Infectious Disease Dynamics Group at Johns Hopkins University

COVIDScenarioPipeline

Public shared code for doing scenario forecasting and creating reports for various governmental entities.

phylosamp

The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkage and sample size calculations for phylogenetic studies.

flepiMoP

The Flexible Epidemic Modeling Pipeline

IDSpatialStats

cholera-mapping-pipeline

Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure

cholera_waves_ssd

flepimop_sample

gavi_vimc_cholera

VIMC cholera model - estimating impact of oral cholera vaccine

globaltoolboxlite

A lite version of the globaltoolbox package for easy use

grande-saline-cholera-serosurvey

Public Repository for Reanalysis of Cholera Serosurvey from Grand Saline Haiti

illumina-vc

minion-vc

Bioinformatics pipeline for Oxford Nanopore sequencing of Vibrio cholerae

rsv-forecast-hub

RSV Scenario Modeling Hub for forecasting

VOCsamplesize

cholera-burden-change-africa

Public repository linked to manuscript on changes in the burden of suspected cholera from 2011-2020 in Africa

cholera-multiplex-panel

cholera_burden_cascade

cholera_positivity

Code and Data for Cholera Positivity Review

CholeraGenomics-AfricaSE

covid_deaths_and_data

Repo for a project focused on outliers in reported data and their impact on our understanding of COVID-19 and ability to model it.

flepimop-documentation

Documentation for JHU-IDD's Flexible Epidemic Modeling Pipeline. Updated through gitbook.com. Browse it on https://iddynamics.gitbook.io/flepimop/

flepiMoP_dockerbuild

Repository containing R environment and other files needed to build a docker image for deploying flepiMoP.

flepiMoP_site

Website for the Flexible Epidemic Modeling Pipeline

nepal_hev

Public code used to map the predicted seroprevalence of hepatitis E virus across Nepal in 2021.

rsv-forecast-hub_website

RSV Forcast Hub website repo

sitakunda-hev

spatialtau

uvira_ocv_coverage_surveys

Challenges with Achieving and Maintaining High Oral Cholera Vaccine Coverage in Uvira, Democratic Republic of Congo: serial cross-sectional representative surveys

uvira_onedose_ocv_ve

One Dose Case-Control Study to Estimate kOCV VE in Uvira, DRC

Uvira_vaccination_validation_2023