Re: [R-sig-eco] singletons and doubletons in vegan

[Canning-Clode, Joao]

Thank you, I think this is what I need. I need to assess the number of species 
represented by exactly one sample (singletons or uniques) and the number of 
species represented by exactly 2 samples (duplicates).

cheers

J
João Canning Clode, Ph.D
Research Associate
Smithsonian Environmental Research Center
647 Contees Wharf Road
Edgewater, MD 21037

Email: canning-clo...@si.edu
Web: www.canning-clode.com

On Feb 1, 2012, at 12:48 PM, Gavin Simpson wrote:

On Wed, 2012-02-01 at 07:32 -0500, Canning-Clode, Joao wrote:
Hi all,

I am running species accumulation curves for several data-sets, and am
also playing with some estimators with this function in vegan:

SF.estimators<-poolaccum(SF.data,permutations=1000)
SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap
plot(SF.estimators) # illustrates graphs for all estimators
summary(SF.estimators,display="jack2") # gives jack2 stats

Does any of you know how can I get the info about singletons and doubletons?

What info do you want?

Working out which spp are singletons and doubletons from the input data
is quite simple for the entire pool of samples (he says, hoping I i]
understood and ii] got this right ;-):

cs <- colSums(SF.data > 0)
singlet <- cs == 1L
doublet <- cs == 2L

singlet[which(singlet)]
doublet[which(doublet)]

E.g.

## Load example data set from vegan
data(BCI)

## compute the column sums
cs <- colSums(BCI > 0)

## logicals for singleton and doubleton
singlet <- cs == 1L
doublet <- cs == 2L

## which species are...
singlet[which(singlet)]
doublet[which(doublet)]

## number of singletons and doubletons...
sum(singlet)
sum(doublet)

HTH

G

best wishes

João

João Canning Clode, Ph.D
Research Associate
Smithsonian Environmental Research Center
647 Contees Wharf Road
Edgewater, MD 21037

Email: 
canning-clo...@si.edu
Web: 
www.canning-clode.com

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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
Pearson Building, [e] 
gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London  [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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Re: [R-sig-eco] singletons and doubletons in vegan

[Jari Oksanen]

On 01/02/2012, at 14:34 PM, Canning-Clode, Joao wrote:

> Hi all,
> 
> I am running species accumulation curves for several data-sets, and am also 
> playing with some estimators with this function in vegan:
> 
> SF.estimators<-poolaccum(SF.data,permutations=1000)
> SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap
> plot(SF.estimators) # illustrates graphs for all estimators
> summary(SF.estimators,display="jack2") # gives jack2 stats
> 
> Does any of you know how can I get the info about singletons and doubletons?
> 
What information do you need? If you want to know the names of singleton and 
doubleton *occurrences* on plots, you can use (with the BCI data in vegan):

freq <- colSums(BCI>0)
which(freq==1)
which(freq==2)

If you want to something similar for counts (individuals), you just change the 
command to find the 'freq'.

If you want to know how many singleton and doubleton species you have in each 
of your sampling units, you can use

rowSums(BCI[, freq==1] > 0)
rowSums(BCI[, freq==2] > 0)

If you want to know how may species have exactly one individual (stem) in a 
sampling unit, just use

rowSums(BCI==1)

Was the information you asked among these things, or do you want to have 
something more?

Cheers, Jari Oksanen
-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa

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Re: [R-sig-eco] singletons and doubletons in vegan

[Gavin Simpson]

On Wed, 2012-02-01 at 07:32 -0500, Canning-Clode, Joao wrote:
> Hi all,
> 
> I am running species accumulation curves for several data-sets, and am
> also playing with some estimators with this function in vegan:
> 
> SF.estimators<-poolaccum(SF.data,permutations=1000)
> SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap
> plot(SF.estimators) # illustrates graphs for all estimators
> summary(SF.estimators,display="jack2") # gives jack2 stats
> 
> Does any of you know how can I get the info about singletons and doubletons?

What info do you want?

Working out which spp are singletons and doubletons from the input data
is quite simple for the entire pool of samples (he says, hoping I i]
understood and ii] got this right ;-):

cs <- colSums(SF.data > 0)
singlet <- cs == 1L
doublet <- cs == 2L

singlet[which(singlet)]
doublet[which(doublet)]

E.g.

## Load example data set from vegan
data(BCI)

## compute the column sums
cs <- colSums(BCI > 0)

## logicals for singleton and doubleton
singlet <- cs == 1L
doublet <- cs == 2L

## which species are...
singlet[which(singlet)]
doublet[which(doublet)]

## number of singletons and doubletons...
sum(singlet)
sum(doublet)

HTH

G

> best wishes
> 
> João
> 
> João Canning Clode, Ph.D
> Research Associate
> Smithsonian Environmental Research Center
> 647 Contees Wharf Road
> Edgewater, MD 21037
> 
> Email: canning-clo...@si.edu
> Web: www.canning-clode.com
> 
> ___
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> 

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%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London  [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

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[R-sig-eco] singletons and doubletons in vegan

[Canning-Clode, Joao]

Hi all,

I am running species accumulation curves for several data-sets, and am also 
playing with some estimators with this function in vegan:

SF.estimators<-poolaccum(SF.data,permutations=1000)
SF.estimators # shows data for Sobs, Chao, both Jacks and bootstrap
plot(SF.estimators) # illustrates graphs for all estimators
summary(SF.estimators,display="jack2") # gives jack2 stats

Does any of you know how can I get the info about singletons and doubletons?

best wishes

João

João Canning Clode, Ph.D
Research Associate
Smithsonian Environmental Research Center
647 Contees Wharf Road
Edgewater, MD 21037

Email: canning-clo...@si.edu
Web: www.canning-clode.com

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