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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
covid-vaccine-impact-orderly
odin.js
Compile odin models to javascriptdemogsurv
Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household surveysepihawkes
contact_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 queuecontext
β»οΈ Reproduce an environmentqueuer
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
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 drjacobycovid19_mainland_China_report
POLICI_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
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 practicalYFestimation
buildr
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