get_Ri: Compute case reproduction numbers (Ri) from outbreaker2...
In o2ools: Tools for 'outbreaker2'
get_Ri R Documentation
Compute case reproduction numbers (Ri) from outbreaker2 chains
Description
This function computes the number of secondary infections caused by each
individual from outbreaker2 MCMC chains. For each MCMC iteration, it counts
how many times each individual appears as an infector (alpha parameter).
Usage
get_Ri(out)
Arguments
out
An object of class outbreaker_chains
Value
A data frame where:
Each row represents an MCMC iteration
Each column represents an individual (named by their identifier)
Values represent the reproduction number (Ri) for that individual
in that iteration
Examples
out_id <- identify(out, ids = linelist$name)
Ri <- get_Ri(out_id)
str(Ri)
o2ools documentation built on June 8, 2025, 10:18 a.m.
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| get_Ri | R Documentation |
Compute case reproduction numbers (Ri) from outbreaker2 chains
Description
This function computes the number of secondary infections caused by each individual from outbreaker2 MCMC chains. For each MCMC iteration, it counts how many times each individual appears as an infector (alpha parameter).
Usage
get_Ri(out)
Arguments
out |
An object of class |
Value
A data frame where:
Each row represents an MCMC iteration
Each column represents an individual (named by their identifier)
Values represent the reproduction number (Ri) for that individual in that iteration
Examples
out_id <- identify(out, ids = linelist$name)
Ri <- get_Ri(out_id)
str(Ri)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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