mpfilter: fit the move persistence state-space model to data after...

In ianjonsen/foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement

fit the move persistence state-space model to data after passing through prefilter

Description

generates initial values for model parameters and unobserved states; structures data and initial values for C++ TMB template; fits state-space model; minimizes the joint log-likelihood via the selected optimizer (nlminb or optim); structures and passes output object to fit_ssm

Usage

mpfilter(
  x,
  model = model,
  time.step = 6,
  parameters = NULL,
  map = NULL,
  fit.to.subset = TRUE,
  control = ssm_control(),
  inner.control = NULL
)

Arguments

x	Argos data passed through prefilter()
time.step	the regular time interval, in hours, to predict to. Alternatively, a vector of prediction times, possibly not regular, must be specified as a data.frame with id and POSIXt dates.
parameters	a list of initial values for all model parameters and unobserved states, default is to let sfilter specify these. Only play with this if you know what you are doing...
map	a named list of parameters as factors that are to be fixed during estimation, e.g., list(psi = factor(NA))
fit.to.subset	fit the SSM to the data subset determined by prefilter (default is TRUE)
control	list of control parameters for the outer optimization (see ssm_control for details)
inner.control	list of control settings for the inner optimization (see ?TMB::MakeADFUN for additional details)
verbose	is deprecated, use ssm_control(verbose = 1) instead, see ssm_control for details
optim	is deprecated, use ssm_control(optim = "optim") instead, see ssm_control for details
optMeth	is deprecated, use ssm_control(method = "L-BFGS-B") instead, see ssm_control for details
lpsi	is deprecated, use ssm_control(lower = list(lpsi = -Inf)) instead, see ssm_control for details

Details

called by fit_mpssm, not intended for general use. mpfilter can only fit to an individual track, use fit_mpssm to fit to multiple tracks (see ?fit_mpssm).

ianjonsen/foieGras documentation built on Jan. 17, 2025, 11:15 p.m.