public archiving

[teixeirak]

Current text:

"All data, code, and results are available through the SCBI-ForestGEO organization on GitHub (https://github.com/SCBI-ForestGEO: SCBI-ForestGEO-Data and McGregor_climate-sensitivity-variation repositories), with static versions corresponding to data and analyses presented here archived in Zenodo (DOIs: 10.5281/zenodo.3604993 and [TBD], respectively "

Thus, upon acceptance, we need to:

(1) make this repo public (2) archive in Zenodo

@mcgregorian1, nothing to do with Zenodo before the first submission.

Do you want to make this whole repo public, or just archive in Zenodo?

[mcgregorian1]

This all sounds good. I was wondering if we should rename this? Should it include my last name explicitly or refer to the paper itself?

[teixeirak]

Up to you. I think including your last name is fine (and helpful), but you might consider changing the "climate-sensitivity-variation" part, as it evolved to focus specifically on drought. That said, it's fine as is.

[mcgregorian1]

Maybe then "McGregor_climate_drought_sensitivity"

[teixeirak]

just "McGregor_drought_sensitivity"

[teixeirak]

Let's also clean up the repo a bit (e.g., delete old stuff). For example, can this folder be deleted?

[mcgregorian1]

Yep it can since we've moved away from using those. I've saved the poster for myself (that was the poster for the VWL annual meeting in March last year). I will look further at other items in the repo.

[mcgregorian1]

I'm looking through the repo to clean it up.

I have created a new folder called "non_publication", which contains all the files (data, scripts, e.g.) that I was originally using for the analysis but now am no longer. I am not sure which of these you'd like to keep. They include:

Data

• [x] PDSI data for winchester, along with a short script for parsing through it.
• [x] P50 data from the TRY database (apparently this file is about 100 MB, and Github won't let me commit it because it's too large. I'm fine with deleting it since we didn't use it, but up to you).
• [x] data on Specific Leaf Area (citation is in the excel file)
• [x] SCBI sapwood data (copied over from another folder)
• [x] The only NEON data I use I kept in the original data/heights/NEON folder. Otherwise, everything here in the non-publication was not used. Is this ok? Did you want to keep the tower diagram pdf in the original?
• [x] the word doc is the supplementary info from your 2015 paper (this is where I got the allometric / trait equations). I assume we wouldn't keep it in the data folder since we'd cite the paper anyways?

Graphs_plots

• [x] I think everything in this folder can be deleted

Scripts

• [x] archive scripts](https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/tree/master/non_publication/scripts) for the full analysis with now-outdated code]
• [x] script to sort the files for Neil when he ran through the .rwl files

Manuscript

• [x] We haven't used the bookdown files for a while since we decided to skip it. I'm fine with deleting this folder but watned to double-check first.
• [x] I moved the original archive folder over here. I think we can delete it as this folder consists of early next steps and paper outlining.

Other questions

• [x] The climate folder contains files that are not used in any of my code (the file that is used (the CRU data) is linked to Ryan's repo and opens from there. It is only used for making the time series plots in Figure 1). However, I noticed from your readme that these should not be edited/removed. Can you elaborate please?

• [x] did you want to keep the PDFs of some of the references?

• [x] I noticed that Table S3 is now the drought stats. Did we decide to not include the candidate_traits anymore as a table?

• [x] We decided to not use the ForestGEOplot jpg correct? That means I can delete it?

• [x] eventually we will want to move the coauthor_review folder to the non-publication folder. Did you want to do that now?

Afterwards

• [ ] the last thing that needs to be done after these are addressed is for me to make new README files

[teixeirak]

Thanks! I'll go through all this later.

[teixeirak]

I just realized that I owe some responses here. Will go through this now. I'll check items that are okay to remove, and add point-by-point responses as needed.

[teixeirak]

@mcgregorian1 , note that references can't be published.

[teixeirak]

[ ] PDSI data for winchester, along with a short script for parsing through it.

Wouldn't hurt to add this to the ForestGEO climate data repo (here, with appropriate README.). But okay to just remove if you don't have time for that.

[mcgregorian1]

@mcgregorian1 , note that references can't be published.

Gotcha. I'll keep an eye out in case there are any rogue PDFs anywhere.

[teixeirak]

* The only NEON data I use I kept in the original data/heights/NEON folder. Otherwise, everything [here](https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/tree/master/non_publication/data/height/NEON) in the non-publication was not used. Is this ok? Did you want to keep the tower diagram pdf in the original?

I'd like to keep these; moved to data folder.

[teixeirak]

* The [climate](https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/tree/master/data/climate) folder contains files that are not used in any of my code (the file that _is_ used (the CRU data) is linked to Ryan's repo and opens from there. It is only used for making the time series plots in Figure 1). However, I noticed from your readme that these should not be edited/removed. Can you elaborate please?

You can delete anything that's not used, but keep the CRU data because its needed for the figure.

[teixeirak]

* did you want to keep the PDFs of some of the [references](https://github.com/SCBI-ForestGEO/McGregor_climate-sensitivity-variation/tree/master/references)?

As noted earlier, those cannot be made public. Please remove here/ keep them in your personal archive.

[teixeirak]

Once final edits are finished, we'll want to remove all of these. Please keep them in a personal archive (and I will too):

[teixeirak]

* the last thing that needs to be done after these are addressed is for me to make new README files

@mcgregorian1 , just a reminder on this.

[teixeirak]

Once final edits are finished, we'll want to remove all of these. Please keep them in a personal archive (and I will too):

I moved all but the for_production folder; that goes later.

[teixeirak]

@mcgregorian1 , actually, publishing and releasing this repo needs to come before finalizing the files, as we need to insert the DOI in the data availability statement.

I have everything I need from the non-publication folder, so you can make sure that you do, and then delete. Once that's done, let me know and I'll do the release.

[mcgregorian1]

I think I'm good to go with this.

[teixeirak]

Ok, thanks! Working on the cleanup/ release now.

[teixeirak]

Okay, repo is public!

[teixeirak]

Okay, it's released, and on Zenodo: https://zenodo.org/record/4070060#.X30QaR17nzI.

This is a pre-release; we'll do final release once all files are finalized.

[mcgregorian1]

Ok! Thank you

[mcgregorian1]

[ ] PDSI data for winchester, along with a short script for parsing through it.

Wouldn't hurt to add this to the ForestGEO climate data repo (here, with appropriate README.). But okay to just remove if you don't have time for that.

I'm wasn't able to get to this tonight. The data in there was other exploratory data that I realized the readme didn't cover. I think the main explainers of it are hidden in an early github issue for this repo.

[teixeirak]

Don't worry about the PDSI data if it's too complicated.