moduleDiagram: Simulation module dependency diagram

In PredictiveEcology/SpaDES.core: Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Simulation module dependency diagram

Description

Create a network diagram illustrating the simplified module dependencies of a simulation. Offers a less detailed view of specific objects than does plotting the depsEdgeList directly with objectDiagram().

Usage

moduleDiagram(sim, type, showParents = TRUE, ...)

## S4 method for signature 'simList,character,logical'
moduleDiagram(sim, type = "plot", showParents = TRUE, ...)

## S4 method for signature 'simList,ANY,ANY'
moduleDiagram(sim, type, showParents = TRUE, ...)

Arguments

sim	A simList object (typically corresponding to a completed simulation).
type	Character string, either "rgl" for igraph::rglplot or "tk" for igraph::tkplot, "Plot" to use quickPlot::Plot() or "plot" to use base::plot(), the default.
showParents	Logical. If TRUE, then any children that are grouped into parent modules will be grouped together by coloured blobs. Internally, this is calling moduleGraph(). Default FALSE.
...	Additional arguments passed to plotting function specified by type.

Value

invoked for its side effect of plotting the module dependency diagram.

Author(s)

Alex Chubaty

See Also

igraph(), moduleGraph() for a version that accounts for parent and children module structure.

Examples

if (requireNamespace("SpaDES.tools", quietly = TRUE) &&
    requireNamespace("NLMR", quietly = TRUE)) {
library(igraph)
times <- list(start = 0, end = 6, "month")
parameters <- list(
  .globals = list(stackName = "landscape"),
  caribouMovement = list(
    .saveObjects = "caribou",
    .saveInitialTime = 1, .saveInterval = 1
  ),
  randomLandscapes = list(.plotInitialTime = NA, nx = 20, ny = 20))

modules <- list("randomLandscapes", "caribouMovement")
paths <- list(
  modulePath = getSampleModules(tempdir())
)

# Set some options so example runs faster
opts <- options(spades.moduleCodeChecks = FALSE, spades.loadReqdPkgs = FALSE)
sim <- simInit(times = times, params = parameters, modules = modules,
               paths = paths)
options(opts)
moduleDiagram(sim)
# Can also use default base::plot
modDia <- depsGraph(sim, plot = TRUE)
# See ?plot.igraph
plot(modDia, layout = layout_as_star)

# Or for more control - here, change the label "_INPUT_" to "DATA"
edgeList <- depsEdgeList(sim)
edgeList <- edgeList[, list(from, to)]
edgeList[from == "_INPUT_", from := "Data"]
edgeList[to == "_INPUT_", to := "Data"]
edgeList <- unique(edgeList)
ig <- graph_from_data_frame(edgeList[, list(from, to)])
plot(ig)
}

PredictiveEcology/SpaDES.core documentation built on April 17, 2024, 8:27 a.m.