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 4 months ago

outbreak

11.97 score 58 stars 11 packages 492 scripts 1.6k downloads

epicontacts - 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 7 months ago

outbreak

8.67 score 15 stars 2 packages 108 scripts 576 downloads

epitrix - 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

8.48 score 11 stars 4 packages 227 scripts 474 downloads

aweek - 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

7.88 score 17 stars 15 packages 118 scripts 1.7k downloads

distcrete - 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

7.37 score 5 stars 7 packages 149 scripts 722 downloads

earlyR - Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

Last updated 4 years ago

6.59 score 9 stars 95 scripts 202 downloads

projections - Project Future Case Incidence

Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.

Last updated 2 years ago

6.47 score 14 stars 174 scripts 397 downloads

epiflows - 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

6.16 score 18 stars 20 scripts 274 downloads

matchmaker - 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

5.43 score 9 stars 2 packages 9 scripts 519 downloads