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 simList,character,logical
moduleDiagram(sim, type = "plot", showParents = TRUE, ...)

# S4 method for 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(), 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/RtmpoLaiAE/sampleModules'
#>   )
#> Paths set to:
#>   options(
#>     rasterTmpDir = '/tmp/RtmpoLaiAE/SpaDES/scratch/raster'
#>     reproducible.cachePath = '/tmp/RtmpoLaiAE/reproducible/cache'
#>     spades.inputPath = '/tmp/RtmpoLaiAE/SpaDES/inputs'
#>     spades.outputPath = '/tmp/RtmpoLaiAE/SpaDES/outputs'
#>     spades.modulePath = '/tmp/RtmpoLaiAE/sampleModules'
#>     spades.scratchPath = '/tmp/RtmpoLaiAE/SpaDES/scratch'
#>   )
#>   terra::terraOptions(tempdir = '/tmp/RtmpoLaiAE/SpaDES/scratch/terra'
#> Apr25 18:01:08 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Apr25 18:01:08 simInit The following .globals were used:
#> Apr25 18:01:08 simInit Key: <global, module>
#> Apr25 18:01:08 simInit              module    global
#> Apr25 18:01:08 simInit              <char>    <char>
#> Apr25 18:01:08 simInit 1:  caribouMovement stackName
#> Apr25 18:01:08 simInit 2: randomLandscapes stackName
#> Elpsed time for simInit: 0.09545803 secs
#> Plot encountered an error; trying base::plot



# }