skeleSim.classes: skeleSim Parameters Class
In christianparobek/skeleSim: Genetic Simulation Engine

Description Slots

An S4 class storing generic parameters used throughout the workflow

title: a title for the simulation. Used in labelling of output files.
date: datestamp for the simulation.
quiet: logical determining whether to limit progress reports.
question: a single character representing type of analytical question being addressed. Can be one of: (n)ull, p(o)wer, (p)erformance.
simulator.type: a single character representing which type of simulator to use. Can be one of: (c)oalescent or (f)orward-time.
simulator: a three character code representing which simulator is being run. Currently codes for fastsimcoal(fsc) and rmetasim(rms) exist.
scenarios: a list of scenario.params objects.
num.sim.reps: number of replicates to run.
sim.func: a function that runs one replicate of the simulator. Must take and return only a skeleSim.params object.
current.scenario: number of current scenario being run.
current.replicate: number of current replicate within current scenario being run.
rep.sample: result of last call to sim.func.
rep.analysis.func: a function that analyzes the results of one simulation replicate.
num.perm.reps: number of permutation replicates to run for population structure statistics.
rep.result: result from last call to rep.analysis.func.
analysis.results: a matrix containing result of all replicate analyses.
sim.summary.func: a function to summarize rep.analysis.
summary.results: a list containign result from call to sim.summary.func.
sim.check.func: a function to check the parameters object prior to running the simualtions
sim.scen.checks: a matrix containing results of 'checks' on scenario elements (T/F)
timing: list containing elapsed time for a simulation
other.checks: a vector containing results of 'checks' on other param object elements
scenario.reps: a two column matrix describing which iteration matches which scenario/replicate
analyses.requested: vector of logicals specifying "Global", "Locus", or "Pairwise" analyses have been requested.
num.pops: number of populations.
pop.size: a vector num.pop long giving size of each population.
sample.size: a vector num.pop long giving the number of samples to take from each population.
migration: a list of one or more num.pop x num.pop matrices giving the migration rates between each population.
locus.type: a character representation of what type of marker to simulate. Can be "dna", "msat", or "snp".
mig.helper: a list of flags and values that are needed for the shiny interface but are not needed for the simulation itself. Makes it easier to keep track of different ways to specify migration matrices for different scenarios. List elements will include migration model, rows and columns of landscape and distance function.
num.loci: number of msat or snp loci to simulate.
sequence.length: number of DNA base pairs to use.
mut.rate: mutation rate for DNA or msat.
simulator.params: an object storing simulator-specific parameters. Can be a list or a simulator-specific class.