epiparameter - Classes and Helper Functions for Working with Epidemiological Parameters

Classes and helper functions for loading, extracting, converting, manipulating, plotting and aggregating epidemiological parameters for infectious diseases. Epidemiological parameters extracted from the literature are loaded from the 'epiparameterDB' R package.

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data-accessdata-packageepidemiologyepiverseprobability-distribution

9.67 score 37 stars 1 dependents 168 scripts 290 downloads

simulist - Simulate Disease Outbreak Line List and Contacts Data

Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age-structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.

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epidemiologyepiverselinelistoutbreaks

7.69 score 11 stars 46 scripts 192 downloads

superspreading - Understand Individual-Level Variation in Infectious Disease Transmission

Estimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions (Kremer et al. (2021) <doi:10.1038/s41598-021-93578-x>), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct (Kucharski et al. (2020) <doi:10.1016/S1473-3099(20)30144-4>), or the cluster size statistics, e.g. what proportion of cases cause X\% of transmission (Lloyd-Smith et al. (2005) <doi:10.1038/nature04153>).

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disease-transmissionepidemiologyepiverse

7.17 score 5 stars 30 scripts 222 downloads

DAISIEprep - Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them.

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data-scienceisland-biogeographyphylogenetics

6.36 score 6 stars 32 scripts 220 downloads

epiparameterDB - Database of Epidemiological Parameters

A data package containing a database of epidemiological parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature.

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data-packageepidemiologyepiverse

6.10 score 3 stars 2 dependents 5 scripts 310 downloads