incidence - Compute, Handle, Plot and Model Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 2 months ago
outbreak
58 stars 12.13 score 29 dependencies 11 dependentsepicontacts - Handling, Visualisation and Analysis of Epidemiological Contacts
A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Last updated 5 months ago
outbreak
15 stars 8.64 score 46 dependencies 2 dependentsepitrix - Small Helpers and Tricks for Epidemics Analysis
A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.
Last updated 2 years ago
epidemiology
11 stars 8.47 score 23 dependencies 4 dependentsaweek - Convert Dates to Arbitrary Week Definitions
Which day a week starts depends heavily on the either the local or professional context. This package is designed to be a lightweight solution to easily switching between week-based date definitions.
Last updated 4 years ago
date-formattingdatesepidemiologytimeseriesweek
17 stars 7.91 score 0 dependencies 14 dependentsdistcrete - Discrete Distribution Approximations
Creates discretised versions of continuous distribution functions by mapping continuous values to an underlying discrete grid, based on a (uniform) frequency of discretisation, a valid discretisation point, and an integration range. For a review of discretisation methods, see Chakraborty (2015) <doi:10.1186/s40488-015-0028-6>.
Last updated 7 years ago
5 stars 7.37 score 0 dependencies 7 dependentsepiflows - Predicting Disease Spread from Flow Data
Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) <doi:10.2807/1560-7917.ES.2017.22.28.30572>. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 1 years ago
outbreak
18 stars 6.16 score 81 dependenciesmatchmaker - Flexible Dictionary-Based Cleaning
Provides flexible dictionary-based cleaning that allows users to specify implicit and explicit missing data, regular expressions for both data and columns, and global matches, while respecting ordering of factors. This package is part of the 'RECON' (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Last updated 5 years ago
9 stars 5.43 score 12 dependencies 2 dependents