epiverse-trace / epiverse-trace/howto
add: how to estimate the proportion of cases that generate 50% of transmission?
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enhancement
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- 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.
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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