Abhishek Senapati's repositories
abhisheksena.github.io
Personal Website
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"
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'
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."
simplagion
Code associated to the paper 'Simplicial models of social contagion' Nat. Commun. (2019)
tsir
Fast code for SIR on temporal networks
WithinBetweenHostCompartmental
Code to accompany publication