Discover mrc-ide/umbrella Open Source project

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Language
R
License
MIT License
Created over 4 years ago
Updated over 1 year ago

mrc-ide

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☂️ Rainfall & Seasonality ☂️

covid-sim

This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London.

C++

1,233

odin

ᚩ A DSL for describing and solving differential equations in R

EpiEstim

A tool to estimate time varying instantaneous reproduction number during epidemics

COVID19_CFR_submission

Repository for all scripts required to replicate the CFR analysis for paper submission.

squire

SEIR transmission model of COVID-19. Documentation at:

covid19-forecasts-orderly

sircovid

C++

individual

R Package for individual based epidemiological models

provisionr

📦📦➡️🏛️ Provision a library of R packages

epireview

PhyDyn

PhyDyn: Epidemiological modelling in BEAST

Java

rrq

🏃🏃🏃 Lightweight Redis queues

skygrowth

Phylodynamic inference

mcstate

✨🧹 Monte-Carlo State Space Models

dust

✨✨✨ Iterate multiple realisations of stochastic models

C++

reactidd

This repository supports epidemiological and disease-dynamic analyses of data from the REal Time Assessment of Community Transmission (REACT) study. It includes both code and data. For code-related enquiries please contact Oliver Eales: [email protected]

dde

🕦🔜🕘 Delay differential equation solver

SIMPLEGEN

Simulating Plasmodium Epidemiological and Genetic Data

bootstrap4-collapse

Just all the css and js you need from Bootstrap4 to implement their collapse functionality.

CSS

ring

💍 Ring buffers

drjacoby

Flexible Markov chain monte carlo via reparameterization

didehpc

☁️💻☁️ Support for the DIDE cluster

nimue

syncr

🔃 R interface to rsync

deterministic-malaria-model

Deterministic malaria model using odin

global-lmic-reports

Global LMIC COVID-19 reports. Updated to include HICs. Previous data is periodically backed up at https://mrcdata.dide.ic.ac.uk/global-lmic-reports/

HTML

naomi

Naomi model for subnational HIV estimation

reestimate_covidIFR_analysis

Repo for work on ICL Report 34 and subsequent Comm Med Methods Paper

spam.mpxv

Stochastic pair approximation model for Monkeypox virus

global-lmic-reports-orderly

COVID-19 forecast reports for LMICs

cinterpolate

📊➡️〰️ Interpolating functions from C, in R

malariasimulation

The malaria model

tfpscanner

Transmission fitness polymorphism scanner

eppasm

EPP Age/Sex Model (EPP-ASM)

Brazil_COVID19_distributions

This repository contains code and data for the "Inference of COVID-19 epidemiological distributions from Brazilian hospital data" manuscript

Python

infectiousdiseasemodels-2022

Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2022

sarscov2-transmission-england

priority-pathogens

https://mrc-ide.github.io/priority-pathogens/

first90release

orderly2

covid-vaccine-impact-orderly

odin.js

Compile odin models to javascript

demogsurv

Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household surveys

epihawkes

contact_patterns

🤝🤧 Systematic review of contact surveys relevant to transmission of respiratory pathogens 🤧🤝

welcome

👋👋👋 Get started at mrc-ide

helios

Simulating far UVC for pathogen control

tfpbrowser

Shiny app for tfpscanner

odin-dust-tutorial

apothecary

💊🏥👌 SEIR Model of COVID-19 Transmission for Modelling Impact of Treatments and Therapeutics 👌🏥💊

shinyq

🌟🚶🚶🚶🌟 shiny application with a queue

context

♻️ Reproduce an environment

queuer

🚶🚶🚶 Prototype general queue

RMAPI

Mapping Averaged Pairwise Information in R

C++

malariaModelFit

Rcpp package containing code for fitting malaria model by MCMC

C++

malariaEquilibrium

covfefe

Flexible simulation of P. falciparum genetic data

C++

conan

📦📦➡️🏛️ Conan the Librarian ⚔️

bhrp

Code for linking Bellman Harris with Renewal Processes

infectiousdiseasemodels-2019

Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases

dopri-js

🕦🔜🕘 Ordinary and delay differential equation solver

TypeScript

shiny_dide

🌟🏥🌟 DIDE shiny server configuration

Shell

PlasmoMAPI

Mapping Plasmodium Spatial Connectivity from Genetic Data

sarscov2-b.1.1.7

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)

HTML

typochallengedata

Analysing data collected in typo challenge

scott

Structured COalescent Transmission Tree simulation

stochasticity-practical

✨📈✨ Shiny application for stochasticity practical

sarscov2-roadmap-england

HTML

OmicronSeverity

Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022

esft

wodin-msc-idm-2023

MissingCases

NetLogo

covid_global_impact

ccmpp.tmb

Cohort component population projection and reconstruction model in TMB

COVIDCurve

Simple Inference of age-specific IFRs for COVID-19 using a Bayesian statistical model

siR

🤒 Individual-based SIR models in R and Rcpp 🤒

typochallenge

☑️📆❎ Typo challenge

odin.dust

Compile odin to dust

drjacoby_training

Holds the material (scripts, lectures etc) for the training workshop on drjacoby

covid19_mainland_China_report

HTML

POLICI_africa_south_america

Shiny app to show African and South American YF coverage

mint

Malaria Indicators Tool

TypeScript

mlesky-experiments

wodin-msc-idm-2022

drat

📦📦📦 drat repository

HTML

spimalot

hermione

MIPanalyzer

Filtering and analysis of MIP data

YFburden

global-lmic-reports-staging

Daily updated LMIC COVID-19 reports (Staging)

HTML

outbreakteachR

Demonstration of analysis associated to "paper outbreak" teaching practical

HTML

YFestimation

buildr

👷📦 Build packages on request

hint-deploy

Deployment tool for hint

Python

leapfrog

Multistate population projection model for demographic estimation.

C++

msc-istda-2019

Introduction to Statistical Thinking and Data Analysis, MSc Epidemiology and MSc Health Data Analytics 2019

HTML

YellowFeverModelEstimation2019

beers

🍻 📦 Beers Interpolation and Subdivision (my first R package)

novel-data-streams

100

heartbeatr

💗💻💗 Redis heartbeat support

mrc-ide/umbrella

mrc-ide

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