Thibaut Jombart's repositories
misc_figures
misc collection of figures used in publication, training etc.
website
My blogdown website
branching_basics
Basic code for branching process simulators.
nhs_pathways_monitoring
Real-time monitoring of potential COVID-19 cases reported through NHS pathways data
contact_tracing_optim
Evaluation of contact tracing optimisation method
covid19_bed_occupancy
Shiny app providing estimates of future bed occupancy given recent admissions
epichange
New method to detect recent changes in incidence trends
misc
Collection of random, potentially useful stuff.
covid19_cases_from_deaths
Shiny app to infer caes from new deaths of COVID-19
OutbreakTools
Basic Tools for the Analysis of Disease Outbreaks
bmmix
Bayesian multinomial mixture model
epirecipes
contributions to Simon Frost's epirecipes
rweekly.org
R Weekly
quicksim
quick outbreak simulation script
video-scripts
Scripts accompanying online videos
lecture-phylogenetics
LaTeX (beamer) slides of a phylogenetics lecture
hugo-initio-site
Example web site for the Hugo-Initio theme
learn
RECON's platform for teaching
adegenet_docker
Docker images for the R package adegenet
outbreaker
Disease outbreak reconstruction from epidemiological and genetic data