[R] Resample with replacement to produce many rarefaction curves with same number of samples

[Luisfo]

Hi Nick,

If you use the following
     raredata <- rarecurve(rrarefy(netdata, sample=100), label=F, 
col=rgb(0, 0, 1, 0.1))
should work for any sample size, e.g. sample=100.
However, you will have a 'warning' if you don't have samples enough, 
because it has not replacement.

If you type 'rrarefy' on the R console (without brackets), or any other 
function name, you will see the R code of the function.
rrarefy uses the function 'sample()' for sampling, but has no option for 
replacement.
I did the following. I created my custom rrarefy function from the original.
rrarefy.custom <- function (x, sample, rep.param=F)
{
   if (!identical(all.equal(x, round(x)), TRUE))
     stop("function is meaningful only for integers (counts)")
   x <- as.matrix(x)
   if (ncol(x) == 1)
     x <- t(x)
   if (length(sample) > 1 && length(sample) != nrow(x))
     stop(gettextf("length of 'sample' and number of rows of 'x' do not 
match"))
   sample <- rep(sample, length = nrow(x))
   colnames(x) <- colnames(x, do.NULL = FALSE)
   nm <- colnames(x)
   if (!rep.param && any(rowSums(x) < sample))
     warning("Some row sums < 'sample' and are not rarefied")
   for (i in 1:nrow(x)) {
     if (rep.param && sum(x[i, ]) <= sample[i])
       next
     row <- sample(rep(nm, times = x[i, ]), sample[i], replace = rep.param)
     row <- table(row)
     ind <- names(row)
     x[i, ] <- 0
     x[i, ind] <- row
   }
   x
}
You can check the differences with the original code if you type 
'rrarefy' on the R console.

So now, if you type the following
     raredata <- rarecurve(rrarefy.custom(netdata, 
sample=100,rep.param=T), label=F, col=rgb(0, 0, 1, 0.1))
you will have the desired behaviour.

WARNING: I do not understand about rarefunction curves or communities in 
your context. So, be careful when resampling. It might not be 
statistically correct.

Regards,
*Luisfo Chiroque*
/PhD Student | PhD Candidate
IMDEA Networks Institute/
http://fourier.networks.imdea.org/people/~luis_nunez/ 
<http://fourier.networks.imdea.org/people/%7Eluis_nunez/>

On 09/07/2016 12:07 AM, Nick Pardikes 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
>
>
>
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