epiverse-trace / epiverse-trace/howto
add: how to estimate the probability of a large outbreak?
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Description
from @adamkucharski
``` r
# how to estimate the probability of a large outbreak?
# 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 ..
#> To retrieve the short citation use the 'get_citation' function
sars_params <- get_parameters(sars)
sars_params
#> mean dispersion
#> 1.63 0.16
# Estimate probability of large outbreak with 5 independent imported cases
probability_epidemic(
R = sars_params[["mean"]],
k = sars_params[["dispersion"]],
num_init_infect = 5
)
#> [1] 0.4722681
```
Created on 2024-01-09 with [reprex v2.0.2](https://reprex.tidyverse.org)
Contributor guide
Research direction
No file or test is named. Start by reviewing the supplied R reprex and the repository's existing how-to guides, using the shown superspreading and epiparameter calls as the entry point; done means a reproducible guide demonstrates estimating the probability of a large outbreak with imported cases.
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