SI cleanup

[teixeirak]

We'll eventually need to fix up SI to conform to journal guidelines (most notably transferring to their template):

Supporting Information

What is Supporting Information (SI)? Data that is integral to the manuscript, but impractical to include within the full text and typeset article (e.g., large-scale data sets and videos), may be presented as SI. All data that is directly relevant to, and necessary for support of the central claims and conclusions of the article, must be presented in the manuscript itself. Please note the following points:

• [x] A Microsoft Word template for SI is available here.
• [x] SI should take the form of Figures, Tables, Methods, Videos/movies or Notes.
• [x] SI must be referred to in the main text in the following format: Supporting Information Fig. S1, Table S1, Video S1, etc., and cited in order numerically by type (Fig. S1, Fig. S2, etc.).
• [x] A brief, single sentence legend for each item of SI should be given at the end of the References.
• [x] Full legends should be included in the SI files, and all text should be consistent with New Phytologist style.
• [x] SI will NOT be copy-edited and must be submitted in final form, ready for publication.
• [x] Citations are not encouraged in SI.
• [x] SI will be reviewed.
• [x] SI cannot be altered after acceptance. Where possible authors should provide a single file containing all the SI, using the template referred to above as a guide.
• [x] Files should be as small as possible and in accessible formats to allow rapid download.
• [x] SI is subject to the same copyright restrictions as published manuscripts.
• [x] SI should not be used to reduce article length.
• [x] Data and information that are peripheral to the conclusions may, subject to Editor approval, be provided as SI.
• [x] Contact np-centraloffice@lancaster.ac.uk for any SI queries

[teixeirak]

A few SI cleanup specifics:

• [x] Table S1 and S2: correct R2.

[teixeirak]

@mcgregorian1 , we should probably put the SI in their standard template for this next submission, which will likely be the final submission.

[mcgregorian1]

I noticed their preference that citations are not included in the SI. Currently we have the R packages cited as part of the appendix...I'm assuming this should be ok?

[teixeirak]

We can leave it in. In case they really don't like it, we'd have to drop the appendix.

[mcgregorian1]

I had assumed the SI word document template they had would be more thorough but it's pretty simple. I'm a little confused by this claim: "If file format allows, please add your supporting information below and submit this template as a Word document. Files in other formats should be submitted as separate files, but please add legend details below as indicated."

Otherwise, it looks to me like things are fine for the SI?

[teixeirak]

Other formats would be things like large data files that won't fit in a word doc. So it is simple: we just need to transfer the content from the pdf/ Rmd to the Word doc. I think that can be done now; don't expect any changes.

[teixeirak]

Note that there's also probably a bit of cleanup with table headings, etc.

[mcgregorian1]

I've done some searching and it seems that outputting to word directly from markdown will not work with the latex formatting we have (but the figures and captions are fine).

Alternatively I've converted to word online from our existing pdf and at first pass the tables seem much better. They still need some formatting fixing, which I can get to.

[teixeirak]

I’d just copy and paste as graphic objects.

[teixeirak]

Just to make sure this is clear, we do NOT need to re-make the tables in word! Just cut and paste from the pdf. We should copy over the text of the table legends, though.

[mcgregorian1]

Do you mean make a snip (/screenshot) from pdf and paste in word?

On Tue, Sep 22, 2020 at 11:08 AM Kristina Anderson-Teixeira < notifications@github.com> wrote:

Just to make sure this is clear, we do NOT need to re-make the tables in word! Just cut and paste from the pdf. We should copy over the text of the table legends, though.

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[teixeirak]

Yes.

[mcgregorian1]

Gotcha. I'm not sure how much time I'll have this afternoon but I will for sure work on this tonight.

On Tue, Sep 22, 2020 at 11:12 AM Kristina Anderson-Teixeira < notifications@github.com> wrote:

Yes.

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Ian McGregor

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College of Natural Resources

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North Carolina State University

2800 Faucette Dr.

Raleigh, NC 27695 USA imcgreg@ncsu.edu | 714-864-1005 | geospatial.ncsu.edu

[teixeirak]

Note that we will have to convert the main article tables to something the journal can work with (word), but we'll do that after its officially accepted.

[mcgregorian1]

The SI didn't need much fixing after converting the pdf to word, so I updated that.

[teixeirak]

@mcgregorian1 , SI currently includes this warning:

May not matter, as we're transferring to word anyway.

[teixeirak]

@mcgregorian1 , just a reminder that we still have these refs showing up in the middle of the SI file:

Again, shouldn't matter since we're moving everything to their word template, but we'll need to make sure we insert them in the final version that goes to press (or the editors will catch it and request in proofs).

[mcgregorian1]

Yes that's just a warning due to having different R versions

On Sat, 26 Sep 2020, 14:59 Kristina Anderson-Teixeira, < notifications@github.com> wrote:

@mcgregorian1 https://github.com/mcgregorian1 , SI currently includes this warning: [image: image] https://user-images.githubusercontent.com/6355854/94348291-dd736e00-0008-11eb-8186-15f36a39e95d.png

May not matter, as we're transferring to word anyway.

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