R/daily-timeseries-plot.R

In OJWatson/paper: Demonstration of analysis associated to "paper outbreak" teaching practical

#' Plot 5x1 multiplot of network at 24 hour intervals
#'
#' \code{daily_timeseries_plot} takes output of \code{first_infection_list} and
#' plots 5x1 plot of infection network at 24 hour intervals
#'
#' @param first_infection_list Infection list outputted by \code{first_infection_list}
#'
#' @export
#'
#'
#'

daily_timeseries_plot <- function(first_infection_list){

  # first we have to ammend those who were never infected to have timing of start and end infection to be infinity
  uninfected <- which(is.na(first_infection_list$linelist$Infection_Hours.since.start))
  first_infection_list$linelist[uninfected,]$Infection_Hours.since.start <- Inf
  first_infection_list$linelist[uninfected,]$End_Infection_Hours.since.start <- Inf

  # create initially network so that node colors can be added to the vertices
  paper.net <- network::network(first_infection_list$contacts,  vertex.attr=first_infection_list$linelist, matrix.type="edgelist",
                                loops=F, multiple=F, ignore.eval = F)

  # Now add the vertices that have no contacts
  network::add.vertices(paper.net, nv = length(uninfected))

  # And set their ID attributes
  network::set.vertex.attribute(paper.net,"ID",value = uninfected,v = uninfected)

  # add vertex color attributes related to onset of infection and recovery
  networkDynamic::activate.vertex.attribute(paper.net,"color","blue",onset=-Inf,terminus=Inf)
  networkDynamic::activate.vertex.attribute(paper.net,"color","red",
                                            onset=first_infection_list$linelist$Infection_Hours.since.start,terminus=Inf)
  networkDynamic::activate.vertex.attribute(paper.net,"color","green",
                                            onset=first_infection_list$linelist$End_Infection_Hours.since.start,terminus=Inf)

  # create network dynamics
  Dyn <- networkDynamic::networkDynamic(
    base.net = paper.net,
    edge.spells=data.frame("onset" = first_infection_list$contacts$Infection_Hours.since.start,
                           "terminus" = range(first_infection_list$linelist$End_Infection_Hours.since.start,finite=T)[2],
                           "tail"=first_infection_list$contacts$From,
                           "head"=first_infection_list$contacts$To),
    vertex.spells=data.frame(onset=0,
                             terminus=range(first_infection_list$linelist$End_Infection_Hours.since.start,finite=T)[2],
                             vertex.id=1:dim(first_infection_list$linelist)[1])
  )

  # all network events
  events <- sort(unique(as.data.frame(Dyn)[,]))

  # create graphical parameters
  par(mai = c(0.8,0,0,0),oma=c(10,0,0,0),cex.main=0.5,cex.lab=2.5)

  # plot the daily time series
  res <- ndtv::filmstrip(Dyn, displaylabels=F,
                  slice.par=list(start=0, end=119,interval=24,
                                 aggregate.dur=24, rule='latest',title="a"),
                  mfrow=c(1,5),vertex.cex=1.5,
                  vertex.col = "color")



}