Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by mrc-ide
A curated list of projects in awesome lists by mrc-ide .
https://github.com/mrc-ide/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.
Last synced: 21 Dec 2024
https://github.com/mrc-ide/odin
ᚩ A DSL for describing and solving differential equations in R
Last synced: 01 Dec 2024
https://github.com/mrc-ide/epiestim
A tool to estimate time varying instantaneous reproduction number during epidemics
Last synced: 20 Dec 2024
https://github.com/mrc-ide/covid19_cfr_submission
Repository for all scripts required to replicate the CFR analysis for paper submission.
Last synced: 06 Nov 2024
https://github.com/mrc-ide/squire
SEIR transmission model of COVID-19. Documentation at:
Last synced: 06 Nov 2024
https://github.com/mrc-ide/individual
R Package for individual based epidemiological models
agent-based-modeling epidemiology individual-based-modelling infectious-diseases r r-package rstats
Last synced: 19 Dec 2024
https://github.com/mrc-ide/provisionr
:package::package::arrow_right::classical_building: Provision a library of R packages
Last synced: 06 Nov 2024
https://github.com/mrc-ide/rrq
:runner::runner::runner: Lightweight Redis queues
Last synced: 06 Nov 2024
https://github.com/mrc-ide/phydyn
PhyDyn: Epidemiological modelling in BEAST
Last synced: 06 Nov 2024
https://github.com/mrc-ide/mcstate
:sparkles::broom: Monte-Carlo State Space Models
Last synced: 06 Nov 2024
https://github.com/mrc-ide/dust
:sparkles::sparkles::sparkles: Iterate multiple realisations of stochastic models
Last synced: 06 Nov 2024
https://github.com/mrc-ide/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]
Last synced: 06 Nov 2024
https://github.com/mrc-ide/dde
:clock1130::soon::clock9: Delay differential equation solver
Last synced: 06 Nov 2024
https://github.com/mrc-ide/drjacoby
Flexible Markov chain monte carlo via reparameterization
Last synced: 06 Nov 2024
https://github.com/mrc-ide/simplegen
Simulating Plasmodium Epidemiological and Genetic Data
Last synced: 06 Nov 2024
https://github.com/mrc-ide/bootstrap4-collapse
Just all the css and js you need from Bootstrap4 to implement their collapse functionality.
Last synced: 06 Nov 2024
https://github.com/mrc-ide/didehpc
:cloud::computer::cloud: Support for the DIDE cluster
Last synced: 06 Nov 2024
https://github.com/mrc-ide/naomi
Naomi model for subnational HIV estimation
Last synced: 06 Nov 2024
https://github.com/mrc-ide/deterministic-malaria-model
Deterministic malaria model using odin
Last synced: 06 Nov 2024
https://github.com/mrc-ide/reestimate_covidifr_analysis
Repo for work on ICL Report 34 and subsequent Comm Med Methods Paper
Last synced: 06 Nov 2024
https://github.com/mrc-ide/cinterpolate
:bar_chart::arrow_right::wavy_dash: Interpolating functions from C, in R
Last synced: 06 Nov 2024
https://github.com/mrc-ide/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/
Last synced: 06 Nov 2024
https://github.com/mrc-ide/spam.mpxv
Stochastic pair approximation model for Monkeypox virus
Last synced: 06 Nov 2024
https://github.com/mrc-ide/global-lmic-reports-orderly
COVID-19 forecast reports for LMICs
Last synced: 06 Nov 2024
https://github.com/mrc-ide/priority-pathogens
https://mrc-ide.github.io/priority-pathogens/
Last synced: 06 Nov 2024
https://github.com/mrc-ide/infectiousdiseasemodels-2022
Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2022
Last synced: 06 Nov 2024
https://github.com/mrc-ide/brazil_covid19_distributions
This repository contains code and data for the "Inference of COVID-19 epidemiological distributions from Brazilian hospital data" manuscript
Last synced: 06 Nov 2024
https://github.com/mrc-ide/demogsurv
Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household surveys
Last synced: 06 Nov 2024
https://github.com/mrc-ide/contact_patterns
🤝🤧 Systematic review of contact surveys relevant to transmission of respiratory pathogens 🤧🤝
Last synced: 06 Nov 2024
https://github.com/mrc-ide/shinyq
:star2::walking::walking::walking::star2: shiny application with a queue
Last synced: 06 Nov 2024
https://github.com/mrc-ide/welcome
:wave::wave::wave: Get started at mrc-ide
Last synced: 06 Nov 2024
https://github.com/mrc-ide/dopri-js
:clock1130::soon::clock9: Ordinary and delay differential equation solver
Last synced: 06 Nov 2024
https://github.com/mrc-ide/covfefe
Flexible simulation of P. falciparum genetic data
Last synced: 06 Nov 2024
https://github.com/mrc-ide/infectiousdiseasemodels-2019
Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases
Last synced: 06 Nov 2024
https://github.com/mrc-ide/queuer
:walking::walking::walking: Prototype general queue
Last synced: 06 Nov 2024
https://github.com/mrc-ide/tfpscanner
Transmission fitness polymorphism scanner
Last synced: 06 Nov 2024
https://github.com/mrc-ide/plasmomapi
Mapping Plasmodium Spatial Connectivity from Genetic Data
Last synced: 06 Nov 2024
https://github.com/mrc-ide/malariamodelfit
Rcpp package containing code for fitting malaria model by MCMC
Last synced: 06 Nov 2024
https://github.com/mrc-ide/conan
:package::package::arrow_right::classical_building: Conan the Librarian :crossed_swords:
Last synced: 06 Nov 2024
https://github.com/mrc-ide/shiny_dide
:star2::hospital::star2: DIDE shiny server configuration
Last synced: 06 Nov 2024
https://github.com/mrc-ide/sarscov2-b.1.1.7
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)
bayesian-inference england epidemiology genetic-data insights paper phylodynamics sarscov2 transmission
Last synced: 06 Nov 2024
https://github.com/mrc-ide/twinkle
:star::arrow_right::sparkles::sparkles::sparkles::sparkles::dizzy: Load balanced shiny server
Last synced: 06 Nov 2024
https://github.com/mrc-ide/apothecary
💊🏥👌 SEIR Model of COVID-19 Transmission for Modelling Impact of Treatments and Therapeutics 👌🏥💊
Last synced: 06 Nov 2024
https://github.com/mrc-ide/covidcurve
Simple Inference of age-specific IFRs for COVID-19 using a Bayesian statistical model
Last synced: 06 Nov 2024
https://github.com/mrc-ide/sir
🤒 Individual-based SIR models in R and Rcpp 🤒
Last synced: 06 Nov 2024
https://github.com/mrc-ide/typochallenge
:ballot_box_with_check::calendar::negative_squared_cross_mark: Typo challenge
Last synced: 06 Nov 2024
https://github.com/mrc-ide/bhrp
Code for linking Bellman Harris with Renewal Processes
Last synced: 06 Nov 2024
https://github.com/mrc-ide/stochasticity-practical
:sparkles::chart_with_upwards_trend::sparkles: Shiny application for stochasticity practical
Last synced: 06 Nov 2024
https://github.com/mrc-ide/typochallengedata
Analysing data collected in typo challenge
Last synced: 06 Nov 2024
https://github.com/mrc-ide/ccmpp.tmb
Cohort component population projection and reconstruction model in TMB
Last synced: 06 Nov 2024
https://github.com/mrc-ide/scott
Structured COalescent Transmission Tree simulation
Last synced: 06 Nov 2024
https://github.com/mrc-ide/omicronseverity
Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022
Last synced: 06 Nov 2024
https://github.com/mrc-ide/leapfrog
Multistate population projection model for demographic estimation.
Last synced: 06 Nov 2024
https://github.com/mrc-ide/polici_africa_south_america
Shiny app to show African and South American YF coverage
Last synced: 06 Nov 2024
https://github.com/mrc-ide/buildr
:construction_worker::package: Build packages on request
Last synced: 06 Nov 2024
https://github.com/mrc-ide/squire.page
Extra functions for use with squire and nimue fits
Last synced: 06 Nov 2024
https://github.com/mrc-ide/pika
Lightweight package for estimating the optimal lag and rolling correlation by grouping variable between two time series
Last synced: 06 Nov 2024
https://github.com/mrc-ide/shiny90
Shiny tool for the first 90 HIV model (https://github.com/mrc-ide/first90)
Last synced: 06 Nov 2024
https://github.com/mrc-ide/heartbeatr
:heartpulse::computer::heartpulse: Redis heartbeat support
Last synced: 06 Nov 2024
https://github.com/mrc-ide/outbreakteachr
Demonstration of analysis associated to "paper outbreak" teaching practical
Last synced: 06 Nov 2024