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backendcovidapp

The backend to the COVID-19 RShiny app (github.com/EU-ECDC/RShinyCovidApp)

california-coronavirus-data

The Los Angeles Times' independent tally of coronavirus cases in California.

comix_data_clean

For cleaning, processing, and serving CoMix data.

covid_homeless_modelling

Code for 'Comparison of infection control strategies to reduce COVID-19 outbreaks in homeless shelters in the United States: a simulation study'

covid_multi_strain

Code for 'Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia'

covid_remaining_burden

Code for 'Unexposed populations and potential COVID-19 hospitalisations and deaths in European countries as per data up to 21st November 2021'

covidest

covidvaccinemodelling

Code for 'Risk factor targeting for vaccine prioritization during the COVID-19 pandemic'

disease_transmission_workflow

Supplementary code for paper "Bayesian workflow for disease transmission model".

epinow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

ethiopiavl

Code for 'Demographic characteristics and prevalence of asymptomatic Leishmania donovani infection in migrant workers working in an endemic area in Northwest Ethiopia'

inla-workshop-glasgow2019

Workshop on spatial and spatio-temporal models using INLA

quantifyingvlnaturalhistory

R code for fitting multi-state Markov model and producing figures in 'Quantification of the natural history of visceral leishmaniasis and consequences for control'

rcpp_intro

A Brief Introduction to Rcpp

seir

SEIR models with odin, dust and mcstate

sir

sircovid

spatiotemporalmodelling2004

Code for 'The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh'

vl_prediction_paper

Analyses used in the paper "A spatio-temporal approach to short-term forecasting of visceral leishmaniasis diagnoses in India"

vlagetrendsanalysis

MATLAB code for performing statistical analyses and fitting reversible catalytic models in 'Age trends in asymptomatic and symptomatic Leishmania donovani infection in the Indian subcontinent: a review and analysis of data from diagnostic and epidemiological studies'

vlspatiotemporalmodelling

Code for 'Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post–kala-azar dermal leishmaniasis'

vlstatisticalanalysis

STATA code for cleaning data and performing statistical analyses in 'Variations in visceral leishmaniasis burden, mortality and the pathway to care within Bihar, India'

warwickvlmodel

MATLAB code for running simulations of Warwick visceral leishmaniasis transmission models in 'Policy recommendations from transmission modelling for the elimination of visceral leishmaniasis in the Indian subcontinent'

warwickvlmodelfitting

MATLAB code for fitting and performing predictions with Warwick visceral leishmaniasis transmission model in 'Elimination of visceral leishmaniasis in the Indian subcontinent: a comparison of predictions from three transmission models'