#' @title Title
#'
#' @description Description
#'
#' @param x A number.
#' @param y A number.
#' @return return value here.
#' @details
#' Additional details here
#' @examples
#' example function call here
#' @export
summary_evo_newick<-function(model,path=getwd(),name=NULL,plot=TRUE){
#plots transmission tree and writes out newick file
#note to run, set evomparams$save_coital_acts=TRUE
if(is.null(model$coital_acts_list[[1]])){
stop("fxn stopping: coital acts list not saved")}
if(sum(model$popsumm[[1]]$new_infections,na.rm=T)==0){
stop("fxn stopping: no new infections occurred")}
bb <- do.call("rbind",model$coital_acts_list[[1]])
cc <- bb[which(bb$infection==1),]
sus <- unique(cc$sus_id)
ix <- match(sus,cc$sus_id)
dd <- cc[ix,]
evo_tm <- data.frame(at=dd$timestep,sus=dd$sus_id,inf=dd$inf_id)
evo_exit_times <- model$pop[[1]]$Time_Death
evo_phylo <- as.phylo.transmat(x=evo_tm,vertex.exit.times = evo_exit_times)
if(plot){
plot(evo_phylo, show.node.label = TRUE,
root.edge=TRUE,
cex = 0.5)
}
if(is.null(name)){
name="EvoNewick.txt"
}else{
name=paste(name,"_EvoNewick.txt",sep="")
}
ape::write.tree(evo_phylo,file=file.path(path,name))
return(evo_tm)
}
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