• Stars
    star
    9
  • Rank 1,939,727 (Top 39 %)
  • Language
    R
  • Created over 4 years ago
  • Updated almost 3 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More 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

แšฉ 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

๐Ÿ“ฆ๐Ÿ“ฆโžก๏ธ๐Ÿ›๏ธ 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

๐Ÿƒ๐Ÿƒ๐Ÿƒ Lightweight Redis queues
R
22
star
13

skygrowth

Phylodynamic inference
R
18
star
14

mcstate

โœจ๐Ÿงน Monte-Carlo State Space Models
R
18
star
15

dust

โœจโœจโœจ 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

๐Ÿ•ฆ๐Ÿ”œ๐Ÿ•˜ 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

๐Ÿ’ Ring buffers
R
12
star
21

drjacoby

Flexible Markov chain monte carlo via reparameterization
R
12
star
22

didehpc

โ˜๏ธ๐Ÿ’ปโ˜๏ธ Support for the DIDE cluster
R
10
star
23

nimue

C
9
star
24

syncr

๐Ÿ”ƒ 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

spam.mpxv

Stochastic pair approximation model for Monkeypox virus
R
8
star
29

global-lmic-reports-orderly

COVID-19 forecast reports for LMICs
R
8
star
30

cinterpolate

๐Ÿ“Šโžก๏ธใ€ฐ๏ธ Interpolating functions from C, in R
R
8
star
31

malariasimulation

The malaria model
R
7
star
32

tfpscanner

Transmission fitness polymorphism scanner
R
7
star
33

eppasm

EPP Age/Sex Model (EPP-ASM)
R
6
star
34

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
35

infectiousdiseasemodels-2022

Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2022
R
6
star
36

sarscov2-transmission-england

R
6
star
37

priority-pathogens

https://mrc-ide.github.io/priority-pathogens/
R
6
star
38

first90release

R
5
star
39

orderly2

R
5
star
40

covid-vaccine-impact-orderly

R
5
star
41

odin.js

Compile odin models to javascript
R
5
star
42

demogsurv

Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household surveys
R
5
star
43

epihawkes

R
5
star
44

contact_patterns

๐Ÿค๐Ÿคง Systematic review of contact surveys relevant to transmission of respiratory pathogens ๐Ÿคง๐Ÿค
R
5
star
45

welcome

๐Ÿ‘‹๐Ÿ‘‹๐Ÿ‘‹ Get started at mrc-ide
5
star
46

helios

Simulating far UVC for pathogen control
R
5
star
47

tfpbrowser

Shiny app for tfpscanner
R
4
star
48

odin-dust-tutorial

R
4
star
49

apothecary

๐Ÿ’Š๐Ÿฅ๐Ÿ‘Œ SEIR Model of COVID-19 Transmission for Modelling Impact of Treatments and Therapeutics ๐Ÿ‘Œ๐Ÿฅ๐Ÿ’Š
C
4
star
50

shinyq

๐ŸŒŸ๐Ÿšถ๐Ÿšถ๐Ÿšถ๐ŸŒŸ shiny application with a queue
R
4
star
51

context

โ™ป๏ธ Reproduce an environment
R
4
star
52

queuer

๐Ÿšถ๐Ÿšถ๐Ÿšถ Prototype general queue
R
4
star
53

RMAPI

Mapping Averaged Pairwise Information in R
C++
4
star
54

malariaModelFit

Rcpp package containing code for fitting malaria model by MCMC
C++
4
star
55

malariaEquilibrium

R
4
star
56

covfefe

Flexible simulation of P. falciparum genetic data
C++
4
star
57

conan

๐Ÿ“ฆ๐Ÿ“ฆโžก๏ธ๐Ÿ›๏ธ Conan the Librarian โš”๏ธ
R
4
star
58

bhrp

Code for linking Bellman Harris with Renewal Processes
R
4
star
59

infectiousdiseasemodels-2019

Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases
R
4
star
60

dopri-js

๐Ÿ•ฆ๐Ÿ”œ๐Ÿ•˜ Ordinary and delay differential equation solver
TypeScript
4
star
61

shiny_dide

๐ŸŒŸ๐Ÿฅ๐ŸŒŸ DIDE shiny server configuration
Shell
4
star
62

PlasmoMAPI

Mapping Plasmodium Spatial Connectivity from Genetic Data
R
4
star
63

sarscov2-b.1.1.7

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)
HTML
4
star
64

typochallengedata

Analysing data collected in typo challenge
R
3
star
65

scott

Structured COalescent Transmission Tree simulation
R
3
star
66

stochasticity-practical

โœจ๐Ÿ“ˆโœจ Shiny application for stochasticity practical
R
3
star
67

sarscov2-roadmap-england

HTML
3
star
68

OmicronSeverity

Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022
R
3
star
69

esft

R
3
star
70

wodin-msc-idm-2023

R
3
star
71

MissingCases

NetLogo
3
star
72

covid_global_impact

covid_global_impact
R
3
star
73

ccmpp.tmb

Cohort component population projection and reconstruction model in TMB
R
3
star
74

COVIDCurve

Simple Inference of age-specific IFRs for COVID-19 using a Bayesian statistical model
R
3
star
75

siR

๐Ÿค’ Individual-based SIR models in R and Rcpp ๐Ÿค’
R
3
star
76

typochallenge

โ˜‘๏ธ๐Ÿ“†โŽ Typo challenge
R
3
star
77

odin.dust

Compile odin to dust
R
3
star
78

drjacoby_training

Holds the material (scripts, lectures etc) for the training workshop on drjacoby
R
3
star
79

covid19_mainland_China_report

HTML
3
star
80

POLICI_africa_south_america

Shiny app to show African and South American YF coverage
R
2
star
81

mint

Malaria Indicators Tool
TypeScript
2
star
82

mlesky-experiments

R
2
star
83

wodin-msc-idm-2022

R
2
star
84

drat

๐Ÿ“ฆ๐Ÿ“ฆ๐Ÿ“ฆ drat repository
HTML
2
star
85

spimalot

R
2
star
86

hermione

R
2
star
87

MIPanalyzer

Filtering and analysis of MIP data
R
2
star
88

YFburden

R
2
star
89

global-lmic-reports-staging

Daily updated LMIC COVID-19 reports (Staging)
HTML
2
star
90

outbreakteachR

Demonstration of analysis associated to "paper outbreak" teaching practical
HTML
2
star
91

YFestimation

R
2
star
92

buildr

๐Ÿ‘ท๐Ÿ“ฆ Build packages on request
R
2
star
93

hint-deploy

Deployment tool for hint
Python
2
star
94

umbrella

โ˜‚๏ธ Rainfall & Seasonality โ˜‚๏ธ
R
2
star
95

leapfrog

Multistate population projection model for demographic estimation.
C++
2
star
96

msc-istda-2019

Introduction to Statistical Thinking and Data Analysis, MSc Epidemiology and MSc Health Data Analytics 2019
HTML
2
star
97

YellowFeverModelEstimation2019

R
2
star
98

beers

๐Ÿป ๐Ÿ“ฆ Beers Interpolation and Subdivision (my first R package)
R
2
star
99

novel-data-streams

2
star
100

heartbeatr

๐Ÿ’—๐Ÿ’ป๐Ÿ’— Redis heartbeat support
R
2
star