This directory contains figures and tables output by the PyR0 model. These outputs are aggregated to weeks, PANGO lineages, and amino acid changes.
Figures and tables are generated by first running preprocessing and inference,
then postprocessing with the following Jupyter notebooks:
mutrans.ipynb ,
mutrans_gene.ipynb ,
mutrans_prediction.ipynb ,
mutrans_backtesting.ipynb .
- Mutation table is ranked by statistical significance. The "mean" field denotes the estimated effect on log growth rate of each mutation.
- Lineage table is ranked by growth rate.
The following plots assess robustness via 2-fold crossvalidation, splitting data into Europe versus (World w/o Europe).
The aggregated model outputs in this directory were generated from data inputs including either GISAID records (https://gisaid.org), an UShER tree placement of those records (http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2), PANGO lineage classifications (https://cov-lineages.org), and case count time series from Johns-Hopkins University (https://github.com/CSSEGISandData/COVID-19). Results in this directory can alternatively be generated using GENBANK records (https://www.ncbi.nlm.nih.gov) instead of GISAID records.
We gratefully acknowledge all data contributors, i.e. the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID initiative [1,2] on which this research is based. A total of 6,466,299 submissions are included in this study. A complete list of the 6,466,299 accession numbers is available in accession_ids.txt.xz.
- GISAID Initiative and global contributors, EpiCoV(TM) human coronavirus 2019 database. GISAID (2020), (available at https://gisaid.org).
- S. Elbe, G. Buckland-Merrett, Data, disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall. 1, 33-46 (2017).
- National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2017 Apr 06]. Available from: https://www.ncbi.nlm.nih.gov