R-universe search: needs:incidence

Showing 11 of total 11 results (show query)

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.

colombia decision-support demographics epiverse outbreak-analysis sdg-3 spatio-temporal-analysis vector-borne-diseases

12 stars 6.94 score 8 scripts

reconhub

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 scripts

reconhub

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.

cpp

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.

openblas cpp openmp

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

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-19 covid-19-data covid-19-india

2.85 score 14 scripts