Simulation: Function to run the simulation portion of SpatialDemography
In akeyel/spatialdemography: A Spatially Explicit Metacommunity Model

This function does the model setup, matrix diagonstics, and simulation portion of spatialdemography.

Simulation(Model.Name, ResultsFile, vdb.data, timefile, write.timefile,
  run.times, run.lbl, start.time, run.path, DispPath, outpath.base, num.sim, S,
  extent, p, landscape, landscape.identifiers, distances, settings, ic, rtd.c,
  locations.file, landscape.dir, SpTraits, tot.sp.num, my.env, env.c.freq,
  is.change, change.count, env.lbl, s.lbl, lnd.lbl, competitiontype, microsites,
  Results, out.metrics, scale.vec, timepoint.vec, scale.cells.lst, resolution,
  log.trans, MaxTime, invasion, num.invaders, cells.to.invade, repro.proportion,
  K_g, multi.species.K, extinction.threshold, edge.type, do.simulation,
  do.diagnostics, testing)

`Model.Name`	The name of the model run
`ResultsFile`	The file that results will be written to.
`vdb.data`	An indicator for whether or not to create visual debugger data
`timefile`	Timing results are written to this file.
`write.timefile`	An indicator for whether the time file should be output.
`run.times`	A list of intermediate times during the model run
`run.lbl`	A list of labels for each of the intermediate times
`start.time`	The starting time for the model
`run.path`	The path for the model run
`DispPath`	The path for the dispersal tables
`outpath.base`	A base path for outputs
`num.sim`	The number of simulations to run
`S`	The number of life stages in the model (MUST BE 4)
`extent`	The length of one side of the square landscape
`p`	The number of cells in the landscape (extent ^ 2)
`landscape`	A list object containing the environmental layer values for each cell in the landscape
`landscape.identifiers`	A list of single letter identifiers for each environmental layer
`distances`	The distances between every pair of cells
`settings`	A dataframe containing the information from the settings file
`ic`	A dataframe containing the information from the initial conditions file
`rtd.c`	An indicator for how to handle response trait diversity. Currently non-functional, use the hard-wired default
`locations.file`	A file indicating species locations. May not be applicable in many circumstances.
`landscape.dir`	A directory pointing to where the landscape files should be written.
`SpTraits`	Species trait data read in from the species file
`tot.sp.num`	The number of species in the species pool (=spe)
`my.env`	Information about the environmental layers
`env.c.freq`	The frequency of environmental change
`is.change`	An indicator for whether or not change will occur in the model (for computational efficiency)
`change.count`	An indicator for the current environmental change step.
`env.lbl`	A vector of labels containing the landscape layer names
`s.lbl`	Another label
`lnd.lbl`	Another label
`competitiontype`	An indicator for what type of competition should be implemented
`microsites`	The number of microsites in the model
`Results`	A dataframe to hold the results from the model
`out.metrics`	A list of metrics to be calculated for the model
`scale.vec`	A list of spatial scales at which to evaluate the model
`timepoint.vec`	A list of timepoints at which to calculate the metrics given in out.metrics
`scale.cells.lst`	A list of cells corresponding to each spatial scale
`resolution`	The resolution to use for rounding (for calculating UTC values)
`log.trans`	Whether or not to log-transform the data. Currently not recommended, as this functionality is untested in multirich package
`MaxTime`	The maximum number of timesteps to run the model for.
`invasion`	How frequently invasion occurs
`num.invaders`	The number of species to have invade
`cells.to.invade`	The number of cells each species will invade
`repro.proportion`	The proportion of the species reproductive potential with which to invade
`K_g`	The carrying capacity in grams
`multi.species.K`	An indicator for whether or not to include a multispecies carrying capacity
`extinction.threshold`	An optional threshold. Below this threshold, a cell's populations will be rounded down to 0.
`edge.type`	The edge type. Currently only ABSORBING and TORUS are supported
`do.simulation`	An indicator for whether or not to run the simulation
`do.diagnostics`	An indicator for whether or not to compute diagnostics
`testing`	An indicator for whether or not a testing run is being conducted