sampleTransmissionTreeFromExiting {nosoi} | R Documentation |
Sample the transmission tree (phylogenetic tree-like) among the exited hosts
Description
Sample a full transmission tree. This function allows for sampling only exited (i.e. inactive) individuals (e.g. when the sampling procedure is destructive or cuts the hosts from the population). Beware because it does not influence the epidemiological process, it only means that the host has been sampled when exiting the simulation.
Usage
sampleTransmissionTreeFromExiting(tree, hosts)
Arguments
tree |
a |
hosts |
a vector of dead hosts to sample |
Details
The tree needs to be produced by function getTransmissionTree
applied on the same nosoiSim
object.
Value
A tree of class treedata
, containing a
phylogenetic tree based on the transmission chain and the mapped data at all the nodes.
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 among non-dead individuals, see sampleTransmissionTree
.
Examples
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
)
## 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)
}