R help - Feb 2011 - Species accumulation curves with differential sampling effort

Hello! I'm a PhD student working with coral reef fish diversity in Mexico.
I want to do species accumulation curves but I have differential sampling
effort for each "sample".
Do you know or have developed an R script that consider the differential
effort of each sample?
PRIMER and other programs use each pack of species as a replica without the
possibility of telling the program that the first group of species (sample)
was collected during a 30 minutes dive and the second group (sample) was
taking after 60 minutes dive and so on.
I would really appreciate any kind of help!
Best regards,
Vanessa  Francisco <"><

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On Feb 21, 2011, at 12:38 PM, Vanessa Francisco wrote:
> Hello! I'm a PhD student working with coral reef fish diversity in  
> Mexico.
Are you hiring?
> I want to do species accumulation curves but I have differential  
> sampling
> effort for each "sample".
> Do you know or have developed an R script that consider the  
> differential
> effort of each sample?
> PRIMER
... not familiar with that package.
> and other programs use each pack of species as a replica without the
> possibility of telling the program that the first group of species  
> (sample)
> was collected during a 30 minutes dive and the second group (sample)  
> was
> taking after 60 minutes dive and so on.
If you were using a glm model with a a log(poisson) link, then adding  
an offset term that was equal to log(time) should sensibly incorporate  
the information for the differential effort.

> I would really appreciate any kind of help!
> Best regards,
> Vanessa  Francisco <"><
-- 

David Winsemius, MD
West Hartford, CT

Hi:

Try the vegan and biodiversityR packages; both contain functions for
producing species accumulation curves.

On Mon, Feb 21, 2011 at 9:38 AM, Vanessa Francisco
<vanewagen@gmail.com>wrote:
> Hello! I'm a PhD student working with coral reef fish diversity in
Mexico.
> I want to do species accumulation curves but I have differential sampling
> effort for each "sample".
> Do you know or have developed an R script that consider the differential
> effort of each sample?
> PRIMER and other programs use each pack of species as a replica without the
> possibility of telling the program that the first group of species (sample)
> was collected during a 30 minutes dive and the second group (sample) was
> taking after 60 minutes dive and so on.
>
One could create a variable in your data frame that quantifies the dive
duration. Whether or not the SAC functions accept weights is something you
could learn from their help pages.

HTH,
Dennis

I would really appreciate any kind of help!
> Best regards,
> Vanessa  Francisco <"><
>
>        [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
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>
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Vanessa Francisco <vanewagen <at> gmail.com> writes:
> 
> Hello! I'm a PhD student working with coral reef fish diversity in
Mexico.
> I want to do species accumulation curves but I have differential sampling
> effort for each "sample".
> Do you know or have developed an R script that consider the differential
> effort of each sample?
> PRIMER and other programs use each pack of species as a replica without the
> possibility of telling the program that the first group of species (sample)
> was collected during a 30 minutes dive and the second group (sample) was
> taking after 60 minutes dive and so on.
> I would really appreciate any kind of help!
Vanessa,

I speak only for the vegan package: I don't know if there is solution
elsewhere
 in R. I can certainly say that this cannot be done in vegan. However, it seems 
like this could be "easily" implemented in some accumulation methods,
but
not with all. Is this weighted SAC published somewhere? If I
"re-invent" it, I'd
like to see what others have done. How keenly and urgently you need this? 
This will require a bit work since the structure of function needs changes 
although the idea is simple, and I'd like to know if that work is of any use
to
anyone before starting. Of course, if this already is in R, I won't do this.

Cheers, Jari Oksanen