likelihood0 {pttstability} | R Documentation |
Default likelihood function
Description
Calculates likelihood of vector y given parameter values in param, based on the particleFilterLL function.
Usage
likelihood0(
param,
y = y,
parseparam = parseparam0,
N = 1000,
detfun = detfun0,
edmdat = NULL,
obsfun = obsfun0,
procfun = procfun0,
neff = FALSE,
lowerbound = (-999)
)
Arguments
param |
An unformatted vector of parameters, to be passed to parseparam function. |
y |
A numeric vector of observed values, from which the likelihood of parameters and functions will be determined. |
parseparam |
A function for transforming the vector param into a form that can be read by particleFilterLL. See particleFilterLL for details. |
N |
Number of particles to simulate. Defaults to 1e3. |
detfun |
A function that simulates deterministic dynamics, which takes in arguments sdet (parameters for deterministic model, taken from pars$proc), and xt, observed abundances at time t. Returns estimated abundances at time t+1 based on deterministic function (either a parametric function or an EDM function). Defaults to detfun0. |
edmdat |
A list including arguments to be passed to S_map_Sugihara1994 - see S_map_Sugihara1994 help file for details. Alternatively, the user can provide a matrix of pre-computed S-map coefficients, in element "smp_cf". Default for edmdat is NULL, which implies that EDM will not be applied - instead, a detfun and pars$det must be included. |
obsfun |
The observation error function to be used: defaults to obsfun0 |
procfun |
The process noise function to be used: defaults to procfun0 |
neff |
Should effective sample size be used to scale likelihood? Defaults to FALSE. TRUE uses automatic sample size, based on correlations in y. Otherwise, can be any positive number. |
lowerbound |
Lower bound for log likelihood. Filter will be re-run if the value falls below this threshold. NOTE - this option may induce a bias in the resulting likelihood (and subsequent parameter) estimates. Should only be set if the lower limit is indicative of filter failure (e.g. if all particles) are degenerate. Defaults to (-Inf) - i.e. no lower limit. |
Value
Log likelihood generated by particleFilterLL function