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
rarefaction.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.
