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(), 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/RtmpIQ0Aky/sampleModules'
#>   )
#> Paths set to:
#>   options(
#>     rasterTmpDir = '/tmp/RtmpIQ0Aky/SpaDES/scratch/raster'
#>     reproducible.cachePath = '/tmp/RtmpIQ0Aky/reproducible/cache'
#>     spades.inputPath = '/tmp/RtmpIQ0Aky/SpaDES/inputs'
#>     spades.outputPath = '/tmp/RtmpIQ0Aky/SpaDES/outputs'
#>     spades.modulePath = '/tmp/RtmpIQ0Aky/sampleModules'
#>     spades.scratchPath = '/tmp/RtmpIQ0Aky/SpaDES/scratch'
#>   )
#>   terra::terraOptions(tempdir = '/tmp/RtmpIQ0Aky/SpaDES/scratch/terra'
#> Jan27 19:03:56 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Jan27 19:03:56 simInit The following .globals were used:
#> Jan27 19:03:56 simInit Key: <global, module>
#> Jan27 19:03:56 simInit               module    global
#> Jan27 19:03:56 simInit               <char>    <char>
#> Jan27 19:03:56 simInit  1:  caribouMovement stackName
#> Jan27 19:03:56 simInit  2: randomLandscapes stackName
#> Elpsed time for simInit: 0.07732439 secs
#> Plot encountered an error; trying base::plot



# }