#' @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
plot_network_fxn <-function(dat,at)
{
#exit if no network plotting
if(dat$param$plot_nw != TRUE){return(dat)}
#exit if not first timestep or not timestep to plot network
if( (at != 2) & ((at %% dat$param$network_print_frequency) != 0)){
return(dat)
}
#exit if "save_network==T" (except if first timestep),
#as plotting doesn't work well on network with complete history
if(dat$param$save_network== TRUE & at>2){return(dat)}
#color from low to high values (spvl, connectivity)
color_vec <- c("white","orange","yellow","red","purple","black")
# Create two plots if we have generic attribute groups
if(!is.logical(dat$param$generic_nodal_att_values))
par(mfrow=c(1,2))
else
par(mfrow=c(1,1))
#get ids of agents on network that are infected
inf_index <- which(dat$attr$status_evo == 1 & dat$attr$active == 1) # No longer used now that I try to colorize the nodes
#position on network
inf_index_id <- dat$attr$id[inf_index]
spvl_breaks=c(0,1e3,1e4,1e5,1e6,1e10)
spvl_label <- as.numeric(cut(dat$pop$V[inf_index_id],breaks=spvl_breaks,
labels=1:5))
#sex-specific symbols
pch_vec <- rep(50,length(dat$attr$status_evo))
pch_vec[dat$attr$sex=="f"]=3
color_ix <- rep("white",length(dat$attr$status_evo))
color_ix[inf_index] <- color_vec[spvl_label]
if(length(which(dat$attr$active ==1))<=100)
plot(dat$nw,vertex.col=color_ix,label="id",label.cex=.85,vertex.sides=pch_vec)
else
plot(dat$nw,vertex.col=color_ix,vertex.sides=pch_vec)
mtext(paste("network at day: ",at," (dark = high VL)"),side=3)
# Plot # 1 -- Nodes colored by connection group
if(!is.logical(dat$param$generic_nodal_att_values)){
inf_index <- which(dat$attr$status_evo >=0 & dat$attr$active ==1)
color_ix <- color_vec[dat$pop$att1[inf_index]]
if(length(which(dat$attr$active ==1))<=100)
plot(dat$nw, vertex.col = color_ix,label="id",label.cex=.85,vertex.sides=pch_vec)
else
plot(dat$nw, vertex.col = color_ix,vertex.sides=pch_vec)
mtext(paste("network at day ",at," (black to yellow: activity grps 1-5)"),side=3)
}
return(dat)
}
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