Showing 14 of total 14 results (show query)
reconhub
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.
Maintained by Tim Taylor. Last updated 8 months ago.
58 stars 12.06 score 504 scripts 11 dependents
mrc-ide
EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Maintained by Anne Cori. Last updated 7 months ago.
95 stars 12.06 score 1.0k scripts 7 dependents
epiverse-trace
epiCo:Statistical and Viz Tools for Vector-Borne Diseases in Colombia
Provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman, M. (1999) <https://iris.paho.org/handle/10665.2/8562>).
Maintained by Juan D. Umaña. Last updated 3 months ago.
colombiadecision-supportdemographicsepiverseoutbreak-analysissdg-3spatio-temporal-analysisvector-borne-diseases
12 stars 6.94 score 8 scriptsreconhub
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>.
Maintained by Thibaut Jombart. Last updated 4 years ago.
9 stars 6.59 score 96 scriptsreconhub
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.
Maintained by Thibaut Jombart. Last updated 4 months ago.
14 stars 6.47 score 175 scripts
epiforecasts
EpiNow:Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
To identify changes in the reproduction number, rate of spread, and doubling time during the course of outbreaks whilst accounting for potential biases due to delays in case reporting.
Maintained by Sam Abbott. Last updated 5 years ago.
33 stars 4.74 score 111 scripts
oswaldogressani
EpiLPS:A Fast and Flexible Bayesian Tool for Estimating Epidemiological Parameters
Estimation of epidemiological parameters with Laplacian-P-splines following the methodology of Gressani et al. (2022) <doi:10.1371/journal.pcbi.1010618>.
Maintained by Oswaldo Gressani. Last updated 5 months ago.
19 stars 4.51 score 17 scripts
ai4ci
ggoutbreak:Estimate Incidence, Proportions and Exponential Growth Rates
Simple statistical models and visualisations for calculating the incidence, proportion, exponential growth rate, and reproduction number of infectious disease case time series. This toolkit was largely developed during the COVID-19 pandemic.
Maintained by Robert Challen. Last updated 2 months ago.
1 stars 4.30 score
epicentre-msf
epivis:Tools for visualising epidemiological data
Static visualisation of patient level linelist data.
Maintained by Paul Campbell. Last updated 5 months ago.
3 stars 4.13 score 3 scripts
maxsal
covid19india:Pulling Clean Data from Covid19india.org
Pull raw and pre-cleaned versions of national and state-level COVID-19 time-series data from covid19india.org <https://www.covid19india.org>. Easily obtain and merge case count data, testing data, and vaccine data. Also assists in calculating the time-varying effective reproduction number with sensible parameters for COVID-19.
Maintained by Max Salvatore. Last updated 3 years ago.
covid-19covid-19-datacovid-19-india
2.85 score 14 scripts
davidchampredon
ern:Effective Reproduction Number Estimation
Estimate the effective reproduction number from wastewater and clinical data sources.
Maintained by David Champredon. Last updated 2 months ago.
2.45 score 14 scriptsmrc-ide
jointlyr:Joint estimation of initial incidence and reproduction number
Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.
Maintained by Sangeeta Bhatia. Last updated 3 years ago.
2.00 score 1 scripts
mrc-ide
rincewind:Utilities for processing forecasts matrices
This package contains utility functions for processing forecasts matrices.
Maintained by Sangeeta Bhatia. Last updated 3 years ago.
1 stars 1.00 score 1 scripts