epiverse-trace / epiverse-trace/howto

add: how to estimate the probability of a large outbreak?

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enhancement
Dominant language
R
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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

Open the contributing 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

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