reachable-nodes: Get the Forward or Backward Reachable Nodes for a Set of...

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Get the Forward or Backward Reachable Nodes for a Set of Nodes

Description

These functions return the Forward or Backward Reachable Nodes of a set of nodes in a network over a time. Warning, these functions ignore nodes without edges in the period of interest. See the ⁠Number of Nodes⁠ section for details It is much faster than iterating tsna::tPath. The distance between to each node can be back calculated using the length of the reachable set at each time step and the fact that the reachable sets are ordered by the time to arrival.

Usage

get_forward_reachable(
  el_cuml,
  from_step,
  to_step,
  nodes = NULL,
  dense_optim = "auto"
)

get_backward_reachable(
  el_cuml,
  from_step,
  to_step,
  nodes = NULL,
  dense_optim = "auto"
)

Arguments

el_cuml	a cumulative edgelist object. That is a data.frame with at least columns: head, tail, start and stop. Start and stop are inclusive.
from_step	the beginning of the time period.
to_step	the end of the time period.
nodes	the subset of nodes to calculate the FRP for. (default = NULL, all nodes)
dense_optim	pre-process the adjacency list to speed up the computations on dense networks. "auto" (default), enable the optimisation when n_edges > n_nodes. "yes" always enables and "no" always disables. The overhead of the optimization is not worth it on sparse networks.

Value

A named list containing: reached: the set of reachable nodes for each of the nodes. lengths: A matrix of length(nodes) rows and one column per timestep + 1 with the length of the reachable set at each step from from_step - 1 to to_step. The first column is always one as the set of reachables at the beginning is just the node itself.

Number of Nodes

To speed up the calculations and lower the memory usage, these functions only take into account nodes with edges in the cumulative edgelist over the period of interest. The nodes are identified in the reached and lengths sublists by names (e.g. node_1093). Nodes without any edges are therefore not calculated as the only node they reach is themselve (length of 1). Take this fact into account when exploring the distribution of Forward Reachable Paths for example. As the nodes with FRP == 1 are not in the output.

Time and Memory Use

These functions may be used to efficiently calculate multiple sets of reachable nodes. As cumulative edgelists are way smaller than full networkDynamic objects, theses functions are suited for large and dense networks. Also, as long as the size of the nodes set is greater than 5, theses functions are faster than iterating over tsna::tPath.

Displaying Progress

These functions are using the progressr package to display its progression. Use progressr::with_progress({ fwd_reach <- get_forward_reachable(el, from = 1, to = 260) }) to display the progress bar. Or see the progressr package for more information and customization.

Examples

## Not run: 

# load a network dynamic object
nd <- readRDS("nd_obj.Rds")
# convert it to a cumulative edgelist
el_cuml <- as_cumulative_edgelist(nd)

# sample 100 node indexes
nnodes <- max(el_cuml$head, el_cuml$tail)
nodes <- sample(nnodes, 100)

# `get_forward_reachable` uses steps [from_step, to_step] inclusive
el_fwd <- get_forward_reachable(el_cuml, 1, 52, nodes)[["reached"]]

# check if the results are consistent with `tsna::tPath`
nodes <- strsplit(names(el_fwd), "_")
for (i in seq_along(el_fwd)) {
  node <- as.integer(nodes[[i]][2])
  t_fwd <- tsna::tPath(
    nd, v = node,
    start = 1, end = 52 + 1, # tPath works from [start, end) right exclusive
    direction = "fwd"
  )

  t_fwd_set <- which(t_fwd$tdist < Inf)
  if(!setequal(el_fwd[[i]], t_fwd_set))
    stop("Missmatch on node: ", node)
}

# Backward:
el_bkwd <- get_backward_reachable(el_cuml, 1, 52, nodes = 1)[["reached"]]
nodes <- strsplit(names(el_bkwd), "_")
t_bkwd <- tsna::tPath(
  nd, v = nodes[i][2],
  start = 1, end = 52 + 1,
  direction = "bkwd", type = "latest.depart"
)
t_bkwd_set <- which(t_bkwd$tdist < Inf)
setequal(el_bkwd[[1]], t_bkwd_set)


## End(Not run)

EpiModel documentation built on Oct. 12, 2024, 1:06 a.m.