Sample the transmission tree (phylogenetic tree-like)

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.

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

# \donttest{
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
)
#> Starting the simulation
#> Initializing ...
#>  running ...
#> Time: 10 (50% of maximum length). Hosts count: 22 (22% of maximum infected hosts).
#> done. 
#> The simulation has run for 16 units of time and a total of 122 hosts have been infected.

## Make sure all needed packages are here
if (requireNamespace("ape", quietly = TRUE)
    || requireNamespace("tidytree", quietly = TRUE)
    || requireNamespace("treeio", quietly = TRUE)) {
  library(ape)
  library(tidytree)
  library(treeio)

  #' ## 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)
  }
# }