vegan::adonis, SS, order of terms

Are the vegan::adonis sums of squares supposed to depend on the order of the
terms?  I'm trying to understand permutational MANOVA, and this
disagrees with my reading of Anderson 2001.

library(vegan)
data(dune)
data(dune.env)
adonis(dune ~ A1 + Management, dune.env)
adonis(dune ~ Management + A1, dune.env)

Any help would be appreciated.

Oliver

Re: vegan::adonis, SS, order of terms

On 01/02/2012, at 06:52 AM, Oliver Soong wrote:

> Are the vegan::adonis sums of squares supposed to depend on the order of the
> terms?  

Yes, the terms are added sequentially, just like in ordinary R anova, and they are order-dependent. The
next release version of vegan will show this information (I just committed the change to R-Forge).

> I'm trying to understand permutational MANOVA, and this
> disagrees with my reading of Anderson 2001.
> 
> library(vegan)
> data(dune)
> data(dune.env)
> adonis(dune ~ A1 + Management, dune.env)
> adonis(dune ~ Management + A1, dune.env)
> 
So *how* does this disagree with your reading?

Cheers, Jari Oksanen
--

-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland

Lecture multivariate statistics for environmental/ecological data in R

Hello,

I have recorded lectures on multivariate statistics for environmental/ecological data with R, loosely
tackling the topics of Legendre & Legendre 1998 and using the vegan package for e.g. ordination,
permutational MANOVA. Topics include multiple regression with the linear and generalized linear
model, MANOVA, permutational MANOVA, distance metrics, NMDS, PCA, Cluster analysis etc.
I make the R code of the lecture, the slides and videos freely available, in case somebody is interested.
http://www.uni-koblenz-landau.de/landau/fb7/umweltwissenschaften/landscape-ecology/Teaching/r-statistics

Any comments welcome - also hints whether there are websites with compilations of R educational material,
where such links should be posted.

Best regards
Ralf Schaefer

------------------------------------------------------------

Prof. Dr. Ralf Bernhard Schäfer
Juniorprofessor for Quantitative Landscape Ecology
Environmental Scientist (M.Sc.)
Institute for Environmental Sciences
University Koblenz-Landau
Fortstrasse 7
76829 Landau
Germany
Mail: schaefer-ralf@...
Phone: ++49 (0) 6341 280-31536
Web: http://tinyurl.com/6dnpxna

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Re: Lecture multivariate statistics for environmental/ecological data in R

Hi Ralf;

Sounds really interesting, however the link seems broken. Could you please
send it again?

Cheers, Ricardo.

2012/2/1 Ralf Schäfer <senator@...>

> Hello,
>
> I have recorded lectures on multivariate statistics for
> environmental/ecological data with R, loosely tackling the topics of
> Legendre & Legendre 1998 and using the vegan package for e.g. ordination,
> permutational MANOVA. Topics include multiple regression with the linear
> and generalized linear model, MANOVA, permutational MANOVA, distance
> metrics, NMDS, PCA, Cluster analysis etc.
> I make the R code of the lecture, the slides and videos freely available,
> in case somebody is interested.
>
> http://www.uni-koblenz-landau.de/landau/fb7/umweltwissenschaften/landscape-ecology/Teaching/r-statistics
>
> Any comments welcome - also hints whether there are websites with
> compilations of R educational material, where such links should be posted.
>
> Best regards
> Ralf Schaefer
>
> ------------------------------------------------------------
>

Re: Lecture multivariate statistics for environmental/ecological data in R

Works for me but may be a line break issue - so here a shortened link:
http://tinyurl.com/br35tgl
Cheers
Ralf

Am 01.02.2012 um 13:01 schrieb Ricardo Solar:

> Hi Ralf;
> 
> Sounds really interesting, however the link seems broken. Could you please send it again?
> 
> Cheers, Ricardo.
> 
> 2012/2/1 Ralf Schäfer <senator@...>
> Hello,
> 
> I have recorded lectures on multivariate statistics for environmental/ecological data with R, loosely
tackling the topics of Legendre & Legendre 1998 and using the vegan package for e.g. ordination,
permutational MANOVA. Topics include multiple regression with the linear and generalized linear
model, MANOVA, permutational MANOVA, distance metrics, NMDS, PCA, Cluster analysis etc.
> I make the R code of the lecture, the slides and videos freely available, in case somebody is interested.
> http://www.uni-koblenz-landau.de/landau/fb7/umweltwissenschaften/landscape-ecology/Teaching/r-statistics
> 
> Any comments welcome - also hints whether there are websites with compilations of R educational
material, where such links should be posted.
> 
> Best regards
> Ralf Schaefer
> 
> ------------------------------------------------------------

singletons and doubletons in vegan

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-clodej@...<mailto:canning-clodej@...>
Web: www.canning-clode.com<http://www.canning-clode.com>

Re: singletons and doubletons in vegan

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)

Re: singletons and doubletons in vegan

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

Re: singletons and doubletons in vegan

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-clodej@...<mailto:canning-clodej@...>
Web: www.canning-clode.com<http://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?

help - vegan taxondive

Dear Members,

I would try to use indices of taxonomic diversity and distinctness to
differentiate two mycorrhizal fungal communities. My problem is up to the*dis
* object required to the function for the calculation. In the function help
I red that "function* taxa2dist* can produce a suitable dist object from a
classification table". How should I should create this classification
table? How it should look-like?
Thank you very much in advance,

Gian

--

-- 
Gian Maria Niccolò Benucci, Ph.D.
Department of Applied Biology
University of Perugia
Borgo XX Giugno, 74
06121 - Perugia, ITALY
Tel: +390755856433
Email: gian.benucci@...

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