epiCo
R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia
epinowcast
Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.
tutorials-middle
Tutorials to learn real-time analysis that includes accessing epidemiological delays, estimating transmission metrics, forecasting, and severity from aggregated incidence data, superspreading from line list and contact data, and simulating transmission chains.
cfr
R package to estimate disease severity and under-reporting in real-time, accounting for reporting delays in epidemic time-series
tutorials-early
Tutorials to learn reading, cleaning and validating case data, and converting line list data to incidence for visualizing epidemic curves.
tutorials-late
Tutorials to learn accessing and analyzing social contact matrices, scenario modelling to simulate disease spread and investigate interventions, and modelling disease burden.
finalsize
R package to calculate the final size of an SIR epidemic in populations with heterogeneity in social contacts and disease susceptibility