Hi Dan,
Just yesterday I noticed in out course that the definition of Gotelli & Colwell differs from our spatially-explicit one. Unfortunately I do not know a reference for ours

Thanks for your advice on the mobr package!
Is it sufficiently mature know to include a vignette or does it make sense to wait some time more until I do that? Which data set would make a good example for the manual?

Best,

Felix

Von: Dan McGlinn [mailto:[email protected]]
Gesendet: Dienstag, 22. November 2016 02:58
An: MoBiodiv/mobr [email protected]
Cc: May, Felix [email protected]; Mention [email protected]
Betreff: [MoBiodiv/mobr] spatially explicit rarefaction reference? (#85)

hey @ngotellihttps://github.com/ngotelli @rueuntalhttps://github.com/rueuntal and @FelixMayhttps://github.com/FelixMay do any of you know of a good reference to cite for our approach to spatially explicit rarefaction. The general concept is described in Chiarucci et al. (2009)http://s3.amazonaws.com/academia.edu.documents/46009003/Spatially_constrained_rarefaction_Incorp20160527-23277-p5ow92.pdf?AWSAccessKeyId=AKIAJ56TQJRTWSMTNPEA&Expires=1479783110&Signature=9oDawdNOIsKYIF9H4EiAkoU%2Fo7A%3D&response-content-disposition=inline%3B%20filename%3DSpatially_constrained_rarefaction_incorp.pdf but they use a different way of defining how to select the next sampled (a k-nearest neighbor approach). Our approach is a bit simpler than their approach is and I'm curious if there is a precedent for it in the literature.

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Hey @FelixMay thanks for the input. I didn't know that @ngotelli and Colwell had a paper that mentioned spatial rarefaction - can you please send along the reference info. I think getting started on a vignette sounds like a great idea. The function names are changing too much at this point. I'm working on adding documentation to the package right now and cleaning up the code. I think the invasive plant dataset that Jon provided is a good demo dataset - I have called it inv_sp and inv_plot_attr for the community and plot attribute datasets respectively. I would like to include this dataset with the package. All of the examples in the code look like the following:

library(mobr)
data(inv_sp)
data(inv_plot_attr)
inv_comm = make_comm_obj(inv_sp, inv_plot_attr)
# etc etc 

My goal now is to finish up the documentation for the most important functions and then to merge the 4cur branch back into master. Then I plan on working on the methods for the continuous explanatory variable case.

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I meant to write that the function names are NOT changing too much at this point.

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Hi Dan,
Oh sorry this was a misunderstanding. I mean the Gotelli & Colwell 2001 Ecol Letters on rarefaction. They introduce species accumulation curves, but these are non-spatial.

Alright, then I try to have a vignette draft before your meeting in December!
At the moment I am in a course and all the students are working with MoBspatial at the moment – I enjoy ;o)

Felix

Von: Dan McGlinn [mailto:[email protected]]
Gesendet: Dienstag, 22. November 2016 16:26
An: MoBiodiv/mobr [email protected]
Cc: May, Felix [email protected]; Mention [email protected]
Betreff: Re: [MoBiodiv/mobr] spatially explicit rarefaction reference? (#85)

Hey @FelixMayhttps://github.com/FelixMay thanks for the input. I didn't know that @ngotellihttps://github.com/ngotelli and Colwell had a paper that mentioned spatial rarefaction - can you please send along the reference info. I think getting started on a vignette sounds like a great idea. The function names are changing too much at this point. I'm working on adding documentation to the package right now and cleaning up the code. I think the invasive plant dataset that Jon provided is a good demo dataset - I have called it inv_sp and inv_plot_attr for the community and plot attribute datasets respectively. I would like to include this dataset with the package. All of the examples in the code look like the following:

library(mobr)

data(inv_sp)

data(inv_plot_attr)

inv_comm = make_comm_obj(inv_sp, inv_plot_attr)

etc etc

My goal now is to finish up the documentation for the most important functions and then to merge the 4cur branch back into master. Then I plan on working on the methods for the continuous explanatory variable case.

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