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

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

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

# \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)
  }
#> 
#> Attaching package: ‘ape’
#> The following objects are masked from ‘package:raster’:
#> 
#>     rotate, zoom
#> 
#> Attaching package: ‘tidytree’
#> The following object is masked from ‘package:raster’:
#> 
#>     select
#> The following object is masked from ‘package:stats’:
#> 
#>     filter
#> Registered S3 method overwritten by 'treeio':
#>   method     from
#>   root.phylo ape 
#> treeio v1.14.3  For help: https://yulab-smu.top/treedata-book/
#> 
#> If you use treeio in published research, please cite:
#> 
#> LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2020, 37(2):599-603. doi: 10.1093/molbev/msz240
#> 
#> Attaching package: ‘treeio’
#> The following object is masked from ‘package:ape’:
#> 
#>     drop.tip
#> The following object is masked from ‘package:raster’:
#> 
#>     mask
#> Warning: `mutate_()` was deprecated in dplyr 0.7.0.
#> Please use `mutate()` instead.
#> See vignette('programming') for more help
# }