Include MLR lineage fitness by trvrb · Pull Request #1169 · nextstrain/ncov (original) (raw)
added 5 commits
This include a script to grab live estimate of MLR lineage fitness and apply this as a tip-level coloring in the tree.
This is mostly updating the description.md files to include sentence describing the MLR fitness coloring.
The mutational fitness analysis relies on results posted to https://github.com/bkotzen/sars-cov2-modeling. However, this analysis hasn't been updated since 2024-07-22. This results in all circulating strains in the key 6m tree to have essentially identical fitness. This makes this coloring not informative and potentially misleading. If these results become updated more frequently, we should restore this analysis. In this case, we should also contact the authors to ask for a more stable GitHub URL. The current strategy of dated analyses with now "latest" tag makes automated updated difficult.
The logistic growth analysis used frequencies of strains in the tree to estimate logistic growth rates. However, analyses at nextstrain.org/sars-cov-2/forecasts use all the available sequence data and provide a more sophisticated estimate of growth rate accounting for competition between circulating viruses. These updated results are available in the mlr_lineage_fitness analysis. The mlr_lineage_fitness results should be substantially more accurate.
Small refactor of fetch_mlr_lineage_fitness script primarily to break out a main() function and to call this function from if __name__ == '__main__':
Explicitly set these entries as Python None rather than the NaN that Pandas wants to do. Then the resulting JSON gets values of null rather than NaN.
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