Re: [R-sig-eco] slope for rarefaction curve
Basic algebrra seems to lead to this function:
rarederatk -
function (x, k)
{
x - x[x0]
J - sum(x)
d - digamma(J-k+1) -digamma(J-x-k+1)
g - lgamma(J-x+1) + lgamma(J-k+1) - lgamma(J-x-k+1)-lgamma(J+1)
d - d*exp(g)
sum(d[is.finite(d)])
}
Here 'x' must be a vector of species abundances for a single site, and 'k' the
sample site at which the
derivative is evaluate. Here a simple test that this seems to work (but please
check):
library(vegan)
data(mite)
rarecurve(mite[1,]) # first sampling point
sum(rarecurve(mite[1,]) # 140, evaluate at 126 individuals
y - rarefy(mite[1,], 126) # 19.47011
b - rarederatk(mite[1,], 126) # derivetive 0.04032 (with warnings)
abline(y-126*b, b) # matches the rarecurve plot
Cheers, Jari Oksanen
From: R-sig-ecology r-sig-ecology-boun...@r-project.org on behalf of Zoltan
Botta-Dukat botta-dukat.zol...@okologia.mta.hu
Sent: 11 May 2015 08:49
To: r-sig-ecology@r-project.org
Subject: Re: [R-sig-eco] slope for rarefaction curve
Dear Simone,
Function rarefy uses the function developed by Hurlbert, thus if you
need slope in a certain point (as your graph suggests) you can calculate
the derivative of this function. It is not an easy job, because
factorials should be derived. See cues here how it can be done:
http://math.stackexchange.com/questions/300526/derivative-of-a-factorial
If you need mean slope in an interval, simply calculate the difference
in the calculated values for the beginning and end of the interval, and
divide the difference by the length of the interval.
Zoltan
2015.05.10. 23:57 keltezéssel, Simone Ruzza írta:
Dear all,
apologies for the total beginner's question. I was wondering if anyone
can give some advice on how to calculate the slope for the last 10% of
the records of a rarefaction curve computed with rarefy from vegan.
Here is a graphic representation of what I would like to do:
https://dl.dropboxusercontent.com/u/33966347/figure.JPG
I have seen that this has been done in a recent paper and I was
wondering if anyone may have any code snippet to do that. Sorry, maybe
this is something really obvious but I have not quite understood how
to do it.
thanks!
Simone
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--
Botta-Dukát Zoltán
Ökológiai és Botanikai Intézet
Magyar Tudományos Akadémia
Ökológiai Kutatóközpont
2163. Vácrátót, Alkotmány u. 2-4.
tel: +36 28 360122/157
fax: +36 28 360110
botta-dukat.zol...@okologia.mta.hu
www.okologia.mta.hu
Zoltán BOTTA-Dukát
Institute of Ecology and Botany
Hungarian Academy of Sciences
Centre for Ecological Research
H-2163 Vácrátót, Alkomány u. 2-4.
HUNGARY
Phone: +36 28 360122/157
Fax..: +36 28 360110
botta-dukat.zol...@okologia.mta.hu
www.okologia.mta.hu
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[R-sig-eco] relate environmental parameters to OTU network
Hi all, I've made a network of OTUs using phyloseq. Now, I'd like to correlate environmental variables to the clusters I observed. Anybody here who has an idea on how to do this exactly? Perhaps there are multiple ways, or if it is possible using another package (network, sna, ...), please let me know. Thanks in advance. Kind regards, Bjorn ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Course: Introduction to zero inflated models with R
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Re: [R-sig-eco] relate environmental parameters to OTU network
Hi Bjorn,
You could check out Local Similarity Analysis (http://meta.usc.edu/softs/lsa/)
or alternatively, network assortativity e.g. in {igraph}
http://www.inside-r.org/packages/cran/igraph/docs/assortativity
Hope it helps,
Cheers,
Johannes
On May 11, 2015, at 4:40 PM, Bjorn Tytgat wrote:
Hi all,
I've made a network of OTUs using phyloseq. Now, I'd like to correlate
environmental variables to the clusters I observed. Anybody here who has an
idea on how to do this exactly? Perhaps there are multiple ways, or if it is
possible using another package (network, sna, ...), please let me know.
Thanks in advance.
Kind regards,
Bjorn
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