Discover ecohealthalliance/awesome-parasite Open Source project

Containerised R workflow template

container-template

doltr

A client for dolt databases

HP3

Repository for Host-Pathogen Phylogeny Project. Paper DOI: 10.1038/nature22975

Tools for working with version-controlled data science workflows

relic

lemis

R package providing access to data on wildlife imports into the United States

ehastyle

R Markdown templates for EHA documents

cites

Quick access to all data in the CITES wildlife trade database

yenpathy

Yen's K Shortest Paths in R, Quickly

C++

flirt

FLIRT uses airline flight schedule data to map the commercial flight network. It shows direct flights from a selected location, and can simulate passengers taking multi-leg itineraries.

Animal outbreak data scraped from the WAHIS database

wahis

diagnostic-dashboard

GRITS uses natural language processing to extract disease-related information from text, including disease names, symptoms, dates, locations, case and death counts, and more.

Tools for working with ODK XLSForms

formstools

mpx-diagnosis

Supplement to: Enhanced surveillance of monkeypox in Bas-Uélé, Democratic Republic of Congo: the limitations of symptom-based case definitions

This code powers the models for the paper "Global hotspots and correlates of emerging zoonotic diseases".

hotspots2

parse-server-amazon-ses-email-adapter

Send parse-server template emails with Amazon SES.

PubCrawler uses the EpiTator framework (known at time of writing as Annie) to resolve toponyms in the PubMed Central Open Access Subset. It was used to create the estimate of reporting bias in the paper "Global hotspots and correlates of emerging zoonotic diseases".

pubcrawler

Jupyter Notebook

mantle

An open-source platform for biosurveillance & One Health research

EcoHealth Alliance Modeling & Analytics Handbook

eha-ma-handbook

spatialsampling

Shiny App for Spatial Sampling

amr-analysis

Global patterns and correlates in the emergence of antimicrobial resistance in humans

metaflu

Functions for Avian Influenza Metapopulation Simulation

amphibian_trade

Documenting amphibian trade into the United States

grits-api

Mobile application for taking trigger based surveys

GoodQuestion

Data and code to support: A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

sars_cov_risk

eidith

⚠️ DEPRECATED ⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr

tater

Manual annotation interface

A Jenkins API wrapper for Meteor

meteor-jenkins

wab-net-website

Data and Code to reproduce the supplementary materials of Carroll et al. 2018, "The Global Virome Project."

GVP_Science

pmcvec

Word embeddings for biomedical scientific literature

Makefile

gideon

Resources for gideon analysis

Automated workflow that triggers for all organizational actions

misc-eha-automations

odk_quality_control

Open Data Kit Data Quality Control Workflows

This project has moved to https://github.com/ecohealthalliance/EpiTator.

annie

repel-infrastructure

Scripts for loading NLP annotations into a SPARQL Database

promed-clustering

Jupyter Notebook

t11

Ruby

grits-net-consume

Materials for EcoHealthNet 2017 Workshop on Eco-Epidemiological Modeling

2017-06-16-ehn-workshop

eidith-cleaning-reports

flirt-simulation-service

bsve-integration

Presentation on Open Data Kit

opendatakit

Test for Target Version and Mermaid Rendering Issues

targets-mermaid-test

Training and evaluation scripts for the EpiTator geoname annotator

geoname-annotator-training

eha-geoname-lookup

Novel infectious Agent Monitoring App

nia-monitor

AMR emergence events data cleaning and compilation

amr-db

Workflow Automation with GitHub Actions

githubactions

CSS

disease-forecasting

predict-behav-report

Template for behavioral data analysis

flirt-consume

Data ingestion project for FLIRT

A UI for curation of geoname annotations

GeoName-Curator

repelpredict

A set of utility functions for working with the container-template-repo template

containerTemplateUtils

lqas

Lot Quality Assurance Sampling (LQAS): Theory and Application

eidr

An R-Universe for EcoHealth Alliance Packages

ecohealthalliance.r-universe.dev

grits-api-release

XLSForm: Tips, tricks, gotchas, and workarounds

xlsform

Automation code related to jenkins and docker based infrastructure

infrastructure

Shell

eh-server-workflow-run

Outlines how you can run various analytic workflows on EHA infrastructure

WABNet-spatial

Code used to produce figures in final report for WABNet project

one-health-stats

bd-econ-backup

complexsurveys

Complex Survey Sampling and Analysis

EcoHealth Realtime Analysis - dashboard for EHA application statistics

ERA

ideeal-app

Client package for accessing REPEL project data

repeldata

ehaproj-template

EIDR Connect takes the data extracted by GRITS and structures it to reconstruct disease events as they are reported across different documents.

eidr-connect