Epidemiology - CRAN Task View

adegenet

Exploratory Analysis of Genetic and Genomic Data

Version 2.1.10

AMR

Antimicrobial Resistance Data Analysis

Version 2.1.1

argo

Accurate Estimation of Influenza Epidemics using Google Search Data

Version 3.0.2

Bernadette

Bayesian Inference and Model Selection for Stochastic Epidemics

Version 1.1.5

bets.covid19

The BETS Model for Early Epidemic Data

Version 1.0.0

bkmr

Bayesian Kernel Machine Regression

Version 0.2.2

coarseDataTools

Analysis of Coarsely Observed Data

Version 0.6-6

colmozzie

Dengue Cases and Climate Variables in Colombo Sri Lanka

Version 1.1.1

corona

Coronavirus ('Rona') Data Exploration

Version 0.3.0

COVID19

R Interface to COVID-19 Data Hub

Version 3.0.3

covid19italy

The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset

Version 0.3.1

covid19sf

The Covid19 San Francisco Dataset

Version 0.1.2

deSolve

Solvers for Initial Value Problems of Differential Equations ('ODE', '...

Version 1.40

DSAIDE

Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology...

Version 0.9.6

earlyR

Estimation of Transmissibility in the Early Stages of a Disease Outbre...

Version 0.0.5

endtoend

Transmissions and Receptions in an End to End Network

Version 2.29

epibasix

Elementary Epidemiological Functions for Epidemiology and Biostatistic...

Version 1.5

epicasting

Ewnet: An Ensemble Wavelet Neural Network for Forecasting and Epicasti...

Version 0.1.0

epiCleanr

A Tidy Solution for Epidemiological Data

Version 0.2.0

epicontacts

Handling, Visualisation and Analysis of Epidemiological Contacts

Version 1.1.4

EpiCurve

Plot an Epidemic Curve

Version 2.4-2

epiDisplay

Epidemiological Data Display Package

Version 3.5.0.2

epidm

UK Epidemiological Data Management

Version 1.0.4

EpiDynamics

Dynamic Models in Epidemiology

Version 0.3.1

EpiEstim

Estimate Time Varying Reproduction Numbers from Epidemic Curves

Version 2.2-4

epiflows

Predicting Disease Spread from Flow Data

Version 0.2.1

EpiILM

Spatial and Network Based Individual Level Models for Epidemics

Version 1.5.2

EpiILMCT

Continuous Time Distance-Based and Network-Based Individual Level Mode...

Version 1.1.7

epimdr

Functions and Data for "Epidemics: Models and Data in R"

Version 0.6-5

epimdr2

Functions and Data for "Epidemics: Models and Data in R (2nd Edition)"

Version 1.0-9

epinet

Epidemic/Network-Related Tools

Version 2.1.11

EpiReport

Epidemiological Report

Version 1.0.2

EpiSignalDetection

Signal Detection Analysis

Version 0.1.2

EpiStats

Tools for Epidemiologists

Version 1.6-2

epitab

Flexible Contingency Tables for Epidemiology

Version 0.2.2

epitools

Epidemiology Tools

Version 0.5-10.1

epitrix

Small Helpers and Tricks for Epidemics Analysis

Version 0.4.0

epitweetr

Early Detection of Public Health Threats from 'Twitter' Data

Version 2.2.16

etm

Empirical Transition Matrix

Version 1.1.1

pomp

Statistical Inference for Partially Observed Markov Processes

Version 5.11

inctools

Incidence Estimation Tools

Version 1.0.15

o2geosocial

Reconstruction of Transmission Chains from Surveillance Data

Version 1.1.3

mediation

Causal Mediation Analysis

Version 4.5.0

mma

Multiple Mediation Analysis

Version 10.7-1

modelSSE

Modelling Infectious Disease Superspreading from Contact Tracing Data

Version 0.1-3

NADA

Nondetects and Data Analysis for Environmental Data

Version 1.6-1.1

nbTransmission

Naive Bayes Transmission Analysis

Version 1.1.4

nosoi

A Forward Agent-Based Transmission Chain Simulator

Version 1.1.2

outbreaker2

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologi...

Version 1.1.3

outbreaks

A Collection of Disease Outbreak Data

Version 1.9.0

powerSurvEpi

Power and Sample Size Calculation for Survival Analysis of Epidemiolog...

Version 0.1.3

SpatialEpi

Methods and Data for Spatial Epidemiology

Version 1.2.8

socialmixr

Social Mixing Matrices for Infectious Disease Modelling

Version 0.4.0

R0

Estimation of R0 and Real-Time Reproduction Number from Epidemics

Version 1.3-1

trendeval

Evaluate Trending Models

Version 0.1.0

trending

Model Temporal Trends

Version 0.1.0

riskCommunicator

G-Computation to Estimate Interpretable Epidemiological Effects

Version 1.0.1

TransPhylo

Inference of Transmission Tree from a Dated Phylogeny

Version 1.4.5

tsiR

An Implementation of the TSIR Model

Version 0.4.3

shinySIR

Interactive Plotting for Mathematical Models of Infectious Disease Spr...

Version 0.1.2

RSurveillance

Design and Analysis of Disease Surveillance Activities

Version 0.2.1

finalsize

Calculate the Final Size of an Epidemic

Version 0.2.1

epikit

Miscellaneous Helper Tools for Epidemiologists

Version 0.1.6

covid19br

Brazilian COVID-19 Pandemic Data

Version 0.1.8

HIMA

High-Dimensional Mediation Analysis

Version 2.3.0

apisensr

Interface to 'episensr' for Sensitivity Analysis of Epidemiological Re...

Version 1.0.0

episensr

Basic Sensitivity Analysis of Epidemiological Results

Version 1.3.0

denguedatahub

A Tidy Format Datasets of Dengue by Country

Version 2.1.1

cholera

Amend, Augment and Aid Analysis of John Snow's Cholera Map

Version 0.8.0

covid19us

Cases of COVID-19 in the United States

Version 0.1.9

covid19swiss

COVID-19 Cases in Switzerland and Principality of Liechtenstein

Version 0.1.0

CovidMutations

Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019)

Version 0.1.3

covid19dbcand

Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R For...

Version 0.1.1

covid19france

Cases of COVID-19 in France

Version 0.1.0

dbparser

Drugs Databases Parser

Version 2.0.3

Epi

Statistical Analysis in Epidemiology

Version 2.58

covid19.analytics

Load and Analyze Live Data from the COVID-19 Pandemic

Version 2.1.3.3

mem

The Moving Epidemic Method

Version 2.18

memapp

The Moving Epidemic Method Web Application

Version 2.16

coronavirus

The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset

Version 0.4.1

odin

ODE Generation and Integration

Version 1.2.6

dde

Solve Delay Differential Equations

Version 1.0.7

epidatr

Client for Delphi's 'Epidata' API

Version 1.2.0

epigrowthfit

Nonlinear Mixed Effects Models of Epidemic Growth

Version 0.15.3

cleanepi

Clean and Standardize Epidemiological Data

Version 1.0.2

linelist

Tagging and Validating Epidemiological Data

Version 1.1.4

cfr

Estimate Disease Severity and Case Ascertainment

Version 0.1.2

epiworldRShiny

A 'shiny' Wrapper of the R Package 'epiworldR'

Version 0.1-0

contactdata

Social Contact Matrices for 177 Countries

Version 1.1.0

incidence

Compute, Handle, Plot and Model Incidence of Dated Events

Version 1.7.5

cmprsk

Subdistribution Analysis of Competing Risks

Version 2.2-12

popEpi

Functions for Epidemiological Analysis using Population Data

Version 0.4.12

SimInf

A Framework for Data-Driven Stochastic Disease Spread Simulations

Version 9.8.1

EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological Parame...

Version 1.6.1

EpiContactTrace

Epidemiological Tool for Contact Tracing

Version 0.18.0

mstate

Data Preparation, Estimation and Prediction in Multi-State Models

Version 0.3.3

epiworldR

Fast Agent-Based Epi Models

Version 0.3-2

malariaAtlas

An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atl...

Version 1.6.3

EpiModel

Mathematical Modeling of Infectious Disease Dynamics

Version 2.5.0

EnvStats

Package for Environmental Statistics, Including US EPA Guidance

Version 3.0.0

surveillance

Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Pheno...

Version 1.24.1

incidence2

Compute, Handle and Plot Incidence of Dated Events

Version 2.6.0

epiR

Tools for the Analysis of Epidemiological Data

Version 2.0.78