remake_fosrec: Function to resample a fossil record from a simulated clade.

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

Description

Function to resample a fossil record from a simulated clade.

Usage

remake_fosrec(sim = sim, samp = function(t, n) {
    0.01
})

Arguments

sim

sets the type parameterization of the rates of speciation and extinction. 'I' and 'II' specifies that the probabilities of extinction and seniority are calculated based on actual durations of intervals, whereas 'III' and 'IV' uses the differences between mid-points of intervals. 'I' and 'III' uses a basic implementation of probability of extinction as 1 - exp(-rate * dt). Models 'II' and 'IV' use a more detailed functional relationship between rate and probability, following Raup (1984): (µ*((exp((lambda-µ)*dt))-1))/(lambda*((exp((lambda-µ)*dt)))-µ). Modeltype 'V' implements a temporally uninformed model, estimating the probabilities directly (or rather their logit).

samp

function detailing sampling rate with arguments (t,n)

Value

The function returns an object of class CMR_model. This most important output is out$probfun which is a function for the posterior. This output can be fed directly into the sampler MCMC_CMR. It also returns Obs and dts as well as the full call (exlcluding default settings), call

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