makeScenarios: Make Scenario Parameters
In EricArcher/ebvSim: Essential Biodiversity Variables Genetic Simulations

Description Usage Arguments Value Note Author(s)

Create data frame of scenario parameters.

makeScenarios(
  num.pops,
  Ne,
  num.samples,
  mig.rate,
  mig.type,
  dvgnc.time,
  marker.type,
  mut.rate,
  num.loci,
  ploidy,
  rmetasim.ngen
)

`num.pops`	number of populations.
`Ne`	effective population size.
`num.samples`	number of samples to simulate. Must be <= Ne.
`mig.rate`	migration rate specified as proportion of population migrating per generaton.
`mig.type`	of migration matrix structure. "island" = rate between all populations is the same. "stepping.stone" = migration only occurs between neighboring populations. Metapopulation is ring shaped, not a linear chain.
`dvgnc.time`	number of generations since divergence.
`marker.type`	type of marker to simulate ("snp").
`mut.rate`	mutation rate of marker in units of # of mutations per generation.
`num.loci`	number of independent loci.
`ploidy`	ploidy of marker. Set to 2 for diploid.
`rmetasim.ngen`	number of generations to run Rmetasim for. Set to `0` to skip Rmetasim.

data frame of scenario specifications.

Each parameter can be a single value or vector of values. Output will be all unique combinations of values, with the following exceptions. Scenarios wth num.samples > Ne are deleted. Scenarios with num.pops = 1 will have mig.rate set to NA.

Eric Archer eric.archer@noaa.gov

EricArcher/ebvSim documentation built on April 9, 2020, 3:39 p.m.