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

[Nick Pardikes]

Hey Luisfo,

This looks great, however I still get the same plot as before (seen
below). The output looks the same. Here is the figure that was
generated from this code:

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
}

raredata <- rarecurve(rrarefy.custom(netdata, sample=100,rep.param=T),
label=F, col=rgb(0, 0, 1, 0.1))

However, I like what you did to the rrarefy function to add the sample
with replacement option.

On Wed, Sep 7, 2016 at 8:17 AM, Luisfo <luisfo89 at yahoo.es> wrote:
> 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/
>
> 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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> and provide commented, minimal, self-contained, reproducible code.
>
>



-- 
Nick Pardikes
PhD Candidate
Program in Ecology, Evolution, and Conservation Biology
University of Nevada
https://nickpardikes.wordpress.com/
nickpardikes at gmail.com
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