R/graphs.R

In robitalec/scale-in-multilayer-networks: Package Accompanying: The Problem And Promise Of Scale In Multilayer Animal Social Networks.

# Graph/network/gbi b'y

#' GBI
#'
#' @param DT 
#' @param id 
#' @param splitList 
#' @param splitBy 
#' @param group 
#'
#' @return
#' @export
#'
#' @examples
list_gbi <- function(DT, id, splitBy, group = 'group') {
  splits <- unique(DT[, .SD, .SDcols = splitBy])
  
  ls <- lapply(seq(nrow(splits)), function(s) {
    gbi <- spatsoc::get_gbi(
      DT = DT[splits[s], on = splitBy],
      group = group,
      id = id
    )
  })
  
  names(ls) <- splits[, do.call(paste, c(.SD, sep = '-'))]
  ls
}


#' Networks
#'
#' @param gbiLs 
#' @param format 
#' @param ai 
#'
#' @return
#' @export
#'
#' @examples
list_nets <- function(gbiLs, format = 'GBI', ai = 'SRI') {
  lapply(
    gbiLs,
    asnipe::get_network,
    data_format = format,
    association_index = ai
  )
}


#' Graphs
#'
#' @param netLs 
#' @param mode 
#' @param diag 
#' @param weighted 
#'
#' @return
#' @export
#'
#' @examples
list_graphs <- function(netLs, mode = 'undirected', diag = FALSE, weighted = TRUE) {
  lapply(
    netLs,
    igraph::graph.adjacency,
    mode = mode,
    diag = diag,
    weighted = weighted
  )
}


#' Edge lists
#'
#' @param edgeLs 
#'
#' @return
#' @export
#'
#' @examples
list_edges <- function(graphLs) {
    edges <- data.table::rbindlist(lapply(graphLs, function(g) {
      igraph::as_data_frame(g)
    }), idcol = 'layer', fill = TRUE)
    spatsoc::dyad_id(edges, 'from', 'to')
    
    edges
}




get_edgelist <- function(DT, group = 'group', id, datetime = 'datetime') {
  all <- DT[, data.table::CJ(left = .SD[[1]], right = .SD[[1]])[left != right], 
            by = group, .SDcols = id]
  
  spatsoc::dyad_id(all, 'left', 'right')
  all[, nbydyad := seq.int(.N), by = c('group', 'dyadID')]
  all[nbydyad == 1]
}