phylo.CAR.groups.fun.agemix: A function that returns age mixing patterns quantities in...

In wdelva/RSimpactHelp: Pre- and Post-simulation helper functions for RSimpact Cyan

Description

A function that returns age mixing patterns quantities in transmission clusters in scenarios where individuals are missing at completly at random

Usage

phylo.CAR.groups.fun.agemix(simpact.trans.net = simpact.trans.net,
  work.dir = work.dir, dirfasttree = dirfasttree,
  sub.dir.rename = sub.dir.rename, limitTransmEvents = 7,
  timewindow = c(30, 40), seq.cov = 70, age.group.15.25 = c(15, 25),
  age.group.25.40 = c(25, 40), age.group.40.50 = c(40, 50))

Arguments

simpact.trans.net	a list of transmission networks produced by transm.network.builder
work.dir	working directory
dirfasttree	directory where is the fastTree tool
sub.dir.rename	subdurectory required when we have to run more than one simulations
limitTransmEvents	Number of minimum transmission events to be considered in each transmission networks
timewindow	Time interval
seq.cov	Percentage of individulas considered for this transmission pattern scenario
age.group.15.25	age group between 15 and 25 years old
age.group.25.40	age group between 25 and 40 years old
age.group.40.50	age group between 40 and 50 years old

Value

a vector of number of men and women in different age group, number of transmissions within all age groups, and mean and SD of age different between infectors and infectees

Examples

w <- phylo.CAR.groups.fun.agemix(simpact.trans.net = simpact.trans.net,
                               work.dir = work.dir,
                               dirfasttree = dirfasttree,
                               sub.dir.rename = sub.dir.rename,
                               limitTransmEvents = 7,
                               timewindow = c(30,40),
                               seq.cov = 70,
                               age.group.15.25 = c(15,25),
                               age.group.25.40 = c(25,40),
                               age.group.40.50 = c(40,50))

wdelva/RSimpactHelp documentation built on Dec. 26, 2019, 3:42 a.m.