HopkinsIDD/Uvira_vaccination_validation_2023

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HopkinsIDD/flepiMoP

The Flexible Epidemic Modeling Pipeline

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HopkinsIDD/flepimop-documentation

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

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HopkinsIDD/rsv-forecast-hub_website

RSV Forcast Hub website repo

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HopkinsIDD/gavi_vimc_cholera

VIMC cholera model - estimating impact of oral cholera vaccine

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HopkinsIDD/nCoV-Sandbox

Language: HTML - Size: 12.3 MB - Last synced: 26 days ago - Pushed: almost 4 years ago - Stars: 16 - Forks: 4

HopkinsIDD/COVID19_Minimal

A minimal repository that contains everything needed to run the COVIDScenarioPipeline on fake data

Language: Makefile - Size: 471 KB - Last synced: 26 days ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 7

HopkinsIDD/uscovid19vacc

COVID-19 Vaccination by age across all states in the US over time.

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HopkinsIDD/globaltoolboxlite

A lite version of the globaltoolbox package for easy use

Language: R - Size: 2.45 MB - Last synced: 26 days ago - Pushed: 6 months ago - Stars: 1 - Forks: 2

HopkinsIDD/Diphtheria Fork of shauntruelove/Diphtheria

Systematic review and reanalysis of diphtheria clinical and epidemiological aspects, including R0 and Vc.

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HopkinsIDD/covidKutupalong

Language: R - Size: 811 KB - Last synced: 26 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

HopkinsIDD/covidSeverity

Tools and estimation of severity metrics

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HopkinsIDD/globaltoolbox

Language: R - Size: 17.6 MB - Last synced: 26 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

HopkinsIDD/covidImportation

Language: R - Size: 33.1 MB - Last synced: 26 days ago - Pushed: over 3 years ago - Stars: 3 - Forks: 5

HopkinsIDD/grande-saline-cholera-serosurvey

Public Repository for Reanalysis of Cholera Serosurvey from Grand Saline Haiti

Language: Jupyter Notebook - Size: 11.2 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 1 - Forks: 0

HopkinsIDD/flepiMoP_site Fork of mmistakes/minimal-mistakes

Website for the Flexible Epidemic Modeling Pipeline

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HopkinsIDD/flepimop_sample

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HopkinsIDD/flepiMoP_dockerbuild

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

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HopkinsIDD/rsv-forecast-hub

RSV Scenario Modeling Hub for forecasting

Language: R - Size: 9.94 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 6

HopkinsIDD/COVIDScenarioPipeline

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

Language: HTML - Size: 512 MB - Last synced: 26 days ago - Pushed: about 1 year ago - Stars: 104 - Forks: 47

HopkinsIDD/MeaslesCanonicalPath

Code and data related to the paper on the canonical to elimination.

Language: R - Size: 82.3 MB - Last synced: 2 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 2

HopkinsIDD/cholera-burden-change-africa

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

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HopkinsIDD/cholera_waves_ssd

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HopkinsIDD/uvira_onedose_ocv_ve

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

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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

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HopkinsIDD/sarscov2-ifr-gva

Code for Geneva SARS-COV-2 IFR Estimates

Language: R - Size: 8.4 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 2

HopkinsIDD/serocovpop

Language: R - Size: 101 KB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 7

HopkinsIDD/mada-multidose-vax

This is the repository for "The challenge of achieving immunity through multiple-dose vaccines in Madagascar"

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HopkinsIDD/cholera-multiplex-panel

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HopkinsIDD/covid19-serodynamics

This repository will contain the dataset and code used to generate the analyses and figures for "Dynamics and significance of the antibody response to SARS-CoV-2 infection".

Language: R - Size: 1.02 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

HopkinsIDD/ncov_incubation

Estimating the incubation time of the novel coronavirus (nCoV-2019) based on traveler data using coarse data tools

Size: 231 MB - Last synced: 6 months ago - Pushed: about 4 years ago - Stars: 57 - Forks: 21

HopkinsIDD/CholeraGenomics-AfricaSE

Size: 1.23 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

HopkinsIDD/sitakunda-hev

Language: R - Size: 193 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 1

HopkinsIDD/IDSpatialStats

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HopkinsIDD/phylosamplesize

Code for Sample Size Calculation for Phylogenetic Case Linkage

Language: R - Size: 129 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

HopkinsIDD/covidRTPCR

Analysis of RT-PCR sensitivity by day since exposure or symptom onset

Language: Stan - Size: 717 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 24 - Forks: 12

HopkinsIDD/illumina-vc

Language: Shell - Size: 94.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

HopkinsIDD/Bangladesh-Cholera-Serosurvey

Code and data from 'Vibrio Cholerae O1 Transmission in Bangladesh: Insights from a Nationally-Representative Serosurvey'

Language: R - Size: 946 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 2

HopkinsIDD/haiti_ocv_JHUmodel

JHU model for examining the effects of mass OCV campaigns in Haiti

Language: R - Size: 222 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

HopkinsIDD/haiti_ocv

primary supplement materials for examining the effects of mass OCV campaigns in Haiti

Size: 5.62 MB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

HopkinsIDD/geotargeting_ocv_ssa

The impact of geographic targeting of oral cholera vaccination in sub-Saharan Africa: a modeling study

Language: R - Size: 15.6 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 0

HopkinsIDD/cholera_burden_cascade

Language: R - Size: 21.9 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

HopkinsIDD/cholera_outbreaks_ssa

Cholera outbreaks in sub-Saharan Africa during 2010-2019: A Descriptive Analysis

Language: R - Size: 29.2 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 2

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.

Language: R - Size: 2.06 MB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 12 - Forks: 2

HopkinsIDD/cholera-mapping-pipeline

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

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HopkinsIDD/ConTESSA

Contact Tracing Evaluation and Strategic Support Application

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HopkinsIDD/cholera-ORS

Source Code and Data for 'Tracking Cholera through Surveillance of Oral Rehydration Solution Sales at Pharmacies: Insights from Urban Bangladesh'

Language: R - Size: 95.7 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 2

HopkinsIDD/EpiForecastStatMech

Exploring methods for merging mechanistic and models to forecast epidemics.

Language: Python - Size: 521 KB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 7 - Forks: 4

HopkinsIDD/spatialtau

Language: R - Size: 43.9 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

HopkinsIDD/COVID19_Test 📦

Language: Python - Size: 717 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

HopkinsIDD/hit-covid

Data and Codebook for the HIT-COVID Project

Size: 66 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 20 - Forks: 7

HopkinsIDD/cholera-systems-serology

A systems serology analysis of correlates of protection against cholera

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HopkinsIDD/cholera_positivity

Code and Data for Cholera Positivity Review

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HopkinsIDD/hepE-bangladesh-national-serosurvey

Language: R - Size: 3.24 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

HopkinsIDD/VOCsamplesize

Language: R - Size: 6.97 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

HopkinsIDD/inperson-schooling-covid-survey

Language: HTML - Size: 86.2 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 2

HopkinsIDD/cholera_seasonality_ssa

Language: HTML - Size: 517 MB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 3

HopkinsIDD/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.

Language: R - Size: 464 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 11 - Forks: 4

HopkinsIDD/minion-vc

Bioinformatics pipeline for Oxford Nanopore sequencing of Vibrio cholerae

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HopkinsIDD/COVID19BurdenFDMN

Size: 1.95 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

HopkinsIDD/COVID19_nonUStemplate

Template repository for creating a non-US setup for the COVID Scenario Pipeline

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HopkinsIDD/tti

COVID19 test-trace-isolate

Language: R - Size: 352 KB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

HopkinsIDD/inperson-schooling-covid-spring-2021

In-person schooling and associated COVID-19 risk in the United States over Spring Semester 2021

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HopkinsIDD/sitakunda-sarscov2-round1

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

HopkinsIDD/juba-sars-cov-2-serosurvey

Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 IgG in Juba, South Sudan, 2020

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HopkinsIDD/bgd_cholera_greyspots

Where are the greyspots in cholera surveillance in Bangladesh?

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HopkinsIDD/hitRcovid

R package to extract hit-covid data

Language: R - Size: 16.8 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

HopkinsIDD/serocovpop-households

Code for Analyses of SARS-COV-2 household transmission in Geneva

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HopkinsIDD/spamd_public

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HopkinsIDD/COVID19_InferenceTest

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HopkinsIDD/cfepi

Code related to "Perfect Counterfactuals for Epidemic Simulations" and the cfepi package

Language: R - Size: 32.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 0

HopkinsIDD/minion-covid

MinION bioinformatics pipeline for un-targeted sequencing of SARS-CoV-2

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HopkinsIDD/COVID19_shenzhen_sero

Language: R - Size: 111 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

HopkinsIDD/leaflet

tile hosting for cholera maps

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HopkinsIDD/covid-dashboard-app

Interactive tool for visualizing COVID-19 intervention scenario models

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HopkinsIDD/covid-science-immuno

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HopkinsIDD/EventBasedEpidemicSimulation

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HopkinsIDD/cholera_burden_africa

Language: Stan - Size: 853 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

HopkinsIDD/EssentialPHServices

Supplementary materials and supporting information for https://doi.org/10.1177/0033354919890862

Size: 25.4 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

HopkinsIDD/rakaimigration

Code for Rakai Study on HIV and Migration Networks

Language: R - Size: 282 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

HopkinsIDD/HIV-Incidence

Characterizing HIV incidence trends across subsaharan Africa

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 1

HopkinsIDD/ForecastFrameworkModels

package for installing models created using ForecastFramework

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HopkinsIDD/ocv-VE-review

Data for Systematic Review and Meta-analysis of Oral Cholera Vaccine Efficacy and Effectivness

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HopkinsIDD/singledose-ocv

Source Code and Data for 'The Impact of a One- versus Two-Dose Oral Cholera Vaccine Regimen in Outbreak Settings: A Modeling Study'

Language: R - Size: 66.4 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 2 - Forks: 0

HopkinsIDD/ZikaLitReview

Data and analytic code for a literature review and pooled analysis aimed at estimating key values in the natural history of Zika virus.

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HopkinsIDD/arichpur_cholera_clustering

Language: R - Size: 14.6 KB - Last synced: 10 months ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

HopkinsIDD/taxonomy-tools

Language: R - Size: 130 KB - Last synced: about 1 year ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

HopkinsIDD/propvac Fork of scottyaz/propvac

OCV Protection and Risk Tool

Language: R - Size: 197 KB - Last synced: about 1 year ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0