log_lik_transmission: Log likelihood of transmission

In mirjamlaager/mrsamcmc: An Implementation of Data Augmented MCMC for Inference on MRSA Transmission

Description

This function calculates the transmission component of the overall log likelihood.

Usage

log_lik_transmission(admissions, colonisations, discharges, statuses,
  antibiotics, cp_no_abx, cp_abx, beta, b, s)

Arguments

admissions	a vector with days of admission of the patients.
colonisations	a vector with days of colonisation of the patients.
discharges	a vector with days of discharge of the patients.
statuses	a vector the statuses on discharge of the patients
antibiotics	a matrix where each row corresponds to a patient and the entries correspond to a day when antibiotics were administered.
cp_no_abx	the number of colonised patients not on antibiotics on the given day.
cp_abx	the number of colonised patients on antibiotics on the given day.
beta	the transmission rate.
b	the multiplicative effect of antibiotics on transmissibility.
s	the multiplicative effect of antibiotics on susceptibility.

mirjamlaager/mrsamcmc documentation built on May 20, 2020, 11:13 a.m.