This repo hosts work on modeling how the composition of viral lineages, such as SARS-CoV-2 Pango lineages, changes over time.
The repo has the following structure:
- a Python package
linmodfor downloading lineage count data, and fitting and evaluating models with this data; and retrospective-forecasting/, with code that uses this package to automate the retrospective evaluation of models.
To run the evaluation: cd retrospective-forecasting && uv run ./run_all.sh.
- See the online docs.
- For use of the restrospective-forecasting pipeline, see the README.
The model is provided with lightly-preprocessed data of variant sequences from humans in the USA, from Nextstrain (data dictionary). An Apache Parquet is provided, with columns date, fd_offset, division, lineage, count. Rows are uniquely identified by (date, division, lineage). date and fd_offset can be computed from each other, given the forecast date.
Note that date is the sample collection date. fd refers to the forecast date. fd_offset is date - fd measured in days. Sequences are filtered to have a collection date no later than the forecast date.
Note also the this codebase uses lineage to refer to a modeling unit (i.e., a collection of sequences treated identically by the model).
| date | fd_offset | division | lineage | count |
|---|---|---|---|---|
| 2024-05-07 | -12 | Arizona | 24A | 1 |
| 2024-05-04 | -15 | Pennsylvania | 24A | 2 |
| ... | ... | ... | ... | ... |
The model must output samples of population-level lineage proportions. An Apache Parquet should be provided, with columns fd_offset, division, lineage, sample_index, and phi (the population proportion), for fd_offset = -30, ..., 14. Rows are uniquely identified by (fd_offset, division, lineage, sample_index).
| fd_offset | division | lineage | sample_index | phi |
|---|---|---|---|---|
| -30 | Alabama | 22B | 1 | 0.000014979599 |
| -30 | Alabama | 22B | 2 | 9.945703e-7 |
| ... | ... | ... | ... | ... |
Scott Olesen ulp7@cdc.gov (CDC/CFA)
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