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Use <bibentry> for handling citations #168

Merged
merged 7 commits into from
Aug 29, 2023
Merged

Use <bibentry> for handling citations #168

merged 7 commits into from
Aug 29, 2023

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joshwlambert
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This PR addresses and closes #156.

This PR updates the citation information in the parameter library and therefore in the <epiparam> class, and uses <bibentry> objects to handle citation information in <epidist> objects.

The data dictionary is updated to check the new title and journal fields in the library.

Tests and documentation are updated to correspond with the functional updates in the package.

@joshwlambert joshwlambert added enhancement New feature or request citations labels Aug 29, 2023
@joshwlambert
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The R CMD check fails on ubuntu (devel), at the {vdiffr} install stage. I believe this is due to the issue logged here: r-lib/vdiffr#137.

I will assume it is fine to merge this without waiting for this individual check to pass, and if the issue persists over time potentially {vdiffr} can be removed from the package.

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@Bisaloo I'm going to merge this PR now in order to not block other developments. Please feel free to leave any comments on the changes and I will address them in a separate PR.

@joshwlambert joshwlambert merged commit 207552c into main Aug 29, 2023
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@joshwlambert joshwlambert deleted the bibentry branch August 29, 2023 17:44
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10 Linton_etal
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Tangential to this PR but are there any plans to list all authors instead of using etal? It would be especially useful if authors want to use the bibtex citation string directly in their manuscript or reference manager.

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Yes, the plan is to store the all bibliographic information. I left it as just the shortened author list for this PR to get the changes into main quicker. I think that the tabular (csv) format is not conducive to a list of names (e.g. one cell for all authors which are semicolon separated perhaps, because one cell per author would not work). Instead using JSON where the authors could be listed within the bibliography of each entry might be better. What do you think to changing from csv to a more structured data format? I don't foresee it being more difficult to maintain or expand a JSON database than csv.

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Make citation field in <epidist> objects be stored as <bibentry>
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