subject:"\[R\] Resample with replacement to produce many rarefaction curves with same number of samples"

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

2016-09-08 Thread Stefan Evert

> On 8 Sep 2016, at 16:25, David L Carlson  wrote:
> 
> Sampling without replacement treats the sample as the population for the 
> purposes of estimating the outcomes at smaller sample sizes. Sampling with 
> replacement (the same as bootstrapping) treats the sample as one possible 
> outcome of a larger population at that sample size. 

But the resamples aren't actually independent samples from the underlying 
population, and in contrast to the usual applications of bootstrapping they 
don't give a good approximation of independent samples if you look at type 
("species") counts.

In my understanding – which may be incomplete – bootstrapping works for a test 
statistic computed from the measurements of a single numeric random variable 
(or perhaps several r.v.) in an i.i.d. sample.  The type count cannot be 
expressed as such a test statistic, hence we get the underestimation bias from 
sampling with replacement.

In NLP, we often use parametric power-law models of the population in order to 
extrapolate type counts (e.g. using this implementation 
http://zipfr.r-forge.r-project.org), but this implies strong (and often 
inappropriate) assumptions about the population.

Best,
Stefan

__
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.

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

2016-09-08 Thread David L Carlson

One way around this would be to use multinomial sampling, but as Stefan 
indicated, the maximum number of species at any size will, of course be 40 (in 
your example):

> set.seed(42)
> # Generate one sample
> census <- round(rlnorm(40))
> sum(census) # Sample size
[1] 76
> sum(as.logical(census)) # No of species present
[1] 31
> 
> # Create probabilities
> census.adj <- census
> # Add .5 to each 0 value
> census.adj[census.adj==0] <- .5
> census.adj <- census.adj/sum(census.adj)
> 
> pcensus <- rmultinom(50, 150, census.adj)
> 
> Species <- apply(pcensus, 2, function(x) sum(as.logical(x)))
> quantile(Species)
  0%  25%  50%  75% 100% 
  29   33   34   36   38

So projecting a sample of 76 to 150 gives an estimated median of 34 species.

-
David L Carlson
Department of Anthropology
Texas A University
College Station, TX 77840-4352

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of David L Carlson
Sent: Thursday, September 8, 2016 9:25 AM
To: Stefan Evert; Nick Pardikes
Cc: R-help Mailing List
Subject: Re: [R] Resample with replacement to produce many rarefaction curves 
with same number of samples

Sampling without replacement will never find more species than there are in 
your original sample either! 

Sampling without replacement treats the sample as the population for the 
purposes of estimating the outcomes at smaller sample sizes. Sampling with 
replacement (the same as bootstrapping) treats the sample as one possible 
outcome of a larger population at that sample size. 

There is another consideration. A zero value means different things at 
different sample sizes. At sample size 10, it means approximately less than 
10%, but at sample size 100, it means approximately less than 1%, and so on. 

-
David L Carlson
Department of Anthropology
Texas A University
College Station, TX 77840-4352

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Stefan Evert
Sent: Thursday, September 8, 2016 7:46 AM
To: Nick Pardikes
Cc: R-help Mailing List
Subject: Re: [R] Resample with replacement to produce many rarefaction curves 
with same number of samples

> On 7 Sep 2016, at 00:07, Nick Pardikes  wrote:
> 
> 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).

Are you sure it makes sense to resample with replacement?  This will 
systematically underestimate the number of species at a given sample size 
(because of the artificial repetition) and will never find more species than 
there are in your original sample.

Best,
Stefan
__
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.

__
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.

__
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.

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

2016-09-08 Thread David L Carlson

Sampling without replacement will never find more species than there are in 
your original sample either! 

Sampling without replacement treats the sample as the population for the 
purposes of estimating the outcomes at smaller sample sizes. Sampling with 
replacement (the same as bootstrapping) treats the sample as one possible 
outcome of a larger population at that sample size. 

There is another consideration. A zero value means different things at 
different sample sizes. At sample size 10, it means approximately less than 
10%, but at sample size 100, it means approximately less than 1%, and so on. 

-
David L Carlson
Department of Anthropology
Texas A University
College Station, TX 77840-4352

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Stefan Evert
Sent: Thursday, September 8, 2016 7:46 AM
To: Nick Pardikes
Cc: R-help Mailing List
Subject: Re: [R] Resample with replacement to produce many rarefaction curves 
with same number of samples

> On 7 Sep 2016, at 00:07, Nick Pardikes  wrote:
> 
> 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).

Are you sure it makes sense to resample with replacement?  This will 
systematically underestimate the number of species at a given sample size 
(because of the artificial repetition) and will never find more species than 
there are in your original sample.

Best,
Stefan
__
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.

__
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.

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

2016-09-08 Thread Stefan Evert

> On 7 Sep 2016, at 00:07, Nick Pardikes  wrote:
> 
> 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).

Are you sure it makes sense to resample with replacement?  This will 
systematically underestimate the number of species at a given sample size 
(because of the artificial repetition) and will never find more species than 
there are in your original sample.

Best,
Stefan
__
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.

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

2016-09-08 Thread Luisfo via R-help

Hi Nick,

Yes, you are right. There's one small bug on my code.
The 'if' within the for-loop is wrong. Try it now with the code below.

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
}

I have test it now before pasting it.

Best,

*Luisfo Chiroque*
/PhD Student | PhD Candidate
IMDEA Networks Institute/
http://fourier.networks.imdea.org/people/~luis_nunez/ 


On 09/07/2016 10:27 PM, Nick Pardikes wrote:
> 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  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)

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

2016-09-08 Thread 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  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
>
>
>
> __
> 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,

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

2016-09-07 Thread Luisfo via R-help

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
>
>
>
> __
> 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.

[[alternative HTML version deleted]]

__
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.

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

2016-09-07 Thread Jim Lemon

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  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/ *
> 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.

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

2016-09-07 Thread Nick Pardikes

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/ *
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.

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

2016-09-07 Thread Nick Pardikes

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/
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.

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

2016-09-07 Thread Nick Pardikes

Greetings,
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/
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.

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

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

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

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

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

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

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

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

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

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

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

11 matches

Site Navigation

Mail list logo

Footer information