bitrugs (version 0.1)

simulate_data_dates: Nosocomial transmission data simulation with fixed dates.

Description

Nosocomial transmission data simulation with fixed dated of admission and discharge. Swab test results and genetic information are generated.

Usage

simulate_data_dates(day_adm, day_dis, p = 0.05, z = 0.8, b = 0.005, gamma = 0.3, 
gamma_gl = 0.03, genpar = 0.8, testdays = 3, model = 2)

Arguments

day_adm

Vector of admission dates (integer values).

day_dis

Vector of discharge dates (integer values). Must be same length as day_adm.

p

Probability of carriage on admission.

z

Swab test sensitivity.

b

Transmission rate.

gamma

Within host/group genetic diversity (geometric distribution parameter).

gamma_gl

Between host/group genetic diversity (geometric distribution parameter).

genpar

Group clustering parameter (model 1), or transmission chain parameter (model 2). See details below.

testdays

Number of days between each carriage test/isolate collection.

model

Genetic diversity model (1: Importation clustering model, 2: Transmission chain model). See details below.

Value

Returns a list of simulated data;

epi

Matrix of epidemiological data, consisting of columns patient ID, day of admission, day of discharge, time of colonization, source of infection, and infection group.

resmat

Matrix of test results. Each row represents the corresponding patient in epi. Each column represents a day, spanning the interval over which data were collected. 0=Negative, 1=Positive, -1=Missing

distmat

Pairwise genetic distance data. Each row and column corresponds to patient ID in patientseqIDs.

patientseqIDs

Vector of patient IDs corresponding to the rows and columns of distmat.

Details

We implement two different models of genetic diversification. Model 1 is the importation clustering model, in which each infected host belongs to a group. The probability that a new importation belongs to a new group is genpar. All hosts within the same transmission chain belong to the same group. Pairwise genetic distances are sampled from geometric distributions with parameters gamma and gamma_gl for within-group and between-group pairs respectively. Model 2 is the transmission chain model, in which genetic distances increase as hosts are further separated in the transmission tree. Genetic distances between hosts separated by k transmission links are drawn independently from the geometric distribution with parameter gamma x genpar^k. Genetic distances between hosts in independent transmission chains are drawn from a geometric distribution with parameter gamma_gl.

See Also

simulate_data to additionally generate admission and discharge dates.

Examples

    admissions <- sort(sample(1:100,100, replace=TRUE))
    discharge <- admissions + rpois(100,5) + 1
    Tsim <- simulate_data_dates(day_adm=admissions, day_dis=discharge, p=0.1,b=0.01)