log_lik_overall: Overall log likelihood for one patient

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

Description

This function calculates the summand of the overall log likelihood that changes when the status of one patient is updated. The constant summands are ignored for efficiency.

Usage

log_lik_overall(admissions, discharges, colonisations, statuses, TP_no_abx,
  TP_abx, test_results_negative, antibiotics, beta, b, s, rho_1, rho_2,
  nPatient, phi, pt)

Arguments

admissions	a vector with days of admission of the patients.
discharges	a vector with days of discharge of the patients.
colonisations	a vector with days of colonisation of the patients.
statuses	a vector the statuses on discharge of the patients
TP_no_abx	the number of true positive tests without antibiotics.
TP_abx	the number of true positive tests with antibiotics.
test_results_negative	a matrix where each row corresponds to a patient and the entries correspond to a day with a negative test result.
antibiotics	a matrix where each row corresponds to a patient and the entries correspond to a day when antibiotics were administered.
beta	the transmission rate.
b	the multiplicative effect of antibiotics on transmissibility.
s	the multiplicative effect of antibiotics on susceptibility.
rho_1	the test sensitivity without antibiotics (baseline).
rho_2	the test sensitivity with antibiotics.
nPatient	the total number of patients.
phi	the probability of a patient beeing colonised on admission.
pt	the patient for which the overall log likelihood is computed.
beta	the transmission rate.

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