modelMedea: Simulates a MEDEA system similar to that observed in...

In coleoguy/MEDEA: Analysis of Medea systems

Description

Returns the results of forward time individual based population genetic simulations.

Usage

modelMedea(max, N, sims, loss, gain, bottleneck, bottleneck.freq, mon.both, fate, pop.init, s, mutation, verbose

Arguments

max	numeric - maximum number of generations to simulate
N	population size to simulate
sims	the number of simulations to run
loss	the per generation per locus probability of losing a MEDEA allele
gain	the per generation per locus probability of gaining a MEDEA allele
bottleneck	the proportion of the population that is lost in a bottleneck event
bottleneck.freq	the frequency of bottleneck events i.e. 7 would mean every 7th genertion a bottleneck occurs
mon.both	if TRUE then the function will return a list the elements of which are matrices reporting the frequency of both MEDEA alleles in every generation of each simulation.
fate	if TRUE then the function will return a matrix with the columns representing the iterations and the rows representing the fate of MEDEA factor A and B.
pop.init	a numeric vector of length 16 describing the initial population. The values should be in the order: ABAB, ABAb, ABaB, ABab, AbAB, AbAb, AbaB, Abab, aBAB, aBAb, aBaB, aBab, abAB, abAb, abaB, abab.
s	this is the selection coefficient of the Medea allele fitness is modeled to be additive: AABB fitness = 1-4*s, AABb fitness = 1-3*s, AAbb fitness = 1-2*s; Aabb fitness = 1-s; aabb fitness = 1
mutation	if TRUE then gain and loss mutations of MEDEA factors are modeled.. currently too slow to use.
verbose	print many print statements for troubleshooting

Details

If this ever is to be published lots of info here about how we imagine the model to work

Value

returns either a matrix or list as described above

Author(s)

Heath Blackmon

coleoguy/MEDEA documentation built on May 13, 2019, 9:50 p.m.