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
9.69 score 37 stars 1 dependents 178 scripts 456 downloads
ringbp - Simulate and Evaluate Targeted Interventions in Infectious Disease Outbreaks
Branching process simulation model of infectious disease transmission with flexible parameterisation of epidemiology and targeted interventions, including isolation, contact tracing and quarantine, to reduce transmission, together with functions to evaluate outbreak control. Introduced in Hellewell et al. (2020) <doi:10.1016/S2214-109X(20)30074-7>.
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controlling-outbreakstransmission
7.94 score 18 stars 24 scripts 351 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
7.67 score 11 stars 44 scripts 343 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
7.21 score 5 stars 33 scripts 335 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
6.43 score 6 stars 37 scripts 300 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 431 downloads