nosoi (version 1.0.0)

sampleTransmissionTree: Sample the transmission tree (phylogenetic tree-like)

Description

Sample a full transmission tree. This function allows for sampling multiple times on the same lineage. When this happens, the sampled ancestor is a tip with length zero.

Usage

sampleTransmissionTree(nosoiInf, tree, samples)

Arguments

nosoiInf

an object of class nosoiSim

tree

a treedata object created by function getTransmissionTree

samples

a data.table object with the following entries:

hosts

Host ID of the individuals to be sampled

times

Times at which each host is sampled

labels

label for the corresponding tip in the tree

Value

A tree of class treedata, containing a phylogenetic tree based on the transmission chain and the mapped data at all the nodes.

Details

The tree needs to be produced by function getTransmissionTree applied on the same nosoiSim object.

See Also

For exporting the annotated tree to other software packages, see functions in treeio (e.g. write.beast).

To get the full transmission matrix, see getTransmissionTree.

For sampling only dead individuals, see sampleTransmissionTreeFromExiting.

Examples

# NOT RUN {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Exit_fct  <- function(t){return(0.08)}
p_Move_fct  <- function(t){return(0.1)}

proba <- function(t,p_max,t_incub){
  if(t <= t_incub){p=0}
  if(t >= t_incub){p=p_max}
  return(p)
}

time_contact = function(t){round(rnorm(1, 3, 1), 0)}

transition.matrix = matrix(c(0, 0.2, 0.4, 0.5, 0, 0.6, 0.5, 0.8, 0),
                           nrow = 3, ncol = 3,
                           dimnames = list(c("A", "B", "C"), c("A", "B", "C")))

set.seed(805)
test.nosoi <- nosoiSim(type="single", popStructure="discrete",
                        length=20,
                        max.infected=100,
                        init.individuals=1,
                        init.structure="A",
                        structure.matrix=transition.matrix,
                        pMove=p_Move_fct,
                        param.pMove=NA,
                        nContact=time_contact,
                        param.nContact=NA,
                        pTrans = proba,
                        param.pTrans = list(p_max=p_max_fct,
                                            t_incub=t_incub_fct),
                        pExit=p_Exit_fct,
                        param.pExit=NA
)

## Full transmission tree
ttreedata <- getTransmissionTree(test.nosoi)
plot(ttreedata@phylo)

## Sampling "non dead" individuals
hID <- c("H-1", "H-7", "H-15", "H-100")
samples <- data.table(hosts = hID,
                      times = c(5.2, 9.3, 10.2, 16),
                      labels = paste0(hID, "-s"))

sampledTree <- sampleTransmissionTree(test.nosoi, ttreedata, samples)
plot(sampledTree@phylo)

## Sampling "dead" individuals
sampledDeadTree <- sampleTransmissionTreeFromExiting(ttreedata, hID)
plot(sampledDeadTree@phylo)
# }
# NOT RUN {
# }