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everhartlab / sclerotinia-366

Analysis for "Population structure and phenotypic variation of *Sclerotinia sclerotiorum* from dry bean (*Phaseolus vulgaris*) in the United States"
https://doi.org/10.7717/peerj.4152
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Referencing specific sections of Supplemental Information #17

Closed zkamvar closed 6 years ago

zkamvar commented 6 years ago

There are a couple of sections in the manuscript that point the reader towards supplemental information, but reviewer 2 pointed out that it's unclear as to where exactly they should be going.

At the time of the review, the paper linked to the OSF repository https://osf.io/ejb5y/, which serves as an archive for this repo.

Here's the example text:

In contrast, when we compared the three cultivars, Beryl, Bunsi, and G122, we found no significant differentiation (Supplementary Information).

I've come up with two solutions (that have been expanded by both Pat Schloss and Ben Marwick, in this twitter thread):

  1. Adding text pointing the reader to a specific section with a citation to the data:

    In contrast, when we compared the three cultivars, Beryl, Bunsi, and G122, we found no significant differentiation (See the section on Host Differentiation in the wmn-differentiation.md file in the Supplemental files https://osf.io/ejb5y/)

  2. Adding a straight up link (as a footnote) pointing to the section:

    In contrast, when we compared the three cultivars, Beryl, Bunsi, and G122, we found no significant differentiation (Supplementary Information^1)

    ^1 https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/wmn-differentiation.md#host-differentiation

Currently, I've opted for 2, but I'm not quite settled yet. I would love to hear opinions.

Hao Ye suggested section numbering. This would be a good option if I were rendering my reports in pdf... though it may be good practice to go back and number the sections before submission ¯\_(ツ)_/¯

zkamvar commented 6 years ago

I believe I have settled on a hybrid between 1 and 2:

https://github.com/everhartlab/sclerotinia-366/blob/16fc8e3797126ed32dee8957f2db24cc14b19b03/doc/manuscript/manuscript.Rmd#L607-L609

In contrast, when we compared the three cultivars, Beryl, Bunsi, and G122, we found no significant differentiation (See section on 'Host Differentiation' in the wmn-differentiation.md[^2] file in the supplemental files [@kamvar2017data]).

[^2]: Direct link: https://github.com/everhartlab/sclerotinia-366/blob/master/results/wmn-differentiation.md#host-differentiation

This way, the permanent link is cited and a convenient visualization of the results is available.

zkamvar commented 6 years ago

This issue has been closed due to the fact that the manuscript has been re-submitted with revisions:

https://peerj.com/preprints/3311v2/