Interesting and probably unwanted behaviour for `strain_interaction_to_cross_immunity`
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 13
- Forks
- 3
- Avg merge
- 19h 43m
- Merged PRs (30d)
- 1
Description
The utils function to convert strain interaction to cross immunity can produce some counterintuitive cross immunity matrix.
import numpy as np
from utils import strain_interaction_to_cross_immunity
interact = np.array([[0.6, 1.0], [0.3, 1.0]])
strain_interaction_to_cross_immunity(2, interact)
# Array([[0. , 0.6, 1. , 0.6],
# [0. , 0.3, 1. , 1. ]], dtype=float32)
So in this case, if we say that the "interaction" for:
- challenging strain 1 to a strain 1 infected is 0.6, and
- challenging strain 1 to strain 2 infected is 1.0
A person who is infected by strain 2 only has cross immunity of 1.0 towards challenging strain 1, but if they are infected by both strain 1 & 2, their cross immunity drops to 0.6 towards challenging strain 1.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating utils.strain_interaction_to_cross_immunity and reproducing the matrix from the issue. Review nearby tests or usage to determine the intended behavior for combined infections; done should include an agreed specification and regression coverage for the interaction cases.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100