nosoi (version 1.0.0)

getTransmissionTree: Gets the full transmission tree (phylogenetic tree-like) from a nosoi simulation

Description

From a nosoi simulated epidemics, this function extracts the full transmission tree in a form mimicking a phylogenetic tree.

Usage

getTransmissionTree(nosoiInf)

Arguments

nosoiInf

an object of class nosoiSim

Value

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

Details

This function uses packages tidytree and treeio, that rely on ape.

See Also

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

To sub-sample this tree, see functions sampleTransmissionTree and 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 {
# }