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2020-cov-tracing

Combined scenarios for COVID transmission

agent-based-epidemic-sim

anderson_may

Companion to Anderson and May (1991) Infectious Diseases of Humans: Dynamics and Control.

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

aws_setup

bash_cheat_sheet

A bash cheat sheet

bu-covid

BU-COVID project

cleanr

"cleanr" package used in cleaning of PopART PC data

closing_gaps_arm_c

Closing gaps analysis for arm C communities

como

CoMo COVID-19 App repository.

como_command_line

Scripts to run the CoMo model as a basic R script and pair with various calibration approaches

como_egypt_analysis

comoodecpp

Implements CoMo Consortium's COVID-19 transmission model in Rcpp.

context_matters

Code for the manuscript "Context Matters: using reinforcement learning to develop human-readable, state-dependent outbreak response policies"

covasim

COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions

covid

Multi-layer network agent-based model of the progression of the COVID19 infection and smartphone-based contact tracing

covid-sim

covid19

Covid19 microsimulation

covid19_r_map_ew

Illustration of a map of England and Wales in R using data on R(t) from LocalCovid19Tracker

covid19model

Code for modelling estimated deaths and cases for COVID19.

covid19uk

dengue-zika-chik_americas

elicitation-1

MMODS Elicitation 1: COVID-19 reopening strategies at the county level in the face of uncertainty

fitode

general purpose ODE fitting tool in R

fmd_realtime_decisionmaking

Code for manuscript "Real-time decision-making during emergency disease outbreaks"

german-nouns

A list of ~100,000 German nouns and their grammatical properties compiled from WiktionaryDE as CSV file. Plus a module to look up the data and parse compound words.

gridsim

Gridsim C++ code for simulating disease spread

gridworld

Reinforcement learning example, solving the gridworld problem

inctools

Incidence Estimation Tools

individual-based-model-for-hiv-among-fsws-and-their-clients

Code for the paper: "HIV incidence and impact of interventions among female sex workers and their clients in the Middle East and North Africa: Mathematical modelling analysis"