Hi Nick,
This is pretty rough, but it may help:
pdf("rd.pdf")
raredata<-rarecurve(cbind(netdata,netdata,netdata),label=FALSE,
col=rgb(0,0,1,0.1),xlim=c(0,100),ylim=c(0,80))
rect(100,0,104,80,col="white",border=NA)
dev.off()Jim On Wed, Sep 7, 2016 at 8:05 AM, Nick Pardikes <nickpardi...@gmail.com> wrote: > I am currently having difficulty producing a graph using rarecurve in the > vegan package. I have produced rarefaction curves (seen below) using the > following code. > > > library(vegan) > > myMat <- round(matrix(rlnorm(2000), 50)) #creates distribution of > communities > > netdata <- as.data.frame(myMat) #generates a matrix of communities (rows), > species (columns) > > raredata <- rarecurve(netdata, label=F, col=rgb(0, 0, 1, 0.1)) #uses > rarecurve to plot a rarefaction for each individual community (n=50) > > > However I would like to produce a graph in which all rarefaction curves end > at the same sample size. For example, in this graph it would be great to > extend the x-axis (sample size) to 100 and have all curves end at this > point. Is there any way to use rarecurve to resample a community (row) with > replacement the same number of times for all 50 communities? With > replacement is important because the communities differ greatly in their > size (number of species). > > > I understand that rarefaction is useful to compare communities with > different sample efforts, but I would still like to generate the figure. My > actual data has 5000 simulated communities that differ greatly in matrix > size and number of samples. > > > Thank you in advance for your help and suggestions. > > > Cheers, > > Nick > > -- > Nick Pardikes > PhD Candidate > Program in Ecology, Evolution, and Conservation Biology > University of Nevada > *https://nickpardikes.wordpress.com/ <https://nickpardikes.wordpress.com/>* > nickpardi...@gmail.com > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
rd.pdf
Description: Adobe PDF document
______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
