Niche and Size Modules no longer running

[ngotelli]

Hi @emhart

Parameters not being read in properly with niche_null_model(dataMacWarb) or with size_null_model(dataRodents). Error occurs both in the console and in the .Rmd vignette. However, cooc_null_model(dataWiFinches) still runs OK.

I tried to push the vignette with this error, but generated a merge conflict. I will wait until this is resolved. :hand: :sleepy:

[emhart]

@ngotelli I don't get any error. Can you post the error that you're getting? However if you're getting a merge conflict, you'll have to resolve it before you can push the vignette. What file is throwing the conflict?

[ngotelli]

Hmm, I was unable to replicate the error this morning, so I am not sure what happened there.

These merge conflicts have happened a few times before, and they may

have to do with the version number that is printed on dev tools or one of the other libraries. I am still learning my way around git (and how to resolve a merge conflict), so I have in those cases just recloned the repo and started fresh.

In the vignette .Rmd, is there any way to suppress the output of the

progress bar? I have tried the switches for echo, warnings, and messages in the chunk header, but the progress bar still shows up, which we definitely don't want to see in the rendered vignette (since it refreshes 20 or 30 times during a run).

Thanks, and enjoy the weekend in sunny California (we are getting more

snow here).

Nick

Quoting Edmund Hart <notifications@github.com>:

@ngotelli[1] I don't get any error. Can you post the error that
you're getting? However if you're getting a merge conflict, you'll
have to resolve it before you can push the vignette. What file is
throwing the conflict?

— Reply to this email directly or view it on GitHub[2].  

 

---

Nicholas J. Gotelli       Office Phone: 802-656-0450
Department of Biology     Lab Phone: 802-656-0451   
University of Vermont     Fax: 802-656-2914
Burlington, VT 05405      e-mail: ngotelli@uvm.edu
********************************************************
Home Page (with manuscript pdfs):

http://www.uvm.edu/~ngotelli/homepage.html

Musician's Corner (with mp3s):

http://www.uvm.edu/~ngotelli/musicpage/music.html

NEW: EcoSimR (free software for null model analysis):

http://www.uvm.edu/~ngotelli/EcoSim/EcoSim.html

---

Links:

[1] https://github.com/ngotelli [2] https://github.com/GotelliLab/EcoSimR/issues/59#issuecomment-78770949

[ngotelli]

Hi @emhart

I pushed up the final version of the Niche Overlap Vignette. Thanks for adding the option to suppress the progress bar. That's pretty essential to be able to use the package in a markdown document! The only real problem I ran into was that plot(type = "niche") doesn't work in the vignette because the figure margins are too large (I have marked the line of code in the .Rmd file). Aaron and I ran into the problem a long time ago when we first started coding the graphics. We adjusted the margins so the niche plot does work with R studio, and I just checked that the plots in EcoSimR do work within a standard .Rmd file in RStudio. They just aren't working in the vignette template.

For now I will move on and try to crank out a co-occurrence module next.

Best,

Nick