Clean up the repo & render submitted version

[gavinsimpson]

Now that we've submitted, we should clean the messy repo up a bit and get rid of all the extraneous files that built up over the weeks.

Delete:

• Neotoma_paper_AD.Rmd -> No longer needed
• Rplots.pdf -> shouldn't have been committed
• TODO.txt -> Most (all) of this is no not needed
• ToDocX_knit.R -> this should be in Makefile & shouldn't link to @SimonGoring's local repo of neotoma
• all.downloads.Rdata -> this is no longer used
• ecology-letters.csl -> not used
• ggmapTemp.png -> not used
• mam.dl.Rdata -> not used
• margins.sty -> not used This is used in the PDF output as I have just dropped the margins in directly via -V
• neotoma_bib.bib.bak -> irrelevant file given VC
• neotoma_paper.Rproj -> not needed, we should add this to .gitignore
• R/ -> no longer used

Move:

• figure_plot.pptx -> this should be in a separate folder of raw materials
• flowchart.png -> figures/ is where this should be and the paper should load it from there
• misc/ & revision_nores/ should be moved to a common folder; perhaps all in misc/

Render:

Render final versions of the submitted paper

• .md (this already done?)
• .pdf
• .docx (this already done)

Finally, tag the repo as a submission so we record this point in the history.

[gavinsimpson]

Before anyone spends a lot /any time on this, I have a branch in my fork which is tackling the issue above.

I intended to do a PR last night but I had a problem with the code erroring out during render(). I'm rerunning with a clean cache but one of the examples needs a lot of data and that takes a while.

[SimonGoring]

Great. Thanks Gavin. Yes, the mammal example is big. @andydawson put in a commented if/else statement that would save the output but I cut it out for the final rendering. I suppose we can put it back in if we want.

Is the error around missing figures? I kept getting that intermittently, but didn't worry too much about it because I had backup figures.

I'm going to go back to the neotoma package too and update the version number & some stuff to indicate which version accompanies the paper text, but I've got some catch-up to do this week, so I appreciate the work cleaning this repo up.

On Thu, Oct 9, 2014 at 10:07 AM, Gavin Simpson notifications@github.com wrote:

Before anyone spends a lot /any time on this, I have a branch in my fork https://github.com/gavinsimpson/neotoma_paper/tree/clean-up which is tackling the issue above.

I intended to do a PR last night but I had a problem with the code erroring out during render(). I'm rerunning with a clean cache but one of the examples needs a lot of data and that takes a while.

— Reply to this email directly or view it on GitHub https://github.com/SimonGoring/neotoma_paper/issues/33#issuecomment-58523579 .

[gavinsimpson]

No worries @SimonGoring. The error was a subscript out of bounds which seems odd and suggests to me that I have a cache issue locally - I had WiFi crap out on me at home last night whilst it was downloading the data for one of the examples.

I think we should snapshot the data as of date of submission (i.e. now). I'll do that once I've checked that I haven't screwed anything up by removing files we really do need. But I'll do that after we tag for the submission code.