jaatha (version 2.7.0)

dm.addSpeciationEvent: Adds a speciation event to a demographic model

Description

You can use this function the create a new population that splits of from an existing population at a given time in the past. The time can be given as parameter or as an expression based on previously generated time points.

Usage

dm.addSpeciationEvent(dm, min.time, max.time, fixed.time, in.population = 1,
  new.time.point = T, new.time.point.name = NA, time.point = NA)

Arguments

dm

The demographic model to which the split should be added.

min.time

If you want to estimate the time point, this will be used as the smallest possible value.

max.time

Same as min.time, but the largest possible value.

fixed.time

If specified, the time.point will not be estimated, but assumed to have the given value.

in.population

The number of the population in which the spilt occurs. See above for more information.

new.time.point

If 'TRUE' a new parameter will be created using the arguments 'min.time' and 'max.time' or 'fixed.time'. It will be named 'new.time.point.name'. If 'FALSE' the argument 'time.point' will be evaluated instead.

new.time.point.name

The name for the new time point.

time.point

Instead of creating a new parameter, you can also set the mutation rate to an expression based on existing parameters. For example setting this to "tau" will use an parameter with name tau that you have previously created. You can also use R expression he

Value

• The demographic model with a split.

Details

Time in measured in Number of 4N0 generations in the past, where N0 is the size of population 1 at time 0.

The command will print the number of the new population, which will be the number of previously existing populations plus one. The first population has number "1".

Examples

dm <- dm.createDemographicModel(c(25,25), 100)
dm <- dm.addSpeciationEvent(dm,0.01,5)
dm <- dm.addMutation(dm,1,20)