skeleSim.classes: skeleSim Parameters Class

Description Slots

Description

An S4 class storing generic parameters used throughout the workflow

Slots

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.


skeleSim documentation built on Nov. 28, 2017, 1:05 a.m.