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paulstaab
/ model_avg_ancestral_pop
Created
June 26, 2015 16:11
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| library(jaatha) | |
| dm <- dm.createDemographicModel(sample.sizes=c(17,17), loci.num=1000, seq.length=1000) | |
| dm <- dm.addSizeChange(dm, 0.05, 10, population = 2,at.time = "0", new.par.name = "q") | |
| dm <- dm.addGrowth(dm, par.new=FALSE, parameter="log(4*q/(1+q))/tau", population=2) | |
| dm <- dm.addSpeciationEvent(dm, 0.1, 5, new.time.point.name = "tau") | |
| dm <- dm.addSizeChange(dm, parameter = "(1 + q) / 2", population=1, at.time="tau", par.new = FALSE) | |
| dm <- dm.addSymmetricMigration(dm, 0.01, 5, new.par.name = "M") | |
| dm <- dm.addMutation(dm, 1, 20, new.par.name = "theta") |
paulstaab
/ decreasing_migration.R
Last active
August 29, 2015 13:57
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| dm <- dm.createDemographicModel(c(25,25), 100, 1000) | |
| dm <- dm.addMutation(dm, 5, 20, new.par.name="theta") | |
| dm <- dm.addRecombination(dm, fixed=5) | |
| # Add parameters for the times and migration | |
| dm <- dm.addParameter(dm, 'tau_0', 0.01, 1) | |
| dm <- dm.addParameter(dm, 'tau_m', 0.1, 5) | |
| dm <- dm.addParameter(dm, 'm', 0.1, 5) | |
| # Add split and decreasing migration |
paulstaab
/ basic_model.R
Last active
December 26, 2015 23:29
Code to create model S1.1 from http://onlinelibrary.wiley.com/doi/10.1002/ece3.722/full
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| nLoci <- 100 | |
| rho <- 5 | |
| dm <- dm.createDemographicModel(c(25,25), nLoci, 1000) | |
| dm <- dm.addMutation(dm, 5, 20, new.par.name="theta") | |
| dm <- dm.addSpeciationEvent(dm, 0.017, 20, new.time.point.name="tau") | |
| dm <- dm.addSymmetricMigration(dm, 0.005, 5, new.par.name="m") | |
| # Everything but a fixed recombination rate does not make sense | |
| dm <- dm.addRecombination(dm, fixed=rho) |