Pinned Repositories
covid-dashboard-app
Interactive tool for visualizing COVID-19 intervention scenario models
covidRTPCR
Analysis of RT-PCR sensitivity by day since exposure or symptom onset
COVIDScenarioPipeline
Public shared code for doing scenario forecasting and creating reports for various governmental entities.
EpiForecastStatMech
Exploring methods for merging mechanistic and models to forecast epidemics.
flepiMoP
The Flexible Epidemic Modeling Pipeline
ForecastFramework
Create modular models. Quickly prototype models whose input includes (multiple) time series data. Create pieces of model use cases separately, and swap out particular models as desired. Create modeling competitions, data processing pipelines, and re-useable models.
hit-covid
Data and Codebook for the HIT-COVID Project
nCoV-Sandbox
ncov_incubation
Estimating the incubation time of the novel coronavirus (nCoV-2019) based on traveler data using coarse data tools
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.
Infectious Disease Dynamics Group at Johns Hopkins University's Repositories
HopkinsIDD/COVIDScenarioPipeline
Public shared code for doing scenario forecasting and creating reports for various governmental entities.
HopkinsIDD/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.
HopkinsIDD/flepiMoP
The Flexible Epidemic Modeling Pipeline
HopkinsIDD/IDSpatialStats
HopkinsIDD/rsv-forecast-hub
RSV Scenario Modeling Hub for forecasting
HopkinsIDD/cholera-mapping-pipeline
Formerly part of cholera-taxonomy. The map creation scripts, packages, and file structure
HopkinsIDD/cholera_waves_ssd
HopkinsIDD/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.
HopkinsIDD/flepimop_sample
HopkinsIDD/gavi_vimc_cholera
VIMC cholera model - estimating impact of oral cholera vaccine
HopkinsIDD/globaltoolboxlite
A lite version of the globaltoolbox package for easy use
HopkinsIDD/grande-saline-cholera-serosurvey
Public Repository for Reanalysis of Cholera Serosurvey from Grand Saline Haiti
HopkinsIDD/illumina-vc
HopkinsIDD/minion-vc
Bioinformatics pipeline for Oxford Nanopore sequencing of Vibrio cholerae
HopkinsIDD/VOCsamplesize
HopkinsIDD/cholera-burden-change-africa
Public repository linked to manuscript on changes in the burden of suspected cholera from 2011-2020 in Africa
HopkinsIDD/cholera-multiplex-panel
HopkinsIDD/cholera_burden_cascade
HopkinsIDD/cholera_positivity
Code and Data for Cholera Positivity Review
HopkinsIDD/CholeraGenomics-AfricaSE
HopkinsIDD/flepimop-documentation
Documentation for JHU-IDD's Flexible Epidemic Modeling Pipeline. Updated through gitbook.com. Browse it on https://iddynamics.gitbook.io/flepimop/
HopkinsIDD/flepiMoP_dockerbuild
Repository containing R environment and other files needed to build a docker image for deploying flepiMoP.
HopkinsIDD/flepiMoP_site
Website for the Flexible Epidemic Modeling Pipeline
HopkinsIDD/nepal_hev
Public code used to map the predicted seroprevalence of hepatitis E virus across Nepal in 2021.
HopkinsIDD/rsv-forecast-hub_website
RSV Forcast Hub website repo
HopkinsIDD/RubellaR0
Estimating the R0 for rubella from global serological data
HopkinsIDD/sitakunda-hev
HopkinsIDD/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
HopkinsIDD/uvira_onedose_ocv_ve
One Dose Case-Control Study to Estimate kOCV VE in Uvira, DRC
HopkinsIDD/Uvira_vaccination_validation_2023