epiverse-trace / epiverse-trace/finalsize

Add brief explaination about the matrix operations

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Documentation Help wanted question
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R
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15
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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

Open the contributing 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

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