jaatha (version 2.7.0)

dm.addGrowth: Adds an growth or decline of the population size of one population to a model.

Description

This function changes the growth factor of a population at given point in time ('at.time'). This factor than applies to the time interval farther into the past from this point.

Usage

dm.addGrowth(dm, min.growth.rate, max.growth.rate, fixed.growth.rate,
  par.new = T, new.par.name = "alpha", parameter, population,
  at.time = "0")

Arguments

dm

The demographic model to which the size change should be added.

min.growth.rate

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

max.growth.rate

Same as min.growth.rate, but the largest possible value.

fixed.growth.rate

If specified, the growth rate will not be estimated, but assumed to have the given value.

par.new

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

new.par.name

Name for the new parameter.

parameter

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 "alpha" will use an parameter with name tau that you have previously created. You can also use R expression

population

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

at.time

The time point at which the size changes.

Value

• The demographic model with a size change.

Details

The population size changes by factor exp(-alpha*t), where alpha is the growth parameter and t is the time since the growth has started. Hence, for positive alpha, the population will 'decline backwards in time' or grow forwards in time. Similar, will decline in forwards time for a negative value of alpha.

If you want to add an instantaneous change of the population size, then use the dm.addSizeChange function.

Examples

# A model with one smaller population
dm <- dm.createThetaTauModel(c(20,37), 88)
dm <- dm.addGrowth(dm, 0.1, 2, population=2, at.time="0")