Simulation module dependency diagram

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().

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

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

# S4 method for class '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.

See also

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

Author

Alex Chubaty

Examples

# \donttest{
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)
}
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:terra’:
#> 
#>     blocks, compare, union
#> The following object is masked from ‘package:testthat’:
#> 
#>     compare
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union
#> Setting:
#>   options(
#>     spades.modulePath = '/tmp/RtmpiqS17z/sampleModules'
#>   )
#> Paths set to:
#>   options(
#>     rasterTmpDir = '/tmp/RtmpiqS17z/SpaDES/scratch/raster'
#>     reproducible.cachePath = '/tmp/RtmpiqS17z/reproducible/cache'
#>     spades.inputPath = '/tmp/RtmpiqS17z/SpaDES/inputs'
#>     spades.outputPath = '/tmp/RtmpiqS17z/SpaDES/outputs'
#>     spades.modulePath = '/tmp/RtmpiqS17z/sampleModules'
#>     spades.scratchPath = '/tmp/RtmpiqS17z/SpaDES/scratch'
#>   )
#>   terra::terraOptions(tempdir = '/tmp/RtmpiqS17z/SpaDES/scratch/terra'
#> Jul28 21:14:16 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Jul28 21:14:16 simInit The following .globals were used:
#> Jul28 21:14:16 simInit Key: <global, module>
#> Jul28 21:14:16 simInit               module    global
#> Jul28 21:14:16 simInit               <char>    <char>
#> Jul28 21:14:16 simInit  1:  caribouMovement stackName
#> Jul28 21:14:16 simInit  2: randomLandscapes stackName
#> Elapsed time for simInit: 0.07564306 secs
#> Plot encountered an error; trying base::plot



# }