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Restructures some introductory text to clarify terms and how earth mover's distance actually works.
Expands a paragraph in the Discussion to mention the increased diversity of H3N2 clades during our test period and the effect that diversity and other evolutionary events may have had on our models. These effects are framed in the context of model overfitting.
Adds best estimated strains by naive model to vaccine comparison figure, adds a new supplemental figure that shows the distance to the future of observed and estimated best strains relative to the corresponding vaccine strains, and quantifies improvement of models over the vaccine strains in the results text. This commit also changes the vaccine strain name annotation in the vaccine comparison figure to use an abbreviation with a larger font and improve overall readability. The abbreviations are now explained in the figure caption.
Adds analyses to the vaccine comparison notebook that include a comparison of relative distance to the future for closest strains vs. vaccine strains and the antigenic distance between those corresponding strains. Also, improves the aesthetics and readability of the vaccine comparison figure and adds the supplemental figure showing relative distance to the future for closest strains vs. vaccine strains.
Adds an analysis to the model results notebook that compares the forecasting accuracy between Northern and Southern Hemispheres.
Updates most citations to use the parenthetical form, adds the eLife document type and bibliography style, updates the model summary table to use the full citation style, and adds a citation for Barrat-Charlaix et al. 2020 which is now available as a preprint.
The eLife template handles placement of these figures without our intervention.
Moves the relative vaccine comparison figure from the supplemental material to a figure supplement, to make comparison between the absolute and relative distances easier.
Promotes some supplemental figures to main figures and moves others to figure supplements for the appropriate main figures. Also promotes most supplemental tables to main tables.
Moves acknowledgments into an appendix, moves the supplemental file reference into the main text, and removes the supplemental text file completely.
Note that the reorganization of supplemental material has broken some references in the compiled PDF. This only seems to be avoidable if the original references remain in the new text which isn't reasonable. Instead, we make do with the missing references for now.
Expands figure supplement captions to be more understandable on their own and cross-references each validation figure to its corresponding part of the cross-validation schematic for simulated and natural populations. This latter change should help readers distinguish between "validation" and "test" results.
Replaces the "best" value judgement with the quantitative "closest" for each closest strain to the future, explains how we calculate these closest strains to the future the first time they are mentioned, and references the equations used. Also expands the interpretation of these closest strains in the vaccine comparison section to clarify that they represent centroids of the observed and estimated future populations.
Simplify upload to eLife by preparing a single latex file.
Simplify eLife document merge by placing all tables in the same top-level directory, but maintain separate table files since these are automatically generated by the repo's workflow.
Previous commits replaced this text in the main manuscript, but I missed the embedded text in these figures.
Simplifies eLife upload and manuscript PDF building by placing all figures in the top-level manuscript directory. This commit also updates the rule used to link these figures from their more human-readable names to use hard links.
Includes eLife digest responses, response letter, and transparent reporting form.
Adds a manually executable notebook with an auspice build for generating the striking image included with the submission and the striking image itself.
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This PR merges all changes associated with revisions requested by reviewers and the related documents for resubmission.