daily_col_prob_precalculated: Compute the probability of acquisition

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

Description

This function calculates the probability of acquisition for a given day and patient using precalculated numbers of colonised patients on and off antibiotics on the given day.

Usage

daily_col_prob_precalculated(admissions, colonisations, discharges,
  statuses, antibiotics, cp_no_abx, cp_abx, beta, b, s, day, pt)

Arguments

admissions	a vector with days of admission 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.
day	the day for which the probability of acquisition is calculated.
pt	the patient for which the probability of acquisition is calculated.
colonsiations	a vector with days of colonisation of the patients.

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