epiverse-trace / epiverse-trace/howto

add: how to estimate the proportion of cases that generate 50% of transmission?

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enhancement
Dominant language
R
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Description

from @adamkucharski

# Get libraries
library(superspreading)
library(epiparameter)

# Load parameters
sars <- epidist_db(disease = "SARS",epi_dist = "offspring_distribution",single_epidist=T)
#> Using Lloyd-Smith J, Schreiber S, Kopp P, Getz W (2005). "Superspreading and
#> the effect of individual variation on disease emergence." _Nature_.
#> doi:10.1038/nature04153 <https://doi.org/10.1038/nature04153>.. 
#> To retrieve the short citation use the 'get_citation' function
sars_params <- get_parameters(sars)
sars_params
#>    mean dispersion 
#>      1.63       0.16 

# proportion of cases that generate 50% of transmission
proportion_transmission(
  R = sars_params[["mean"]],
  k = sars_params[["dispersion"]],
  percent_transmission=0.5,
)
#>      R    k prop_50
#> 1 1.63 0.16    4.8%

Created on 2024-01-09 with reprex v2.0.2

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Research direction

No target file is named; start by reviewing the repository's existing how-to guides and the R example in this issue, including the superspreading and epiparameter packages. Done means adding a reproducible guide that explains how to estimate the proportion of cases responsible for 50% of transmission and reproduces the shown result.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
documentation
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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