Package: epichains 0.1.0.9000

James M. Azam

epichains: Simulating and Analysing Transmission Chain Statistics Using Branching Process Models

Provides methods to simulate and analyse the size and length of branching processes with an arbitrary offspring distribution. These can be used, for example, to analyse the distribution of chain sizes or length of infectious disease outbreaks, as discussed in Farrington et al. (2003) <doi:10.1093/biostatistics/4.2.279>.

Authors:James M. Azam [aut, cre, cph], Sebastian Funk [aut], Flavio Finger [aut], Zhian N. Kamvar [ctb], Hugo Gruson [ctb, rev], Karim Mané [rev], Pratik Gupte [rev], Joshua W. Lambert [rev]

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epichains.pdf |epichains.html
epichains/json (API)
NEWS

# Install 'epichains' in R:
install.packages('epichains', repos = c('https://epiverse-trace.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/epiverse-trace/epichains/issues

Datasets:
  • covid19_sa - COVID-19 Data Repository for South Africa

On CRAN:

branching-processesepidemic-dynamicsepidemic-modellingepidemic-simulationsepidemiologyepidemiology-modelsoutbreak-simulatortransmission-chaintransmission-chain-reconstruction

6 exports 6 stars 6.46 score 2 dependencies 4 scripts

Last updated 11 days agofrom:0933849bbd. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 30 2024
R-4.5-winOKSep 30 2024
R-4.5-linuxOKSep 30 2024
R-4.4-winOKSep 30 2024
R-4.4-macOKSep 30 2024
R-4.3-winOKSep 30 2024
R-4.3-macOKSep 30 2024

Exports:dborellikelihoodrborelrgborelsimulate_chain_statssimulate_chains

Dependencies:backportscheckmate

Design Principles for {epichains}

Rendered fromdesign-principles.Rmdusingknitr::rmarkdownon Sep 30 2024.

Last update: 2024-06-21
Started: 2024-05-15

Getting started with epichains

Rendered fromepichains.Rmdusingknitr::rmarkdownon Sep 30 2024.

Last update: 2024-05-23
Started: 2023-09-02

Literature on branching process applications

Rendered frombranching_process_literature.Rmdusingknitr::rmarkdownon Sep 30 2024.

Last update: 2024-06-21
Started: 2023-09-25

Modelling disease control interventions

Rendered frominterventions.Rmdusingknitr::rmarkdownon Sep 30 2024.

Last update: 2024-07-10
Started: 2023-11-10

Projecting infectious disease incidence: a COVID-19 example

Rendered fromprojecting_incidence.Rmdusingknitr::rmarkdownon Sep 30 2024.

Last update: 2024-06-21
Started: 2023-03-06

Theoretical background for epichains

Rendered fromtheoretical_background.Rmdusingknitr::rmarkdownon Sep 30 2024.

Last update: 2024-07-10
Started: 2023-09-25