Repo explorer · mrc-ide · UK Public Sector GitHub Observatory

All 596 public repositories. Commits, authors and file counts come from the mirrored git history; type and team come from the GOV.UK Developer Documentation where it covers the repository. Type to filter; click a column heading to sort.

Repository	Language	Git size	Commits	Authors	Files	Status
global-lmic-reports Global LMIC COVID-19 reports. Updated to include HICs. Previous data is periodically backed up a	HTML	24.2 GB	140	5	4,641	active
covid-vaccine-impact-orderly	R	21.4 GB	79	5	2,047	active
global-lmic-meffs	R	6.5 GB	18	3	5,222	active
covid19-short-term-forecasts Short term forecasts of COVID-19 deaths in multiple countries	HTML	5.7 GB	129	5	3,804	active
nimue_global_fits	-	4.6 GB	32	1	370	active
alphavirus-panama Endemic Alphavirus in Panama	R	2.0 GB	19	3	67	active
covid-19-the-economist-global-excess-deaths-model The Economist's model to estimate excess deaths to the covid-19 pandemic	R	1.5 GB	130	6	15	active
india-ascertainment Analysis of COVID-19 mortality in India	R	1.5 GB	10	1	1,924	active
helios Simulating far UVC for pathogen control	R	1.3 GB	852	16	439	active CI
contact_patterns 🤝🤧 Systematic review of contact surveys relevant to transmission of respiratory pathogens 🤧🤝	R	1.3 GB	70	4	233	active
cepi_variant_proof_vaccine_C19	R	1.2 GB	2	1	4,858	active
ivRmectin Malaria modelling framework to assess the impact of endectocide interventions	C	852.5 MB	280	7	46	active
VIMC_malaria Imperial group malaria modelling for the Vaccine Impact Modelling Consortium	HTML	779.0 MB	157	5	57	active
HIV_EndGame_SA	C++	643.1 MB	160	4	197	active
diseaseX_modelling 🦠🌍😷Modelling the deployment of medical countermeasures against a hypothetical "Disease X" caused	R	595.1 MB	320	5	9,203	active
covid-mortality-ascertainment Research compendium for analysis of COVID-19 mortality ascertainment	R	549.5 MB	39	6	25	active
global-lmic-reports-staging Daily updated LMIC COVID-19 reports (Staging)	HTML	527.3 MB	1	1	2,192	active
covid-alternative-mortality Repository for analysis of alternative sources of COVID-19 mortality	R	515.1 MB	67	5	146	active
cepi_retrospective_analysis	R	399.8 MB	90	5	332	active
safir squire and friends individual rewrite	R	365.8 MB	528	12	219	active CI
pfhrp2_sample_submission This repository contains all code to reproduce the analysis in the associated submission: "Bayes	R	365.7 MB	12	3	222	active
MAP_raster_to_admin Repo for converting MAP ITN use (or other raster data) to admin data	R	364.6 MB	14	4	461	active
YF_VIMC_Burden_Orderly Orderly framework for running VIMC yellow fever burden calculations using the YEP package	R	361.3 MB	46	1	157	active
MINT_data_selector Data and function to quickly select data for the MINT web interface	R	349.0 MB	24	2	21	active
reestimate_covidIFR_analysis Repo for work on ICL Report 34 and subsequent Comm Med Methods Paper	R	324.1 MB	919	6	166	active
global-lmic-results Results dump from https://github.com/mrc-ide/global-lmic-reports-orderly	R	316.0 MB	29	5	487	active
naomi.resources	R	315.2 MB	115	7	221	active CI
referenced-TI Code for the referenced thermodynamic integration (TI) method of calculating model evidence	Jupyter Notebook	313.7 MB	6	2	246	active
PLOS_GPH_Assessing_YF_Outbreak_Potential Repository of data and code for paper to be published in PLOS GPH	R	292.4 MB	9	2	86	active
drjacoby_submission Scripts to carry out all analysis and reproduce tables and figures for the drjacoby manuscript s	HTML	284.8 MB	59	3	52	active
PGEforge A community-driven resource for enhancing Plasmodium genomic epidemiology analysis	JavaScript	281.6 MB	548	32	505	active CI
SA_longterm_HTS Code for reproducing results in HTS reduction paper	C++	256.0 MB	20	2	191	active
YellowFeverDynamics	C++	228.3 MB	333	2	173	active CI
leaptfrog Multistate population projection model for demographic estimation.	C++	227.2 MB	360	7	56	active CI
mcstate :sparkles::broom: Monte-Carlo State Space Models	R	221.4 MB	1,415	19	129	active CI
malariasimple	C++	215.6 MB	77	4	88	active CI
tb-elim	MATLAB	199.1 MB	450	3	304	active
foresite-orderly Orderly implementation of foresite malaria site files	R	194.1 MB	223	2	58	active
PhyDyn PhyDyn: Epidemiological modelling in BEAST	Java	193.1 MB	162	13	140	active
YEP A package for running a dynamic SEIRV model of yellow fever and inferring model parameters	R	192.2 MB	417	3	85	active CI
arbomap Web application displaying dengue indicators	TypeScript	192.0 MB	765	12	472	active CI
syria-covid-ascertainment	HTML	183.7 MB	10	2	119	active
malaria_trial_pk Bespoke MCMC for estimating pk parameters from trial data	R	172.9 MB	375	7	52	active
eppasm EPP Age/Sex Model (EPP-ASM)	R	170.1 MB	746	27	94	active CI
GRFFmap	HTML	157.9 MB	153	4	94	active
Brazil_COVID19_distributions This repository contains code and data for the "Inference of COVID-19 epidemiological distributi	Python	152.3 MB	15	3	126	active
mlesky-experiments	R	152.2 MB	37	6	29	active
global-lmic-reports-orderly COVID-19 forecast reports for LMICs	R	145.7 MB	1,117	11	90	active
malariasimulation The malaria model	R	137.3 MB	1,831	42	203	active CI docker
global_lmic_projections_esft	-	135.9 MB	9	1	580	active
apothecary 💊🏥👌 SEIR Model of COVID-19 Transmission for Modelling Impact of Treatments and Therapeutics 👌🏥💊	C	130.6 MB	181	7	516	active
tfpbrowser Shiny app for tfpscanner	R	128.3 MB	382	17	4,248	active CI
DRpower Sample size calculation and power analysis for drug- and diagnostic resistance studies	R	127.5 MB	128	3	163	active CI
priority-pathogens https://mrc-ide.github.io/priority-pathogens/	R	126.8 MB	1,937	43	300	active CI docker
mpoxseir	C++	120.5 MB	729	16	69	active CI
ZamCovid_CEPI_extended_dominance Extended dominance analysis of 100DM in Kabwe, Zambia	HTML	114.5 MB	3	2	139	active
eppasm-leapfrog EPP Age/Sex Model (EPP-ASM)	R	114.3 MB	441	13	123	active CI
covid-sim This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infec	C++	113.0 MB	2,041	54	229	active CI docker
covid_global_impact covid_global_impact	R	106.2 MB	69	5	76	active
naomi Naomi model for subnational HIV estimation	R	105.5 MB	3,020	26	337	active CI docker
hrp2malaRia pfhrp2 deletion malaria modelling	R	103.9 MB	29	4	55	active
naomi.zaf Naomi model for subnational HIV estimation -- South Africa district estimates version	R	103.0 MB	2,690	24	334	active CI docker
POLICI (PO)pulation (L)evel (I)mmunization (C)overage (I)mperial College London - Tool for visualisatio	R	101.6 MB	11	3	32	active
drat :package::package::package: drat repository	HTML	98.3 MB	392	2	313	active
YellowFeverModelEstimation2019	R	90.1 MB	141	2	42	active
POLICI_africa_south_america Shiny app to show African and South American YF coverage	R	85.9 MB	20	1	26	active
PlasmoMAPI_submission Holds scripts etc. needed to reproduce all figures and tables from the PlasmoMAPI submission.	R	82.7 MB	11	2	34	active
stateMINT malaria simulation state space emulator	Python	82.4 MB	57	5	64	active CI
mlscluster mlscluster: multilevel selection clustering algorithm	R	82.0 MB	42	2	32	active
esft	R	77.4 MB	201	6	92	active
covid_booster_strategies Codebase for the manuscript on covid booster dose strategies submitted December 2022	R	76.9 MB	14	3	200	active
threemc threeMC: Matt's Model for Male Circumcision	R	75.7 MB	1,066	8	113	active CI
COVID_SIR A repo comparing Deterministic and Stochastic SIR pipelines for fitting to data	R	72.3 MB	8	2	108	active
covid_booster_analysis_safir	R	70.9 MB	2	2	108	active
sircovid	C++	68.3 MB	4,153	33	136	active CI docker
HISTONCHO Code to support compiling, cleaning and plotting onchocerciasis intervention histories	R	66.8 MB	22	2	69	active
Dengue_TimorLeste Code to reproduce the analyses for sero-catalytic and spatial modeling of dengue force of infect	R	66.2 MB	33	3	19	active
MINTe-python	Python	58.8 MB	18	3	26	active
AMMS2022 This repository holds all of the code for the Applied Malaria Molecular Surveillance (AMMS) 2022	HTML	57.8 MB	139	9	117	active
DRpowerSite An extension of the DRpower method to allow site-specific prevalence to be estimated	R	56.4 MB	5	3	11	active
MixDiff	R	54.1 MB	477	12	74	active
grout Geo tile server	TypeScript	52.6 MB	148	3	297	active CI docker
zaf-circumcision-paper	R	49.6 MB	15	1	388	active
msvalidation Long running validation vignettes for the malariasimulation package	Dockerfile	49.4 MB	27	5	9	active CI docker
YF_WHO_risk_reports	R	48.7 MB	42	2	37	active
matchGADM	R	45.9 MB	33	3	54	active
Gina_pkpd_trials	R	45.6 MB	13	4	14	active
MMS-SD_workshop This repository holds all of the code for the Malaria Molecular Surveillance Study Design (MMS-S	HTML	43.8 MB	152	6	234	active CI
estiMINT-python	Python	43.2 MB	82	4	43	active CI
epiestims	HTML	42.5 MB	521	12	278	active
Delfino Delfino: Trajectory-Based Epidemiological Simulation	Jupyter Notebook	42.2 MB	127	10	57	active docker
global_covid_vaccine_booster_paper	R	39.1 MB	3	2	79	active
covid19_South_Korea_report Data to run the analysis of the Imperial College London Report on South Korea's response to COVI	-	38.5 MB	26	2	191	active
backsearchr	R	37.5 MB	12	1	30	active
commal Severe malarial anaemia in the community	R	37.4 MB	52	1	25	active
public-events-zombie-sim2-java	Java	37.0 MB	21	3	68	active
tfgh_retrospective_analysis Retrospective COVID vaccine impact analysis	HTML	34.7 MB	5	1	412	active
covid_vaccine_dose_analysis	R	33.4 MB	74	4	1,013	active
sarscov2-datastreams-england	R	33.0 MB	27	3	177	active
Overall-and-Serotype-Specific-Dengue-Transmission-Trends-in-Mexico-2016-2023	R	32.5 MB	52	2	27	active
csavr-mortality	R	31.9 MB	40	1	30	active
squire.page Extra functions for use with squire and nimue fits	C	31.0 MB	142	6	150	active CI
covid19-forecasts-orderly	R	30.0 MB	1,312	16	252	active
sarscov2-severity-england	R	29.9 MB	6	3	112	active
EpiEstim A tool to estimate time varying instantaneous reproduction number during epidemics	R	29.4 MB	1,170	43	158	active CI
covid19_mainland_China_report	HTML	29.3 MB	15	3	3,797	active
Brazil-arbovirus-meteo This repository accompanies the paper 'Spatiotemporal relationships between extreme weather even	R	29.1 MB	21	3	19	active
peeps 👩🏽‍🤝‍🧑🏽 Malaria model demography 👩🏾‍🤝‍🧑🏿	R	28.5 MB	67	5	33	active CI
drjacoby Flexible Markov chain monte carlo via reparameterization	R	28.1 MB	481	6	241	active CI
gonovax	R	28.1 MB	1,584	10	223	active CI
epicyst Cysticercosis modelling project	R	27.7 MB	149	6	53	active CI
cmdstanr CmdStanR: the R interface to CmdStan	R	26.2 MB	2,570	29	369	active CI
simpleepp Simplified stylized implementation of UNAIDS Estimation and Projection Package (EPP) model	R	25.2 MB	73	3	5	active
dust-bench	R	24.6 MB	50	1	81	active
EPIONCHO.IBM EPIONCHO-IBM is an individual-based dynamic transmission model for onchocerciasis.	R	24.4 MB	255	10	60	active
alphaepi Epidemiological analysis of HIV population cohort ata	R	24.1 MB	26	5	33	active
markovid Inference of durations and flows from UK hospitalisation data	R	22.6 MB	245	6	58	active CI
odin-monty-workshop-2025 Website for the Odin-Monty workshop - 24th & 25th March 2025	R	20.8 MB	135	6	58	active CI
odin-monty	R	20.7 MB	343	7	62	active CI
threemc-orderly Orderly project for mrc-ide/circumcision-coverage	R	20.7 MB	610	11	230	active
naomi1 Archive of naomi 1.x.x model	R	20.0 MB	1,025	11	203	archived docker
malaria_optimal_allocation	R	19.7 MB	6	2	34	active
weave 🧶 GPs for routine data 🧶	R	19.3 MB	193	2	67	active CI
specio :rainbow: Spectrum IO for EPP model for HIV epidemic estimates	R	18.9 MB	139	6	157	active
popim POPulation IMmunity	R	18.8 MB	282	3	77	active CI
malaria_no_more Code used to produce data for Malaria No More artwork	R	18.8 MB	88	3	31	active
hsbibm Hierarchical simulation-based inference benchmark	Python	18.7 MB	81	9	128	active CI
odin ᚩ A DSL for describing and solving differential equations in R	R	18.0 MB	1,744	18	204	active CI docker
mvw Malariaverse workshop	R	17.8 MB	64	2	204	active CI
covid19-forecasts-orderly-shiny Shiny app collating the outputs of mrc-ide/covid19-forecasts-orderly	-	17.6 MB	11	4	9	active
stochastic-deterministic-epidemics	R	16.9 MB	32	3	125	active
covid_vaccine_allocation Within-country prioritisation, global allocation, and public health impact of a vaccine against	R	16.7 MB	21	3	145	active
drjacoby_training Holds the material (scripts, lectures etc) for the training workshop on drjacoby	R	16.7 MB	9	2	27	active
msc-istda-2019 Introduction to Statistical Thinking and Data Analysis, MSc Epidemiology and MSc Health Data Ana	HTML	16.5 MB	76	8	128	active
rtss_prioritisation	R	16.3 MB	12	3	87	active
mpox-clade1-vax-analysis Repository accompanying the paper: "Epidemiological characteristics and vaccination impact scena	R	15.7 MB	13	5	166	active
hintr2 Re-implementation of hint using pkgapi	R	15.6 MB	112	2	115	archived docker
individual R Package for individual based epidemiological models	R	15.4 MB	846	16	147	active CI docker
Dengue-Epidemiology-and-Transmission-Intensity Code and data to simulate & fit dengue constant-in-time FOI catalytic model. Produces the analys	R	15.2 MB	97	1	20	active
icl-hbv_v2 Updated repository for the HBV model developed at Imperial College London	MATLAB	15.2 MB	59	5	39	active
EpiEstimApp Source code for the EpiEstim app.	R	15.1 MB	481	10	110	active CI docker
hintr.comparisons A repo to hold a test to compare hintr and its refactored hintr2	R	14.9 MB	4	1	43	active docker
icl-hbv The HBV model developed at Imperial College London	MATLAB	14.5 MB	21	4	20	active
SIMPLEGEN Simulating Plasmodium Epidemiological and Genetic Data	R	14.4 MB	295	8	251	active CI
sarscov2-b.1.1.7 Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)	HTML	14.4 MB	23	6	76	active
reactidd This repository supports epidemiological and disease-dynamic analyses of data from the REal Time	R	14.3 MB	233	13	598	active
hiv-inference-website HIV Inference Group Website	SCSS	14.0 MB	105	22	632	active
rodent Plug-and-play R package for Rt estimation using a Bayesian SIR model with explicit change points	R	13.2 MB	75	2	81	active CI
DSY_YF_outbreak_risk2 Calculations of outbreak risk for Djibouti, Somalia and Yemen.	R	13.1 MB	5	2	104	active
epireview	R	13.0 MB	1,161	38	159	active CI
squire SEIR transmission model of COVID-19. Documentation at:	R	12.9 MB	924	70	201	active CI
monty Monte Carlo Models :goat:	R	12.7 MB	1,543	9	262	active CI
demogsurv Analysis of demographic indicators from Demographic and Health Surveys (DHS) and other household	R	12.6 MB	100	5	42	active CI
pyorderly	Python	12.1 MB	464	17	144	active CI
COVIDCurve Simple Inference of age-specific IFRs for COVID-19 using a Bayesian statistical model	R	12.0 MB	408	6	87	active CI
tmb.example Example of running TMB in a docker container	R	12.0 MB	3	1	20	active docker
spatialbranchr What the Package Does (One Line, Title Case)	C++	11.8 MB	43	3	82	active CI
infectiousdiseasemodels-lusaka-2022	R	11.6 MB	16	2	77	active
dust-gpu-prototype Prototype code for CUDA version of dust	C++	11.5 MB	27	3	26	active
packit Web app for serving outpack and/or orderly2 metadata	TypeScript	11.4 MB	2,549	20	873	active CI docker
stochasticity-practical :sparkles::chart_with_upwards_trend::sparkles: Shiny application for stochasticity practical	R	11.2 MB	79	4	33	active
orderly :hospital::ambulance: Lightweight Reproducible Reporting for R	R	11.1 MB	1,306	16	252	active CI
who_covid_vacc_rfp	R	10.6 MB	9	2	100	active
ZamCovid_kabwe_manuscript Public repository for the Kabwe COVID-19 modelling manuscript.	R	10.1 MB	3	2	96	active
hipercow :cow::computer::cow:	R	9.9 MB	1,282	9	234	active CI
kuenm kuenm: An R package for detailed calibration and construction of Maxent Ecological Niche Models.	TeX	9.9 MB	264	5	141	active
malsimtutorial Course materials for malariasimulation modelling workshop on June 11	R	9.8 MB	68	8	134	active CI
leapfrog-hiv	R	9.1 MB	77	4	40	active CI
wodin odin on the web	TypeScript	8.6 MB	2,678	17	480	active CI docker
mpox-workshop-repo Wodin repo for the March 2026 mpox workshop in DRC	R	8.5 MB	79	9	172	active
child_covid19_lit_review Code and results associated with systematic literature review	HTML	8.4 MB	7	3	76	active
odin-monty-pasteur-2025 Presentation and material for odin-monty introduction to Institut Pasteur 24th September 2025	R	8.4 MB	29	2	25	active CI
threemc_example Self contained threemc example, to diagnose large memory usage.	C++	8.3 MB	37	6	15	active
naomi.utils Utility Functions For Naomi Datasets	R	8.3 MB	198	16	106	active docker
ebolasurvey Survey for expert elicitation of Ebola outbreak and cost parameters	R	8.3 MB	103	3	395	active
cowflu :cow::customs:	R	8.2 MB	298	6	64	active CI
MIPanalyzer Filtering and analysis of MIP data	R	8.2 MB	66	4	186	active CI
adcomp AD computation with Template Model Builder (TMB)	C++	8.1 MB	1,437	39	1,284	active
covid19-si-shiny	R	8.1 MB	19	4	21	active
ccmpp.tmb Cohort component population projection and reconstruction model in TMB	R	7.9 MB	75	3	40	active CI
malariasimulation_comp Sandbox for malaria model version comparison	R	7.9 MB	9	1	23	active
wodin-quito-workshop Wodin repo of the IDMAPP-LATAM workshop in Quito 2025	R	7.8 MB	57	7	172	active
dfertility	C++	7.8 MB	180	2	60	active
rminte R wrapper for minte python package	R	7.7 MB	32	1	60	active CI
r21_vacc_antibody_model	R	7.6 MB	3	2	61	active
pika Lightweight package for estimating the optimal lag and rolling correlation by grouping variable	R	7.5 MB	116	4	45	active CI
RMAPI Mapping Averaged Pairwise Information in R	C++	7.5 MB	97	6	181	archived
hint-adr-poc Proof of concept for SSO integration	Python	7.4 MB	17	3	25	active docker
scene 🎬 Malariaverse scenario builder 🎬	R	7.4 MB	59	3	36	active CI
RTSS-CE Cost-effectiveness of RTS,S vs. scale-up of existing interventions.	R	7.0 MB	200	4	94	active
deterministic-malaria-model-1 Custom seasonality input as vector	C	7.0 MB	245	18	88	active CI
gf 🌍Global🌎Fund🌏 malaria modelling	R	7.0 MB	257	30	113	active CI
mint Malaria Indicators Tool	TypeScript	6.9 MB	669	16	192	active docker
deterministic-malaria-model Deterministic malaria model using odin	C	6.9 MB	540	33	88	active CI
Africa_MMS_design Holds analysis associated with a paper attempting to put bounds on how much malaria molecular su	R	6.8 MB	2	1	50	active
conan2 :package::package::arrow_right::classical_building: Conan the Librarian :crossed_swords:	R	6.8 MB	180	5	54	archived CI
profvis Visualize R profiling data	JavaScript	6.6 MB	601	16	175	active CI
malariaverse 💫 The Malariaverse 💫	CSS	6.6 MB	33	1	47	active
Tapestry	C++	6.6 MB	177	3	417	active CI
jointlyr	C++	6.5 MB	11	4	24	active
sarscov2-transmission-england	R	6.3 MB	4	3	52	active
YF_parameter_estimates	-	6.2 MB	4	2	8	active
public-events-microbit-epidemic :computer::radio::syringe::chart_with_upwards_trend: Proximity-driven epidemic over bluetooth	Java	6.0 MB	162	3	112	active
odin2	R	6.0 MB	955	11	108	active CI
PlasmoSim A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data fr	C++	6.0 MB	75	5	128	active CI
aloe 🌿 Prototype malaria output software tool 🌿	R	5.6 MB	61	1	43	active CI
PlasmoMAPI Mapping Plasmodium Spatial Connectivity from Genetic Data	R	5.5 MB	88	3	162	active
didehpc-pkgs	R	5.4 MB	37	1	87	active
orderly-tutorial	R	5.4 MB	32	3	35	active CI
covid_efficacy	R	5.4 MB	3	1	30	active
netz 🦟🛏 all things bet net 🛏🦟	R	5.3 MB	127	8	51	active CI
virtual-ecology-workbench Toolkit for creating agent-based simulations of plankton ecosystems	Java	5.2 MB	5	1	228	active
ForesiteExplorer	R	5.2 MB	31	4	11	active
dust :sparkles::sparkles::sparkles: Iterate multiple realisations of stochastic models	C++	5.2 MB	2,427	16	280	active CI docker
hivmappr Small-area estimation of HIV prevalence, ART coverage, and HIV incidence	Stan	5.1 MB	33	2	29	active
wastewatchR Branching-process based framework to evaluate the utility of wastewater-based surveillance for e	R	5.1 MB	54	4	39	active
malariaModelFit Rcpp package containing code for fitting malaria model by MCMC	C++	5.1 MB	119	2	126	active
rtss_impact_cea_2021 🦟❌ Update of analysis from Penny et al 2015 ❌🦟	R	5.0 MB	34	1	64	active
Vo_serology	R	4.9 MB	21	2	50	active
odin-dust-tutorial	R	4.8 MB	46	4	26	active
covid19-si	R	4.8 MB	619	5	109	active
dde :clock1130::soon::clock9: Delay differential equation solver	R	4.8 MB	361	8	70	active CI
dust2	R	4.7 MB	971	12	212	active CI
geojsonio Convert many data formats to & from GeoJSON & TopoJSON	R	4.7 MB	846	19	164	active CI docker
inference-data	R	4.5 MB	143	6	108	active
auth-api An API for issuing authentication and authorization tokens	Kotlin	4.5 MB	12	2	148	active
human_tsol_FoI_modelling Project to fit catalytic models to human taenia solium age-(sero)prevalence data to estimate per	R	4.5 MB	23	1	18	active
odin-monty-hpru-2025 Presentation and material for odin-monty introduction for February 2025 HPRU meeting	R	4.4 MB	43	7	19	active CI
odin.dust Compile odin to dust	R	4.3 MB	643	17	57	active CI
cometr	R	4.3 MB	51	4	223	active CI docker
sarscov2-multiregion	R	4.2 MB	57	3	64	active
site 🌎 malariaverse 🌍 site-files 🌏	R	4.0 MB	301	13	153	active CI
emu_trainer	R	4.0 MB	6	1	12	active
wodin-shortcourse-2025 Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases	R	3.8 MB	14	4	180	active
wodin-shortcourse-2026	R	3.8 MB	1	1	189	active
STAVE Spatial-temporal aggregate variant encoding	R	3.8 MB	45	3	276	active CI
nimue	C	3.8 MB	223	20	78	active CI
hypatia Individual-based COVID transmission model	R	3.8 MB	218	9	51	active CI
anatembea AnteNatal Assessment of Temporal malaria Epidemiology using Mechanistic models, Bayesian Estimat	R	3.7 MB	169	5	62	active CI
short-course-website The short course website	PHP	3.7 MB	134	6	112	active
global_covid_vaccine_booster	R	3.6 MB	3	2	69	active
malariafit	R	3.4 MB	3	1	51	active
mint-v2 Malaria intervention tool V2	TypeScript	3.4 MB	610	4	330	active CI docker
rrq :runner::runner::runner: Lightweight Redis queues	R	3.4 MB	1,071	16	173	active CI docker
climate_norovirus_litreview	R	3.4 MB	67	1	24	active
SGP_covid19_mental_health Inequalities in Mental Health: Age-related Trends Across Pandemic Phases in Singapore	-	3.4 MB	7	2	8	active
wodin-royal-society	HTML	3.3 MB	52	4	38	active
LID_mapping_falciparum_resistance Data accompanying accepted paper	-	3.2 MB	3	1	5	active
ring :ring: Ring buffers	R	3.2 MB	284	10	74	active CI
google-form-post-cordova-plugin Cordova plugin to submit a response to a Google Form	Java	3.2 MB	43	4	16	active
covid-titre-efficacy	R	3.2 MB	6	3	20	active
umbrella ☂️ Rainfall & Seasonality ☂️	R	3.2 MB	104	5	40	active CI docker
om 🕉 optimise malaria 🕉	R	3.1 MB	66	3	41	active CI
boostr 💉 Vaccine antibody efficacy model 💉	R	3.1 MB	25	2	28	active CI
EPIONCHO-IBM-CTS	R	3.0 MB	12	4	3	active
treasure 👑 malaria commodities & unit costing 👑	R	3.0 MB	140	3	90	active CI
first90release	R	3.0 MB	165	12	115	active CI
china-exit-covid-19 Code, data, and supplemental material for the analysis of China's exit from their strict social	R	3.0 MB	8	3	86	active
spimalot	R	2.9 MB	1,998	27	153	active CI
currentsee 🌊 CE Sankey flows 💸	R	2.9 MB	128	3	72	active CI
naomi-dev	R	2.9 MB	9	3	35	active
postie ✉️ malariasimulation post processing ✉️	R	2.9 MB	67	4	52	active CI
RCodingSupport Utility package to accompany the R Coding Support module	HTML	2.9 MB	10	2	104	active
infectiousdiseasemodels-2022 Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2022	R	2.8 MB	24	5	63	active
noticeboard DIDE noticeboard website	HTML	2.8 MB	202	13	27	active CI
wodin-shortcourse-2023 Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2023	R	2.8 MB	66	6	114	active CI
outbreakteachR Demonstration of analysis associated to "paper outbreak" teaching practical	HTML	2.8 MB	33	3	52	active
comet comet	TypeScript	2.7 MB	277	8	132	active docker
autodiff_odin	R	2.7 MB	166	4	35	active
sarscov2-vaccine-delay	R	2.6 MB	3	1	75	active
conan :package::package::arrow_right::classical_building: Conan the Librarian :crossed_swords:	R	2.5 MB	172	5	54	active CI
mob	C++	2.4 MB	90	4	93	active CI
cali 🌴 Good vibes and model calibration 🌴	R	2.3 MB	91	4	40	active CI
sarscov2-roadmap-england	HTML	2.2 MB	1	1	62	active
odin-dust-plots Code to generate plots for 'Reproducible parallel inference and simulation of stochastic state s	HTML	2.1 MB	15	4	28	active
infectiousdiseasemodels-vietnam-2025 Modelling and Analysis of Serological Data Workshop, OUCRU Vietnam, Nov 2025	HTML	2.0 MB	23	2	79	active
infectiousdiseasemodels-singapore Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases	R	2.0 MB	28	2	47	active
R-for-IDM-Intro	HTML	1.9 MB	15	2	4	active
orderly.sharedfile	R	1.9 MB	26	7	26	active CI
covid-uk-mobility-report Code to plot the figures and run the statistical analysis in: Anonymised & aggregated crowd leve	R	1.9 MB	9	3	22	active
infectiousdiseasemodels-2019 Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases	R	1.9 MB	70	5	65	active
infectiousdiseasemodels-2021 Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2021	R	1.9 MB	27	6	61	active
wodin-shortcourse-2024 Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2024	R	1.8 MB	14	3	170	active
infectiousdiseasemodels-asiadenguesummit-2026 Modelling Serological Data Workshop, Asia Dengue Summit 2026, Singapore	HTML	1.8 MB	14	2	77	active
infectiousdiseasemodels-brazil Brazil 2022 short course	HTML	1.8 MB	25	4	68	active
dengue_vaccine_comparison	Stan	1.8 MB	179	3	25	active
moz.utils	R	1.7 MB	51	3	21	active CI
malawi-idm-2022	R	1.6 MB	3	1	19	active
wodin-gambia-idm-2023	R	1.6 MB	5	2	24	active
DENV_risk_maps :world_map: Global mapping of dengue transmission intensity	R	1.6 MB	2,215	3	196	active
kp-data-shiny	R	1.6 MB	19	2	10	active
mipmapper Methods for analysing MIP data.	R	1.6 MB	55	3	77	active
epireviewdb Database for {epireview}	R	1.6 MB	12	2	48	active CI
mechanistic_yf_workshop_SI Supplementary material for "Mechanistic yellow fever modelling under climate change in Brazil an	-	1.5 MB	5	2	3	active
vaccinequity_litreview	R	1.4 MB	42	3	16	active
starmeds	R	1.4 MB	23	2	9	active
twinkle :star::arrow_right::sparkles::sparkles::sparkles::sparkles::dizzy: Manage and update shiny appli	R	1.4 MB	421	5	51	active CI docker
ZamCovid	C++	1.3 MB	66	3	63	active
hipercow-py	Python	1.3 MB	488	4	82	active CI
cart 🐴 malaria cartographic information 🐴	R	1.3 MB	24	2	30	active CI
Contact_matrix_data Collated contact matrix data by country	R	1.3 MB	1	1	4	active
test-wodin-builder-config	R	1.2 MB	14	2	32	active CI
didehpc :cloud::computer::cloud: Support for the DIDE cluster	R	1.2 MB	611	13	10	archived CI
easy_map_poc Proof of concept easy map	R	1.2 MB	6	1	6	active
sircovid2	C++	1.2 MB	276	8	79	archived CI
denguetak	C++	1.2 MB	36	2	26	active
marathon	Rust	1.2 MB	45	6	33	active CI
COVID19_CFR_submission Repository for all scripts required to replicate the CFR analysis for paper submission.	R	1.1 MB	29	4	41	active
lostturnip Find your lost roots	C++	1.1 MB	24	2	28	active CI
paramap-api	TypeScript	1.1 MB	19	3	12	active CI docker
outpack-r	R	1.1 MB	609	11	107	active CI
squire_js JS interface for squire	JavaScript	1.1 MB	169	8	31	active CI docker
easymap A web app for easily visualising area data	TypeScript	1.0 MB	59	3	56	active CI
iccm Integrated Community Case Management	-	1.0 MB	135	1	1	active
massR21_serval Modelling of the SERVAL trial of R21 mass vaccination in Burkina Faso and The Gambia	R	1.0 MB	27	3	5	active
typochallenge :ballot_box_with_check::calendar::negative_squared_cross_mark: Typo challenge	R	1.0 MB	278	7	37	active
africa_LSM_impact Looking at the impact of larval source management for Ellies paper (working title) "The potentia	R	919.6 kB	3	1	16	active
ppmcmc 🦟✨⛓🎲 Plasmodium particle Markov chain chain Monte Carlo	C++	862.2 kB	17	7	26	active CI
wodin-static-demo	R	853.0 kB	6	2	11	active CI
snapalette	R	831.5 kB	28	2	52	active
skadi-chart	TypeScript	826.4 kB	571	4	36	active CI
skadi-demo	HTML	823.3 kB	4	1	29	active
safir3 A version of safir with individual infectiousness	R	812.0 kB	11	1	46	active
genecastR Estimates changes in allele prevalence under selection using time series genetic data.	R	789.5 kB	21	2	58	active CI
mintr	R	789.5 kB	696	17	75	active CI docker
tfmpe Tokenised Flow Matching for Posterior Estimation	Python	740.4 kB	125	4	74	active CI
dopri-js :clock1130::soon::clock9: Ordinary and delay differential equation solver	TypeScript	668.7 kB	167	9	36	active CI
ebolasim_public	C	657.4 kB	73	6	28	active
hindsite 🌎 site 🌍 post-processing 🌏	R	653.3 kB	39	2	84	active CI
WNV_biodiversity_EM Data and code for analysing the association between avian biodiversity and West Nile Virus circu	R	652.3 kB	1	1	20	active
odin-js	TypeScript	625.7 kB	198	6	39	active CI
packit-deploy	Python	617.5 kB	366	17	50	active CI docker
chronofix	R	612.4 kB	520	5	47	active CI
flodia 🌊🌊 Compartmental model flow diagrams in base R	R	609.3 kB	160	4	141	active CI
outpack_server Rust server for outpack	Rust	604.2 kB	428	17	79	active CI docker
naomi.extensions Core Naomi model functionality for use in web app	R	599.0 kB	9	2	30	active docker
odin.ui	R	561.2 kB	649	7	103	active docker
shiny90 Shiny tool for the first 90 HIV model (https://github.com/mrc-ide/first90)	R	560.1 kB	768	13	74	active
context :recycle: Reproduce an environment	R	546.8 kB	301	7	73	active CI
cinterpolate :bar_chart::arrow_right::wavy_dash: Interpolating functions from C, in R	C	545.8 kB	53	3	34	active CI
skygrowth Phylodynamic inference	R	532.5 kB	44	8	33	active
VAE_PopGen Inference under the lattice model in population genetics via Variational Auto-Encoders (VAEs)	Jupyter Notebook	491.5 kB	12	6	16	active
safir2 squire and friends individual rewrite rewrite	R	482.3 kB	41	3	71	active CI
mpoxRingVax	R	464.9 kB	44	1	20	active
beers :beers: :package: Beers Interpolation and Subdivision (my first R package)	R	451.6 kB	24	4	24	active CI
dust-js Dust in JavaScript	TypeScript	444.4 kB	117	8	34	active CI
mint-emulator A Neural Network Emulator to Support MINT Output Analysis	Python	443.4 kB	26	5	19	active
memprof Monitor system or process memory over time	R	417.8 kB	29	3	26	active CI
coop 🐔 COnstrained OPtimisation 🐔	R	408.6 kB	37	1	60	active CI
contents-of-care	R	406.5 kB	155	2	70	active docker
hint-generic-chart-prototypes	TypeScript	392.2 kB	21	3	34	active
mrc-ide.github.io	Python	380.9 kB	40	3	41	active
mode	C++	378.9 kB	262	7	43	active CI
dust-random-bench	C++	377.9 kB	25	2	15	active
malaria-tools New version of Malaria Tools being developed in 2018	HTML	369.7 kB	129	4	33	active
public-events-zombie-sim-android Android app to control Zombie Sim 2 remotely	Java	369.7 kB	10	2	80	active
mrc-imperial-poster-template	TeX	365.6 kB	2	1	19	active
gasworks	C++	354.3 kB	299	3	70	active CI
mpoxspam https://mrc-ide.github.io/mpoxspam/	C++	350.2 kB	203	7	48	active CI
orderly.runner Small HTTP server for running orderly reports	R	349.2 kB	345	22	68	active CI docker
Rambler	C++	346.1 kB	30	2	37	active CI
nimue_js A javascript interface to nimue (a covid vaccine model)	JavaScript	344.1 kB	77	8	40	active CI docker
qdenga_impact	R	340.0 kB	52	2	35	active
ebola_shiny Survey for expert elicitation of Ebola outbreak and cost parameters	R	333.8 kB	71	5	4	active
excalibur	R	323.6 kB	155	3	63	active CI
global_raster_tools :earth_africa: :world_map: Tools for handling shape files/rasterisation globally at 1/120 degree	Java	314.4 kB	20	1	74	active
chronofix-analysis	R	313.3 kB	213	7	22	active
hivmodels.net Static assets for hivmodel.net	CSS	312.3 kB	22	2	9	active
mics-datasets Repository of MICS survey datasets	HTML	307.2 kB	20	3	17	active
mint-emulator-api A simple flask API to interact with trained emulator models for MINT.	Python	302.1 kB	13	2	11	active
vivax Individual-based model for P. vivax malaria transmission	C++	302.1 kB	66	7	58	active docker
naomi.options	R	289.8 kB	172	12	49	active CI
covfefe Flexible simulation of P. falciparum genetic data	C++	285.7 kB	51	1	82	active
skadi	-	281.6 kB	61	2	1	active
db Rcpp error debug minimal example	C++	275.5 kB	4	2	10	active
odin.js Compile odin models to javascript	R	273.4 kB	210	7	61	archived
outpack.orderly	R	272.4 kB	166	13	35	active CI docker
shinyrob	R	270.3 kB	16	2	20	active
bootstrap4-collapse Just all the css and js you need from Bootstrap4 to implement their collapse functionality.	CSS	268.3 kB	31	3	11	active
queuer :walking::walking::walking: Prototype general queue	R	266.2 kB	166	7	41	active CI
ssa-incidence-paper	R	254.0 kB	2	1	8	active
shiny-dide :star2::hospital::star2: DIDE shiny server configuration	Shell	246.8 kB	308	26	12	active
dustgpu	Makefile	242.7 kB	139	2	13	active
public-events-herd-immunity-android_v2 V2 of Herd Immunity Android Controller	Java	242.7 kB	2	2	60	active
hermione	R	240.6 kB	37	4	53	active
siR 🤒 Individual-based SIR models in R and Rcpp 🤒	R	236.5 kB	134	1	80	active
denclim odin.dust dengue climate model compiled as package	C++	235.5 kB	15	1	14	active
GLAM	R	233.5 kB	51	3	50	active CI
hipercow-api 🐮💻🐮 Web API for supporting cluster use via hipercow	C#	232.4 kB	98	2	63	active CI
YF_climateChange	R	231.4 kB	149	2	49	active
YEPaux R package containing auxiliary functions for use with YellowFeverDynamics package.	R	230.4 kB	102	2	41	active
malariaEquilibriumVivax	R	227.3 kB	65	8	43	active
orderly_training	R	226.3 kB	25	5	19	active
us-covid19-forecasts-orderly US forecasts	R	219.1 kB	95	5	39	active
vimcmalaria helper functions for VIMC malaria workflow	R	216.1 kB	147	4	63	active
genecastR_paper Holds all code to reproduce results for the genecastR paper.	-	215.0 kB	2	2	5	active
londonMSM_tree_simulator Coalescent simulation of London MSM trees	R	210.9 kB	6	4	13	active
odin.api	R	205.8 kB	161	7	46	active CI docker
Zika_vaccine Designing clinical disease vaccine efficacy trials for Zika	R	202.8 kB	224	2	31	active
outpack	Python	189.4 kB	21	7	15	active CI
mockr Drop-in replacement for testthat::with_mock()	R	185.3 kB	249	7	47	archived CI
GLAM-test Repository for testing the {mrc-ide/GLAM} package including generation of test data, validation	R	182.3 kB	58	3	19	active
who_rfp_topic_IV	R	181.2 kB	4	2	10	active
provisionr :package::package::arrow_right::classical_building: Provision a library of R packages	R	177.2 kB	167	2	59	active
heartbeatr :heartpulse::computer::heartpulse: Redis heartbeat support	R	176.1 kB	130	6	38	active CI
tfpscanner Transmission fitness polymorphism scanner	R	174.1 kB	170	9	54	active CI
covid19-si-orderly	R	172.0 kB	94	4	152	active
shortcourse-2019	R	171.0 kB	33	3	35	active
wodin-epimodels	Shell	171.0 kB	150	10	8	active
NHP_in_brazil	R	166.9 kB	64	3	55	active
malaria_mortality_SR systematic review of RCTs on malaria mortality and all-cause mortality	R	162.8 kB	7	2	9	active
orderly.db	R	162.8 kB	99	7	38	active CI
wodin-demo-config	HTML	161.8 kB	18	5	22	active
example_site_file_project Skeleton for malaria site file work	R	154.6 kB	6	1	21	active
serialization A kotlin package for de/serializing large CSV files with variable column headers into fixed typ	Kotlin	154.6 kB	19	2	53	active
malaria-sites-orderly	R	150.5 kB	23	3	24	active
singapore_shortcourse_2022 Repo for the Singapore Shortcourse 2022	R	148.5 kB	2	1	58	active
sircovid-gpu-hack	C++	146.4 kB	65	3	51	active
wodin-shortcourse Experimental wodin-based version of the short course app	R	144.4 kB	2	1	45	active
viralload	R	139.3 kB	75	5	29	active CI
genescaper Allele frequency mapping and outlier detection	R	132.1 kB	32	3	62	active CI
kelp SeaweedFS R client	R	123.9 kB	55	3	32	active CI
public-events-herd-immunity-mainapp The main Java app for the Herd Immunity (Bouncing Ball) game	Java	119.8 kB	9	3	28	active
migrate-packit--perms-from-orderly-web	Python	113.7 kB	37	2	28	active
variantstring Defines variant string format, a convenient format for encoding multi-locus genotypes	R	110.6 kB	60	5	43	active CI
covid_vaccine_hesitancy	R	108.5 kB	2	2	11	active
decart Domestic case Estimates from Cases Among Returning Travellers - Java application	Java	102.4 kB	2	1	20	active
gonovaxdust	C++	101.4 kB	29	4	26	active CI
YFestimation	R	98.3 kB	32	2	75	active
outpack.server	R	96.3 kB	34	6	39	archived CI docker
wodin-demo Demo instance of wodin	Shell	89.1 kB	28	3	19	active
msio Samples malariasimulation inputs and calculates corresponding outputs for surrogate modelling.	R	88.1 kB	33	3	26	active CI docker
mockcpp An R package for integrating trompeloeil as a mocking framework for testthat/catch c++ tests	C++	82.9 kB	19	3	45	active CI docker
nda-examples	C++	82.9 kB	5	3	13	active
buildr :construction_worker::package: Build packages on request	R	81.9 kB	83	3	32	active
grout-deploy Deployment tool for grout	Python	79.9 kB	41	3	18	active CI
malariaEquilibrium	R	79.9 kB	27	5	27	active
pkgbuilder Binary R packages as a HTTP service	R	79.9 kB	55	2	35	active CI
spam.mpxv Stochastic pair approximation model for Monkeypox virus	R	78.8 kB	16	5	12	active
malariavaxTrials	R	76.8 kB	13	2	41	active
twinkle-cli CLI for configuring the Twinkle shiny server	Kotlin	76.8 kB	15	2	24	active CI
privilege_walk	R	75.8 kB	18	2	6	active
SriLanka_FOI This repository hosts a Shiny web application to explore dengue transmission intensity in Sri La	R	74.8 kB	8	1	6	active
public-events-zombie-sim-c The Zombie Spatial Simulator Core	C++	74.8 kB	2	1	10	active
odin-news	-	70.7 kB	12	2	10	active CI
msc-idm-2021	R	69.6 kB	36	3	38	active
mpiRC Wrapper for calling MPI functions from R	R	68.6 kB	54	2	102	active
wodin-gambia-idm-2024	R	68.6 kB	12	4	44	active
COVID19_surveillance_sensitivity	R	66.6 kB	11	3	10	active
wodin-deploy Deploy tool for wodin	Python	66.6 kB	45	3	6	active
MissingCases	NetLogo	59.4 kB	14	3	29	active
mrc-ide-vault	Shell	59.4 kB	29	4	8	active
msc-idm-2020	R	59.4 kB	22	3	36	active
weighter	R	59.4 kB	11	2	39	active
YFburden	R	58.4 kB	61	5	31	active
cloth 👖 A product of weave 👖	R	58.4 kB	20	1	9	active
wodin-msc-idm-2023	R	58.4 kB	23	3	37	active
rtss_vacc_antibody_model Implementation of the RTS,S vaccine antibody model developed by MT White (https://doi.org/10.101	R	57.3 kB	2	2	7	active
dustmpi	C++	56.3 kB	36	4	24	active CI
orderly.sharepoint	R	56.3 kB	20	4	20	active CI
epihawkes	R	55.3 kB	4	2	85	active
PGEhammer A series of utility functions that improve the experience of working with other software tools i	R	52.2 kB	48	6	51	active CI
MMSpower MMS power package	R	50.2 kB	21	1	23	active CI
mint-news News site for updates to MINT and mintr	-	50.2 kB	5	4	10	active CI
rrq.kelp SeaweedFS backed file store for rrq	R	50.2 kB	24	3	23	active CI
orderly.helper	R	49.2 kB	16	5	22	active CI
rincewind Utilities for processing forecasts, does a lot of things semi-competently	R	49.2 kB	61	3	21	active
roundtable	-	49.2 kB	26	1	4	archived
typochallengedata Analysing data collected in typo challenge	R	49.2 kB	38	7	7	active
dj11	R	48.1 kB	27	1	22	active
eigen1	R	48.1 kB	23	4	25	active CI
netdiagnostics :microscope: Net sensitivity and specificity for test combinations	R	48.1 kB	17	3	43	active
remotesave	R	48.1 kB	26	2	26	active
wodin-msc-idm-2024	R	46.1 kB	12	4	37	active
hiv-orderly-proxy	Shell	45.1 kB	29	2	11	active docker
wodin-proxy	Shell	45.1 kB	31	1	14	active docker
mrc-ide.r-universe.dev	-	44.0 kB	77	14	1	active
rmnist :one::writing_hand: R interface to the 'MNIST' collection of handwritten digits	R	44.0 kB	22	3	18	active CI
xoshiro	Makefile	44.0 kB	11	2	15	archived CI
didehpc-cmdline-tool Command-line tools wrapping MS HPC Pack for job management	C#	43.0 kB	18	1	17	active
wodin-msc-idm-2022	R	43.0 kB	19	2	31	active
ATACCC-kinetic-model-and-data ATACCC kinetic model and data	R	42.0 kB	1	1	11	active
malaria_model_onboarding	R	42.0 kB	16	2	8	active
msc-idm-2022	R	42.0 kB	5	2	38	active
dengue_dynamics_angola Containing the data and code enabling replication of the analyses carried out in the manuscript	R	41.0 kB	10	2	13	active
msc-idm-2019	R	39.9 kB	8	2	33	active
dengue_meta_analysis	R	38.9 kB	7	2	14	active
mint-deploy	Shell	36.9 kB	35	5	6	active
wodin-malawi-idm-2022	R	35.8 kB	15	2	24	active
hiv-orderly-web Orderly web configuration for hiv-orderly	Shell	33.8 kB	58	5	12	active
titanic2	-	33.8 kB	2	1	7	active
individual-test	C++	31.7 kB	16	1	18	active
odin.gsl	Makefile	31.7 kB	17	2	10	archived
broad-fungalgroup Broad Fungal Genomics group scripts	Python	30.7 kB	30	7	12	active
repatriation-covid-19 Collated data on repatriation flights from Wuhan, China, between 29th Jan - 27th Feb	-	30.7 kB	9	1	3	active
wodin-msc-idm-2025	R	30.7 kB	4	2	37	active
buildkite-reporter-test Example repo for testing testthat.buildkite reporter	Shell	29.7 kB	10	2	23	active docker
evd-2026-outbreak-size	R	29.7 kB	12	2	5	active
contact_sampling_polio_surveillance	R	28.7 kB	2	1	8	active
outpack.http	Shell	26.6 kB	4	2	22	active CI docker
2019-nCoV	-	25.6 kB	7	2	5	active
FoI_bayesian Fitting force-of-infection (models) to age-(sero)prevalence data, incorporating diagnostic uncer	R	25.6 kB	4	1	5	active
glodide Submission of Global LMIC Reports via Orderly To DIDE Cluster	R	25.6 kB	13	5	11	active
wodin-msc-idm-2026	R	25.6 kB	1	1	37	active
assessr	R	24.6 kB	27	2	22	active
syncr :arrows_clockwise: R interface to rsync	R	24.6 kB	17	2	20	active
wodin-acomvec-2023	R	24.6 kB	4	1	24	active
ckan-extrafields An extra field customisation for departmental use of CKAN 2.9.0	Python	23.6 kB	1	1	31	active
orderly3.vault	Makefile	22.5 kB	4	2	15	active CI
mrc-ide-redis	Shell	21.5 kB	1	1	5	active
nlcali	R	21.5 kB	5	2	17	active
OmicronSeverity Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022	R	19.5 kB	1	1	6	active
early-japan Repository of data used for study into the early phase of the COVID-19 epidemic in Japan	-	19.5 kB	3	2	2	active
node-20-docker A Dockerfile and script for building an image that has both node and docker installed	Shell	19.5 kB	32	7	5	active docker
YF_mcstate_example Example of yellow fever model fitting implemented using mcstate	C++	18.4 kB	3	2	9	active
deduplicater Tools for Opinionated Deduplication of Tabular Records	R	18.4 kB	3	1	14	active
demography-orderly Orderly implementation of malaria demography	R	18.4 kB	4	1	13	active
mpox-orderly-web	Shell	18.4 kB	12	1	6	active
popimconnect R package to convert between the population structures used in the YF model and in package vip	R	18.4 kB	18	2	17	active
promed-covid	R	18.4 kB	7	2	15	active
welcome :wave::wave::wave: Get started at mrc-ide	-	18.4 kB	25	3	1	active
wodin-buc-2023	R	18.4 kB	5	3	8	active
BobTestPackage Simple test package	R	17.4 kB	16	3	17	active CI
inference-data-orderly-image Docker image build for inference-data orderly	Dockerfile	17.4 kB	14	2	13	active docker
learnr_test Testing learnR tutorial with DRpower with the DIDE shiny server (Shazia, Rich and Emma)	HTML	17.4 kB	3	3	5	active
packit-config	-	17.4 kB	24	4	5	active
ascertainr	R	16.4 kB	8	2	18	active
hintr-loadbalancer	Shell	16.4 kB	21	4	12	active CI docker
udsm-imperial-2025	HTML	16.4 kB	3	1	6	active
covid19-forecasts-orderly-image	Dockerfile	15.4 kB	12	6	13	active docker
modelapi	R	15.4 kB	10	2	28	active docker
node-docker A Dockerfile and script for building an image that has both node and docker installed	Shell	15.4 kB	26	6	5	active docker
agestructuredEPICYST_analysis Analysis code to support producing results (plots and tables) for manuscript submitted (Dixon et	R	14.3 kB	3	1	8	active
hiv-orderly Docker image build for HIV orderly	Dockerfile	14.3 kB	18	2	13	active docker
malaria-orderly-image	Dockerfile	14.3 kB	12	4	17	active docker
naomi-pipelines Repo for naomi buildkite pipelines	-	14.3 kB	34	4	5	active
covid19-forecasts-orderly-web	Shell	13.3 kB	10	1	8	active
shinyq :star2::walking::walking::walking::star2: shiny application with a queue	R	13.3 kB	18	3	6	active
testthat.buildkite Buildkite reporter for testthat	R	13.3 kB	15	3	11	active
fertility-orderly-image Docker image build for osymandius/fertility_orderly	R	11.3 kB	12	4	13	active docker
parrotmetric :bird::chart_with_upwards_trend::bird: Parametric plots in R (For teaching / R Book Club only!)	R	11.3 kB	10	3	14	active
scott Structured COalescent Transmission Tree simulation	R	11.3 kB	10	3	8	active
gavi_covid_forecast	R	10.2 kB	9	4	9	active
malaria-orderly-web Config and deployment for Malaria Orderly Web instance	-	10.2 kB	13	2	2	active
RECON_TB_to_odin Re-writing the RECON TB practical (https://www.reconlearn.org/post/practical-tb.html) to run in	R	9.2 kB	3	1	17	active
ebola_example	R	9.2 kB	4	2	7	active
naomi-troubleshooting	HTML	8.2 kB	12	2	5	active
auth-db A dockerised postgres database with a schema to support authentication and authorization for any	Shell	7.2 kB	4	1	16	active docker
bhrp Code for linking Bellman Harris with Renewal Processes	R	6.1 kB	2	1	8	active
git-workflow-demo A repo for demonstrating how we use git to collaborate	R	6.1 kB	19	13	3	active
mpox_clade_i_severity Data and analysis code for "Age-patterns of severity of clade I mpox in historically endemic cou	R	6.1 kB	1	1	4	active
sim Not a repository anyone should actually use for anything	C++	6.1 kB	6	1	12	active
threemc-orderly-image Docker image build for threemc orderly	Shell	6.1 kB	6	2	11	active docker
valgrindr docker image with valgrind for debugging package with C++ code on Mac OS	Dockerfile	6.1 kB	7	2	5	active docker
git-training-biscuits Repo for git training	-	5.1 kB	12	2	2	active
gpu-cluster-showcase	Python	5.1 kB	2	1	5	active
hipercow-tlo	Python	5.1 kB	3	1	9	active CI
mint-mockups	HTML	5.1 kB	3	1	3	active
orderly-tutor-orderly-web Orderly-web for orderly.dide.ic.ac.uk	Shell	5.1 kB	4	1	6	active
podin-demo Config demo for podin tool	HTML	5.1 kB	3	1	9	active CI
wodin-builder-action	-	5.1 kB	16	1	2	active
covid-italy-dashboard	R	4.1 kB	3	1	4	active
git-example	R	4.1 kB	6	2	3	active
orderly-action A GitHub action for using orderly and Packit	R	4.1 kB	2	1	6	active CI
orderly-tutor-image Docker image for orderly-tutor / orderly.dide.ic.ac.uk	Dockerfile	4.1 kB	3	2	12	active docker
rcrng	Makefile	4.1 kB	3	1	13	active
docker-official-images	Shell	3.1 kB	6	1	3	active CI
drjacobench ⏲ Drjacoby benchmarking ⏲	R	3.1 kB	1	1	11	active
epireview.data	-	3.1 kB	5	1	13	active
git_demo	R	3.1 kB	10	1	5	active
matchbox	Makefile	3.1 kB	2	1	13	active
mockr.onload Example of mockr not working with .onLoad interactively	R	3.1 kB	3	1	11	active
mpox_sa	R	3.1 kB	4	1	3	active
renamer	-	3.1 kB	4	1	1	active
aloe_deploy deploy aloe apps	R	2.0 kB	3	1	8	active
comet-deploy	Shell	2.0 kB	1	1	5	active
context.rrq	Makefile	2.0 kB	1	1	11	active
hintr-profile	Shell	2.0 kB	1	1	8	active
lilith-test	R	2.0 kB	6	2	3	active
mint-data A public repository for the model simulation data used in MINT, the malaria intervention tool. (	-	2.0 kB	2	1	2	active
odin.batch	Makefile	2.0 kB	1	1	10	active
MMStools This repos is still in the early stages of development. Eventually, it is intended to host a ser	-	1.0 kB	1	1	2	active
covid_booster_analysis_safir_refit	-	1.0 kB	1	1	2	active
covid_npi_lifting_manuscript	-	1.0 kB	1	1	3	active
get-unstuck	-	1.0 kB	4	1	1	active
git-rebase-demo	-	1.0 kB	4	1	3	active
git-training-biscuit repo for git training	-	1.0 kB	8	1	2	active
migrate_duckdb	Shell	1.0 kB	1	1	7	active docker
novel-data-streams	-	1.0 kB	4	1	2	active
orderly-tutor Orderly repo for teaching sessions using orderly.dide.ic.ac.uk	-	1.0 kB	2	2	4	active
wodin-base-image	Dockerfile	1.0 kB	2	1	3	active CI docker
git-training-yalini biscuits	-	0 B	3	1	1	active
hiv-docs Documentation for HIV group	-	0 B	2	1	1	active
odin-app	R	0 B	1	1	5	active
shiny :star2::books::star2: documentation and (eventually) scripts for our shiny setup	-	0 B	1	1	1	active
thecount Joint Inference Framework for R0 and Epidemic Size	-	0 B	0	0	0	active