In mrc-ide/hypatia: Individual-Based Model of COVID Transmission

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
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hypatia

The goal of hypatia is to enable SQUIRE to be run on an individual basis rather than aggregate

Installation

install_github('mrc-ide/individual')
library(individual)

Example

Get parameters from SQUIRE

  R0 <- 2
  time_period <- 1000
  tt_contact_matrix <- 0
  contact_matrix_set <- squire::contact_matrices[[1]]

  pop <- hypatia:::get_population("Afghanistan")

  psq <- hypatia:::get_parameters(
    population = pop$n,
    R0 = R0,
    time_period = time_period,
    contact_matrix_set = contact_matrix_set,
    tt_contact_matrix = tt_contact_matrix
  )