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42 search results found

Covid 19_unified Dataset ⭐ 168

Unified COVID-19 Dataset

Cholera ⭐ 138

R Package for Analyzing John Snow's 1854 Cholera Map

Pm_covid ⭐ 102

Public Available Code and Data to Reproduce Analyses in "Air pollution and COVID-19 mortality in the United States: Strengths and limitations of an ecological regression analysis."

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

Sars2pack ⭐ 56

An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources

Bayesian spatial analysis

Epinowcast ⭐ 47

Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

Data2019ncov ⭐ 38

COVID-19 Pandemic Data R Package

A framework for data-driven stochastic disease spread simulations

Report templates and helper functions for applied epidemiology

Taiwan Covid 19 ⭐ 27

Analysis and visualization of Taiwan’s COVID-19 data

Individual ⭐ 27

R Package for individual based epidemiological models

Epiparameter ⭐ 18

R package with epidemiological parameters for infectious diseases

Covid19_npi_china ⭐ 18

Code for: The effect of human mobility and control measures on the COVID-19 epidemic in China

R Outbreak Info ⭐ 16

R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.

National_causal ⭐ 15

Public Available Code to Conduct Analyses in "Evaluating the Impact of Long-term Exposure to Fine Particulate Matter on Mortality Among the Elderly."

Epidemiology ⭐ 14

CRAN Task View: Epidemiology

Ephtrackr ⭐ 14

R interface to the CDC National Public Health Tracking Network API

Epiestimapp ⭐ 14

Source code for the EpiEstim app.

Repository for the R for Epidemiology book

Epigraphdb R ⭐ 12

R package for epigraphdb

R package to estimate disease severity and under-reporting in real-time, accounting for reporting delays in epidemic time-series

Convert dates to arbitrary week definitions 📆

Estimater ⭐ 9

R package for estimation and monitoring of the effective reproduction number in a pathogen outbreak/epidemic

Basic sensitivity analysis of epidemiological results in R

Finalsize ⭐ 9

R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility

Global Late Blight Metamodelling ⭐ 9

R Scripts and supporting data for creating metamodels, as published in Ecosphere, and using them to generate global estimates of potato late blight risk based on climate data as published in Global Change Biology.

Epi.branch.sim ⭐ 8

Stochastic epidemiological branching simulation

Small Helpers and Tricks for Epidemics Analysis

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies

R package for easier interactions with the Go.Data API

An R package for epidemiological analysis using population data

Vaccineff ⭐ 6

R package with tools for estimating vaccine effectiveness and vaccine related metrics

Bcepirate ⭐ 6

Tools for Standardized Rates in Population Health Surveillance and Epidemiology

Tmleworkshop ⭐ 6

Targeted maximum likelihood estimation (TMLE) enables the integration of machine learning approaches in comparative effectiveness studies. It is a doubly robust method, making use of both the outcome model and propensity score model to generate an unbiased estimate as long as at least one of the models is correctly specified.

Methods for simulating and analysing the sizes and lengths of chains from branching process models

Freqtables ⭐ 6

Quickly make tables of descriptive statistics (i.e., counts, percentages, confidence intervals) for categorical variables. This package is designed to work in a tidyverse pipeline, and consideration has been given to get results from R to Microsoft Word ® with minimal pain.

Incidence Estimation Tools

Practical R For Epidemiologists ⭐ 5

Practical R for Epidemiologists

Epidemiology Tools ⭐ 5

A list of tools to assist with epidemiology research

An R package for importing epi data into R.

Contactdata ⭐ 5

R package with social contact data for 177 regions (Prem et al. 2017; Prem et al. 2021)

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