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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.odin
α© A DSL for describing and solving differential equations in REpiEstim
A tool to estimate time varying instantaneous reproduction number during epidemicsCOVID19_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
individual
R Package for individual based epidemiological modelsprovisionr
π¦π¦β‘οΈποΈ Provision a library of R packagesepireview
PhyDyn
PhyDyn: Epidemiological modelling in BEASTrrq
πππ Lightweight Redis queuesskygrowth
Phylodynamic inferencemcstate
β¨π§Ή Monte-Carlo State Space Modelsdust
β¨β¨β¨ Iterate multiple realisations of stochastic modelsreactidd
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
π¦ππ Delay differential equation solverSIMPLEGEN
Simulating Plasmodium Epidemiological and Genetic Databootstrap4-collapse
Just all the css and js you need from Bootstrap4 to implement their collapse functionality.ring
π Ring buffersdrjacoby
Flexible Markov chain monte carlo via reparameterizationdidehpc
βοΈπ»βοΈ Support for the DIDE clusternimue
syncr
π R interface to rsyncdeterministic-malaria-model
Deterministic malaria model using odinglobal-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/naomi
Naomi model for subnational HIV estimationreestimate_covidIFR_analysis
Repo for work on ICL Report 34 and subsequent Comm Med Methods Paperspam.mpxv
Stochastic pair approximation model for Monkeypox virusglobal-lmic-reports-orderly
COVID-19 forecast reports for LMICscinterpolate
πβ‘οΈγ°οΈ Interpolating functions from C, in Rmalariasimulation
The malaria modeltfpscanner
Transmission fitness polymorphism scannereppasm
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" manuscriptinfectiousdiseasemodels-2022
Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2022sarscov2-transmission-england
priority-pathogens
https://mrc-ide.github.io/priority-pathogens/first90release
epihawkes
covid-vaccine-impact-orderly
orderly2
odin.js
Compile odin models to javascriptdemogsurv
Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household surveyscontact_patterns
π€π€§ Systematic review of contact surveys relevant to transmission of respiratory pathogens π€§π€welcome
πππ Get started at mrc-idehelios
Simulating far UVC for pathogen controltfpbrowser
Shiny app for tfpscannerodin-dust-tutorial
apothecary
ππ₯π SEIR Model of COVID-19 Transmission for Modelling Impact of Treatments and Therapeutics ππ₯πshinyq
ππΆπΆπΆπ shiny application with a queuequeuer
πΆπΆπΆ Prototype general queueRMAPI
Mapping Averaged Pairwise Information in RmalariaModelFit
Rcpp package containing code for fitting malaria model by MCMCmalariaEquilibrium
covfefe
Flexible simulation of P. falciparum genetic dataconan
π¦π¦β‘οΈποΈ Conan the Librarian βοΈbhrp
Code for linking Bellman Harris with Renewal Processesinfectiousdiseasemodels-2019
Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseasesdopri-js
π¦ππ Ordinary and delay differential equation solvershiny_dide
ππ₯π DIDE shiny server configurationPlasmoMAPI
Mapping Plasmodium Spatial Connectivity from Genetic Datasarscov2-b.1.1.7
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)typochallengedata
Analysing data collected in typo challengescott
Structured COalescent Transmission Tree simulationstochasticity-practical
β¨πβ¨ Shiny application for stochasticity practicalsarscov2-roadmap-england
OmicronSeverity
Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022esft
wodin-msc-idm-2023
covid19_mainland_China_report
MissingCases
covid_global_impact
covid_global_impactccmpp.tmb
Cohort component population projection and reconstruction model in TMBCOVIDCurve
Simple Inference of age-specific IFRs for COVID-19 using a Bayesian statistical modelsiR
π€ Individual-based SIR models in R and Rcpp π€typochallenge
βοΈπβ Typo challengeodin.dust
Compile odin to dustdrjacoby_training
Holds the material (scripts, lectures etc) for the training workshop on drjacobyPOLICI_africa_south_america
Shiny app to show African and South American YF coveragemint
Malaria Indicators Toolmlesky-experiments
wodin-msc-idm-2022
drat
π¦π¦π¦ drat repositoryspimalot
hermione
YFestimation
MIPanalyzer
Filtering and analysis of MIP dataYFburden
global-lmic-reports-staging
Daily updated LMIC COVID-19 reports (Staging)outbreakteachR
Demonstration of analysis associated to "paper outbreak" teaching practicalbuildr
π·π¦ Build packages on requesthint-deploy
Deployment tool for hintumbrella
βοΈ Rainfall & Seasonality βοΈleapfrog
Multistate population projection model for demographic estimation.msc-istda-2019
Introduction to Statistical Thinking and Data Analysis, MSc Epidemiology and MSc Health Data Analytics 2019YellowFeverModelEstimation2019
beers
π» π¦ Beers Interpolation and Subdivision (my first R package)novel-data-streams
heartbeatr
ππ»π Redis heartbeat supportLove Open Source and this site? Check out how you can help us