Package: modelSSE 0.1-3

Shi Zhao

modelSSE: Modelling Infectious Disease Superspreading from Contact Tracing Data

Comprehensive analytical tools are provided to characterize infectious disease superspreading from contact tracing surveillance data. The underlying theoretical frameworks of this toolkit include branching process with transmission heterogeneity (Lloyd-Smith et al. (2005) <doi:10.1038/nature04153>), case cluster size distribution (Nishiura et al. (2012) <doi:10.1016/j.jtbi.2011.10.039>, Blumberg et al. (2014) <doi:10.1371/journal.ppat.1004452>, and Kucharski and Althaus (2015) <doi:10.2807/1560-7917.ES2015.20.25.21167>), and decomposition of reproduction number (Zhao et al. (2022) <doi:10.1371/journal.pcbi.1010281>).

Authors:Shi Zhao [aut, cre]

modelSSE_0.1-3.tar.gz
modelSSE_0.1-3.tar.gz(r-4.5-noble)modelSSE_0.1-3.tar.gz(r-4.4-noble)
modelSSE_0.1-3.tgz(r-4.4-emscripten)modelSSE_0.1-3.tgz(r-4.3-emscripten)
modelSSE.pdf |modelSSE.html
modelSSE/json (API)

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

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 178 downloads 19 exports 1 dependencies

Last updated 1 years agofrom:06c8e3521f. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 09 2024
R-4.5-linuxNOTEDec 09 2024

Exports:convert.epipara.to.delapparad_nextgenclusterdistnd_offspringdistnd_outbreakdistnd_reproductiondistnmostinfectiousPoveralllikelihoodp_nextgenclusterdistnp_offspringdistnp_outbreakdistnparaest.MCMCparaest.MLq_nextgenclusterdistnq_offspringdistnq_outbreakdistnr_nextgenclusterdistnr_offspringdistnr_outbreakdistntailoffspringQ

Dependencies:Delaporte

Readme and manuals

Help Manual

Help pageTopics
A dataset of COVID-19 outbreak in Hong KongCOVID19_JanApr2020_HongKong
The next-generation cluster size distributiond_nextgenclusterdistn p_nextgenclusterdistn q_nextgenclusterdistn r_nextgenclusterdistn
The offspring distributiond_offspringdistn p_offspringdistn q_offspringdistn r_offspringdistn
The final outbreak size distributiond_outbreakdistn p_outbreakdistn q_outbreakdistn r_outbreakdistn
The distribution of individual reproduction numberd_reproductiondistn
A dataset of MERS outbreaks in the Middle East regionMERS_2013_MEregion
A dataset of mpox outbreaks in DRCmpox_19801984_DRC
The likelihood functionoveralllikelihood
To estimate model parameters using Markov chain Monte Carlo approachparaest.MCMC
To estimate model parameters using maximum likelihood approachparaest.ML
A dataset of smallpox outbreaks in Europesmallpox_19581973_Europe
The "20/80" rulemostinfectiousP tailoffspringQ