phylosamp
R package designed to help users conduct and evaluate sample size calculations for phylogenetic studies. Presently, the functions can be used to calculate sample size in three types of scenarios that frequently arise when analyzing pathogen genomic data: 1) trying to determining if pathogen infections are linked by transmission, 2) trying to estimate the frequency…
SeverityEstimate
R package designed to help epidemiologists estimate the severity of an outbreak when using multiple surveillance methods.
simple_gam_utilities
Some utilities for smoothing time series: monotonic smooths and fast derivative estimations
TabularEpi
Python framework for rapid creation and protyping of scalable models in a flexible, object oriented, environment
tti
An extension of the tti R package, originally designed to support public health departments in assessing the impact of test–trace–isolate strategies, with added functionality to account for heterogeneous populations.
vaxflux
Python package for modeling and forecasting seasonal vaccination rates, namely flu vaccination uptake.
Flexible Epidemic Modeling Pipeline (flepiMoP)
Simulates a wide range of compartmental models of infectious disease transmission. The disease transmission and observation models are defined by a no-code configuration file, which allows models of varying complexity to be specified quickly and consistently, from simple problems described by SIR-style models in a single population to more complicated models of multiple pathogen strains…
IDSpatialStats
R package designed to help epidemiologists assess the scale of spatial and temporal dependence in epidemic case occurrence data. The current implementation of the package includes a function which simulates infectious disease spread as a spatial branching process, along with two novel spatial statistics that estimate: 1) the mean of the spatial transmission kernel, which…
Target Agnostic