Package: branchingprocess 0.2.0

Damon Toth

branchingprocess: Calculate Outbreak Probabilities for a Branching Process Model

Quantify outbreak risk posed by individual importers of a transmissible pathogen. Input parameters of negative binomial offspring distributions for the number of transmissions from each infected individual and initial number of infected. Calculate probabilities of final outbreak size and generations of transmission, as described in Toth et al. (2015) <doi:10.3201/eid2108.150170> and Toth et al. (2016) <doi:10.1016/j.epidem.2016.04.002>.

Authors:Damon Toth [aut, cre], Erin Clancey [ctb], Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics [fnd]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
branchingprocess/json (API)

# Install 'branchingprocess' in R:

install.packages('branchingprocess', repos = c('https://epiforesite.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiforesite/branchingprocess/issues

Pkgdown/docs site:https://epiforesite.github.io

On CRAN:

4.18 score 4 scripts 373 downloads 13 exports 0 dependencies

Last updated from:9a2147b8e3. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	101
source / vignettes	OK	175
linux-release	OK	105
macos-release	OK	105
macos-oldrel	OK	87
windows-devel	OK	64
windows-release	OK	63
windows-oldrel	OK	57
wasm-release	OK	83

Exports:pExtinct pFinalSize pFinalSizeAndGen pFinalSizeAndGenSwitch1 pFinalSizeAndGenSwitch2 pFinalSizeSwitch1 pFinalSizeSwitch2 pGen pGenSwitch1 pGenSwitch2 pNextGenSize pSizeAtGen pSizeAtGenSwitch1

Dependencies:

H5N1 Example

Rendered fromH5N1Example.Rmdusingknitr::rmarkdown

Last update: 2025-04-22
Started: 2024-08-06

Help page	Topics
Probability that one initial case leads to an outbreak that eventually dies out (stochastic extinction)	pExtinct
Final outbreak size probability	pFinalSize
Joint probability of outbreak final size and number of transmission generations	pFinalSizeAndGen
Joint probability of outbreak final size and number of transmission generations with offspring distribution parameters switched after generation one	pFinalSizeAndGenSwitch1
Joint probability of outbreak final size and number of transmission generations with offspring distribution parameters switched after generation two	pFinalSizeAndGenSwitch2
Probability of final outbreak size with offspring distribution parameters switched after generation one	pFinalSizeSwitch1
Probability of final outbreak size with offspring distribution parameters switched after two generations of transmission	pFinalSizeSwitch2
Probability that one initial case leads to an outbreak lasting less than g generations of transmission.	pGen
Probability that one initial case leads to an outbreak lasting less than g generations of transmission, with offspring distribution parameters switched after generation one.	pGenSwitch1
Probability that one initial case leads to an outbreak lasting less than g generations of transmission, with offspring distribution parameters switched after generation two.	pGenSwitch2
Probability of y total transmission directly from x independent infected individuals	pNextGenSize
Probability that n initial cases lead to an outbreak that lasts at least g generations of transmission AND has exactly j total cases after generation g	pSizeAtGen
Probability that n initial cases lead to an outbreak that lasts at least g generations of transmission AND has exactly j total cases after generation g, with offspring distribution parameters switched after generation one	pSizeAtGenSwitch1

Package: branchingprocess 0.2.0

branchingprocess: Calculate Outbreak Probabilities for a Branching Process Model

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