DAISIE_loglik_integrand {DAISIE} | R Documentation |
Integrand to be integrated to calculate the log likelihood for the relaxed rate model.
Description
Integrand to be integrated to calculate the log likelihood for the relaxed rate model.
Usage
DAISIE_loglik_integrand(
DAISIE_par,
pars1,
pars2,
brts,
stac,
missnumspec,
methode,
abstolint,
reltolint,
verbose,
pick,
par_mean,
par_sd
)
Arguments
DAISIE_par |
A numeric parameter to evaluate the integral of the function. |
pars1 |
Vector of model parameters: |
pars2 |
Vector of settings: |
brts |
Numeric vector of branching times |
stac |
Numeric of Endemicity status |
missnumspec |
Numeric of missing species |
methode |
Method of the ODE-solver. Supported Boost |
abstolint |
Numeric absolute tolerance of the integration |
reltolint |
Numeric relative tolerance of the integration |
verbose |
A numeric vector of length 1, which in simulations and 'DAISIEdataprep()' can be '1' or '0', where '1' gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed. The default: '0' does not print, '1' prints the initial likelihood and the settings that were selected (which parameters are to be optimised, fixed or shifted), '2' prints the same as '1 and also the intermediate output of the parameters and loglikelihood, while '3' the same as '2' and prints intermediate progress during likelihood computation. |
pick |
Numeric determining which parameter is selected for the relaxed-rate model |
Value
A numeric