MRC Centre for Global Infectious Disease Analysis (@mrc-ide)
Guthub

mrc-ide

Twitter logo Share LinkedIn logo Share Facebook logo Share

Top repositories

1

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
star
2

odin

ᚩ A DSL for describing and solving differential equations in R
R
98
star
3

EpiEstim

A tool to estimate time varying instantaneous reproduction number during epidemics
R
94
star
4

COVID19_CFR_submission

Repository for all scripts required to replicate the CFR analysis for paper submission.
R
71
star
5

squire

SEIR transmission model of COVID-19. Documentation at:
R
50
star
6

covid19-forecasts-orderly

R
29
star
7

sircovid

C++
28
star
8

individual

R Package for individual based epidemiological models
R
27
star
9

provisionr

📦📦➡️🏛️ Provision a library of R packages
R
27
star
10

epireview

R
26
star
11

PhyDyn

PhyDyn: Epidemiological modelling in BEAST
Java
22
star
12

rrq

🏃🏃🏃 Lightweight Redis queues
R
22
star
13

skygrowth

Phylodynamic inference
R
18
star
14

mcstate

✨🧹 Monte-Carlo State Space Models
R
18
star
15

dust

✨✨✨ Iterate multiple realisations of stochastic models
C++
18
star
16

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]
R
15
star
17

dde

🕦🔜🕘 Delay differential equation solver
R
14
star
18

SIMPLEGEN

Simulating Plasmodium Epidemiological and Genetic Data
R
12
star
19

bootstrap4-collapse

Just all the css and js you need from Bootstrap4 to implement their collapse functionality.
CSS
12
star
20

ring

💍 Ring buffers
R
12
star
21

drjacoby

Flexible Markov chain monte carlo via reparameterization
R
12
star
22

didehpc

☁️💻☁️ Support for the DIDE cluster
R
10
star
23

nimue

C
9
star
24

syncr

🔃 R interface to rsync
R
9
star
25

deterministic-malaria-model

Deterministic malaria model using odin
C
9
star
26

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
9
star
27

naomi

Naomi model for subnational HIV estimation
R
9
star
28

reestimate_covidIFR_analysis

Repo for work on ICL Report 34 and subsequent Comm Med Methods Paper
R
9
star
29

spam.mpxv

Stochastic pair approximation model for Monkeypox virus
R
8
star
30

global-lmic-reports-orderly

COVID-19 forecast reports for LMICs
R
8
star
31

cinterpolate

📊➡️〰️ Interpolating functions from C, in R
R
8
star
32

malariasimulation

The malaria model
R
7
star
33

tfpscanner

Transmission fitness polymorphism scanner
R
7
star
34

eppasm

EPP Age/Sex Model (EPP-ASM)
R
6
star
35

Brazil_COVID19_distributions

This repository contains code and data for the "Inference of COVID-19 epidemiological distributions from Brazilian hospital data" manuscript
Python
6
star
36

infectiousdiseasemodels-2022

Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2022
R
6
star
37

sarscov2-transmission-england

R
6
star
38

priority-pathogens

https://mrc-ide.github.io/priority-pathogens/
R
6
star
39

first90release

R
5
star
40

orderly2

R
5
star
41

covid-vaccine-impact-orderly

R
5
star
42

odin.js

Compile odin models to javascript
R
5
star
43

demogsurv

Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household surveys
R
5
star
44

epihawkes

R
5
star
45

contact_patterns

🤝🤧 Systematic review of contact surveys relevant to transmission of respiratory pathogens 🤧🤝
R
5
star
46

welcome

👋👋👋 Get started at mrc-ide
5
star
47

helios

Simulating far UVC for pathogen control
R
5
star
48

tfpbrowser

Shiny app for tfpscanner
R
4
star
49

odin-dust-tutorial

R
4
star
50

apothecary

💊🏥👌 SEIR Model of COVID-19 Transmission for Modelling Impact of Treatments and Therapeutics 👌🏥💊
C
4
star
51

shinyq

🌟🚶🚶🚶🌟 shiny application with a queue
R
4
star
52

context

♻️ Reproduce an environment
R
4
star
53

queuer

🚶🚶🚶 Prototype general queue
R
4
star
54

RMAPI

Mapping Averaged Pairwise Information in R
C++
4
star
55

malariaModelFit

Rcpp package containing code for fitting malaria model by MCMC
C++
4
star
56

malariaEquilibrium

R
4
star
57

covfefe

Flexible simulation of P. falciparum genetic data
C++
4
star
58

conan

📦📦➡️🏛️ Conan the Librarian ⚔️
R
4
star
59

bhrp

Code for linking Bellman Harris with Renewal Processes
R
4
star
60

infectiousdiseasemodels-2019

Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases
R
4
star
61

dopri-js

🕦🔜🕘 Ordinary and delay differential equation solver
TypeScript
4
star
62

shiny_dide

🌟🏥🌟 DIDE shiny server configuration
Shell
4
star
63

PlasmoMAPI

Mapping Plasmodium Spatial Connectivity from Genetic Data
R
4
star
64

sarscov2-b.1.1.7

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)
HTML
4
star
65

typochallengedata

Analysing data collected in typo challenge
R
3
star
66

scott

Structured COalescent Transmission Tree simulation
R
3
star
67

stochasticity-practical

✨📈✨ Shiny application for stochasticity practical
R
3
star
68

sarscov2-roadmap-england

HTML
3
star
69

OmicronSeverity

Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022
R
3
star
70

esft

R
3
star
71

wodin-msc-idm-2023

R
3
star
72

MissingCases

NetLogo
3
star
73

covid_global_impact

covid_global_impact
R
3
star
74

ccmpp.tmb

Cohort component population projection and reconstruction model in TMB
R
3
star
75

COVIDCurve

Simple Inference of age-specific IFRs for COVID-19 using a Bayesian statistical model
R
3
star
76

siR

🤒 Individual-based SIR models in R and Rcpp 🤒
R
3
star
77

typochallenge

☑️📆❎ Typo challenge
R
3
star
78

odin.dust

Compile odin to dust
R
3
star
79

drjacoby_training

Holds the material (scripts, lectures etc) for the training workshop on drjacoby
R
3
star
80

covid19_mainland_China_report

HTML
3
star
81

POLICI_africa_south_america

Shiny app to show African and South American YF coverage
R
2
star
82

mint

Malaria Indicators Tool
TypeScript
2
star
83

mlesky-experiments

R
2
star
84

wodin-msc-idm-2022

R
2
star
85

drat

📦📦📦 drat repository
HTML
2
star
86

spimalot

R
2
star
87

hermione

R
2
star
88

MIPanalyzer

Filtering and analysis of MIP data
R
2
star
89

YFburden

R
2
star
90

global-lmic-reports-staging

Daily updated LMIC COVID-19 reports (Staging)
HTML
2
star
91

outbreakteachR

Demonstration of analysis associated to "paper outbreak" teaching practical
HTML
2
star
92

YFestimation

R
2
star
93

buildr

👷📦 Build packages on request
R
2
star
94

hint-deploy

Deployment tool for hint
Python
2
star
95

umbrella

☂️ Rainfall & Seasonality ☂️
R
2
star
96

leapfrog

Multistate population projection model for demographic estimation.
C++
2
star
97

msc-istda-2019

Introduction to Statistical Thinking and Data Analysis, MSc Epidemiology and MSc Health Data Analytics 2019
HTML
2
star
98

YellowFeverModelEstimation2019

R
2
star
99

beers

🍻 📦 Beers Interpolation and Subdivision (my first R package)
R
2
star
100

novel-data-streams

2
star