#### Growth parameters: the "Growth" force

This submenu allows you to turn on and off estimation of population growth rates, and to set starting parameters.

If there is a single population in your data, Lamarc will estimate a single growth rate for it. If there are multiple populations, Lamarc will estimate one independent growth rate per population.

If the type of Growth is exponential (the only type currently allowed) then if we label growth as g, then the relationship between Theta at a time t > 0 in the past and Theta at the present day (t = 0) is:

Theta(t) = Thetapresent day e-gt

This means that a positive value of g represents a growing population, and a negative value, a shrinking one.

Time is measured in units of mutations (i.e., 1 t is the average number of generations it takes one site to accumulate one mutation), and g is measured in the inverse units of time. If mu is known, divide generations by mu to get units of t, or conversely, multiply t*mu to get a number of generations.

Additionally, its now possible to choose between a "Stick" or "Curve" implementation for the chosen type of growth. Generally, if possible, one should always use the "Curve" implementation as the "Stick" is just an approximation to the "Curve". We provide it because in some cases only the "Stick" is available and...

Starting parameter input for growth is similar to that for Theta, except that no quick pairwise calculators are available; you will have to either accept default values or enter values of your own. Avoid highly negative values (less than -10) as these have some risk of producing infinitely long trees which must then be rejected.

Type of Growth Growth implemented via