Description Usage Arguments Details Value See Also Examples
Nosocomial transmission data simulation with fixed dated of admission and discharge. Swab test results and genetic information are generated.
1 2 | 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)
|
day_adm |
Vector of admission dates (integer values). |
day_dis |
Vector of discharge dates (integer values). Must be same length as |
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. |
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
.
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 |
distmat |
Pairwise genetic distance data. Each row and column corresponds to patient ID in |
patientseqIDs |
Vector of patient IDs corresponding to the rows and columns of |
simulate_data
to additionally generate admission and discharge dates.
1 2 3 |
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