R help - Sep 2016 - Resample with replacement to produce many rarefaction curves with same number of samples

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/>*
nickpardikes at gmail.com
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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 <nickpardikes at 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/>*
> nickpardikes at gmail.com
>
> ______________________________________________
> R-help at 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.
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