epiverse-trace / epiverse-trace/finalsize
Add brief explaination about the matrix operations
- Dominant language
- R
- Stars
- 15
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
Description
I suggest adding a coloured box, code folding, or redirecting to an external reference for the following questions:
- Why contact matrix is transposed?
https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/finalsize.Rmd#L100
- Why largest eigenvalue in the contact matrix should be 1.0?
https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/finalsize.Rmd#L104-L107
- Is it part of a normalization procedure or it aims to resemble a probability of contact between 0-1?
- Can you explain further about the statement:
> To ensure that the overall epidemic dynamics correctly reflect the assumed value of R0
- Why divide the contact matrix with its respective age group population size?
https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/finalsize.Rmd#L109-L112
- Can you explain further about the statement:
> To reflect the assumption that each individual in group {j} make contacts at random with individuals in group {i}
- Are both operations of a preliminary process recommended for all formal analyses? Probably depends on the input format, but this reason is strong enough to create a function for this task?
Contributor guide
Research direction
Start by reading the referenced sections of vignettes/finalsize.Rmd around lines 100-112 and review the five existing comments for context. Document why the contact matrix is transposed, normalized by its largest eigenvalue, and divided by age-group population size, and clarify whether these preprocessing steps should be a reusable function or remain guidance for input-specific analyses.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100