min=radius,max=plotdim[2]-radius) num.ind=length(data$gx) place=numeric() dist=((data$gx-xlo)^2+(data$gy-ylo)^2)^0.5 dist.n=dist=radius place=(1:num.ind)[dist.n] sample.new=data[place,] sample.new=sample.new[is.na(sample.new$tag)==F,] if(graph){ plot(data$gx,data$gy,xlab=x,ylab=y) points(sample.new$gx,sample.new$gy,type=p, col=blue) } cat(Random sample point is,c(xlo,ylo),sep= ,\n) return(sample.new) } Sample Nest sampling spp.area.onetime=function(data,side) { randsample=subset(data,data$gx=0data$gxsidedata$gy=0data$gyside) no.ind=length(randsample$sp) no.spp=length(unique(randsample$sp)) abund=numeric() splist=unique(randsample$sp) for (i in 1:no.spp) {abund[i]=length(randsample$sp[randsample$sp==splist[i]]) } p=abund/sum(abund) shannon=-sum(p*log(p)) simpson=1-sum(p^2) return(c(side^2/1e4,no.ind,no.spp,shannon,simpson)) } ############ Sample Variogram result=sample.side(bci,side=20,plotdim=c(500,500)) result[1:4,] library(geoR) abund=result[,1:3] abund.geo=as.geodata(abund) dist=seq(0,500,20) abund.var=variog(abund.geo,dir=0,uvec=dist) ##comput