settings.file: Settings File
In akeyel/spatialdemography: A Spatially Explicit Metacommunity Model

This file contains settings for one or more model scenairios. Each row in this file corresponds to a scenario

Input	Description
Scenario	A label for each scenario. Needs to correspond & be in the same order as the Scenario input in the initial conditions file.
GenerateVisualDebuggerData	An indicator variable. When 0, additional diagnostics are not produced. When 1, additional diagnostics are produced.
GenerateNewSpecies	When 1, new species are generated based on the Species Instructions File sp.instr.file and the Species Response Instructions File sp.resp.instr.file. Otherwise, a pointer should be given to indicate which existing Species File (sp.file) to use (the pointer is a short piece of code in the Species file name that follows species_file_ and precedes any ending (e.g., date).
GenerateNewLandscape	When 1, new landscape files are generated based on the Environmental Layers File (env.file).
ignore.rtd	(optional) An indicator variable for whether response trait diversity should be taken into account when assigning species. If 1, specified response trait diversity levels will be met (or an error will be given if they cannot be met), if 0, the model will proceed without respect to those inputs. Not applicable when species locations are read in from file.
initial.n	(optional, if column is absent, defaults to a value of 1.) An indicator for how initial species numbers should be assigned. If absent or 1, 10 times as many juveniles and 100 times as many seeds will be produced (relative to adult numbers). If 2, a starting biomass is specified in the initial.conditions.file and this biomass is divided evenly among all three life stages. Each life stage starts with a number of individuals equal to 1/3 starting biomass divided by the biomass of an individual (floor division).
loc.extraction	(optional) Indicates how extraction from file should proceed. Extraction types are: 1. Read in all life stages from file. 2. Read in locations (presence) from file, but set up abundances based on settings in initial.n. 3. Read in adult locations from file, and set up juveniles and seeds based on settings in initial.n.
timestep.extraction	The time step to be extracted from file
include.copula	(optional) An indicator for whether generation via a copula is desired. Number should indicate the number of different copulas desired.
N.sim.dispersal.table	The number of random draws to be used for obtaining simu-lated dispersal probabilities.
RunSimulation	When 1, this indicates that the simulation portion of the model should be run, otherwise the simulation is not con-ducted.
RunMatrixDiagnostics	When 1, this indicates that additional matrix diagnostics should be computed and written to file, otherwise these are not computed.
Write.Timefile	When 0 or absent, no timing is done. When 1, the total scenario time is written to file. When 2, total scenario time and run time details are output to file.