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abc_r

abhisheksena.github.io

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computational-infectious-disease

The companion repository to Computational Modeling of Infectious Disease by Chris von Csefalvay

covid_multi_strain

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

cross_border_mobility

demo

dengue_foi

Example code to estimate force of infection from age-stratified incidence data, as described in "Opportunities for improved surveillance and control of infectious diseases from age-specific case data: insight from dengue".

deterministic-malaria-model

Deterministic malaria model using odin

disease_transitions

Early-warning signals of disease transitions

epicluster

Bayesian nonparametric methods for learning rapid changes in disease transmission

heterogeneous-exposure-hons

Modules and scripts to model contagions on higher-order networks with heterogeneous exposure

intro-pmcmc

Endo A. et al., "Introduction to the particle Markov-chain Monte Carlo." Epidemics, 2019.

odin-dust-plots

Code to generate plots for 'Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate'

odin_tutorial

optimal_resource

MATLAB scripts for generating the figures presented in the manuscript "Quantification of optimal resource allocation strategies for controlling epidemics"

param-estimation-sir

Example R, Python, and Matlab code for ML estimation with an SIR model, as well as for examining identifiability and uncertainty using the Fisher information matrix and profile likelihoods.

patchsim

Code for simulating the metapopulation SEIR model. Sample network for US national simulation included.

rate-of-incidence-ews

code to accompany "Prospects for detecting early warning signals in discrete event sequence data: application to epidemiological incidence data."

sarscov2-transmission-england

simplagion

Code associated to the paper 'Simplicial models of social contagion' Nat. Commun. (2019)

spatially-connected-rt

tsir

Fast code for SIR on temporal networks

withinbetweenhostcompartmental

Code to accompany publication