pradel_unvd_gam: Internal function used to calculate the likelihood of the...

In josteist/Compadre: Analysis of Macroevolutionary Rates of Speciation, Extinction and Sampling using Capture-Mark-Recapture techniques

Description

Internal function used to calculate the likelihood of the Pradel CMR model using the seniority as input.

Usage

pradel_unvd_gam(gam, ext, p, u, n, v, d, minval = 1e-05)

Arguments

gam	Seniority in the Pradel model. Either one value or one for each of the n-1 last intervals.
ext	Extinction probabilities. Same size as fec.
p	Sampling probabilities.
u, n, v, d	Values for number observations, each of length equal to number of intervals. u - number of taxa first observed, n - number of taxa observed, v - number of taxa observed for last time. d should be vector of 0's.
minval	Minimum probabilities used for calculations. No probabilities are allowed be be smaller than minval or larger than 1-minval. Defaults to 1e-5.

Value

Returns $LogL (log likelihood), and $Ll.numerator and $Ll.denominator.

josteist/Compadre documentation built on June 3, 2021, 1:02 p.m.