Description Usage Arguments Value Examples
View source: R/phylo.AR.groups.fun.agemix.R
A function that returns age mixing patterns quantities in transmission clusters in scenarios where individuals are missing at random
1 2 3 4 5 6 | phylo.AR.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, seq.gender.ratio = 0.7,
age.group.15.25 = c(15, 25), age.group.25.40 = c(25, 40),
age.group.40.50 = c(40, 50))
|
simpact.trans.net |
a list of transmission networks produced by |
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 |
seq.gender.ratio |
Gender ratio |
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 |
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
1 2 3 4 5 6 7 8 9 10 11 | w <- phylo.AR.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,
seq.gender.ratio = 0.7,
age.group.15.25 = c(15,25),
age.group.25.40 = c(25,40),
age.group.40.50 = c(40,50))
|
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