fit_mpm: fit a *Move Persistence Model* ('mpm')

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 a Move Persistence Model (mpm)

Description

fit a random walk with time-varying move persistence to temporally regular or irregular location data

Usage

fit_mpm(
  x,
  what = "predicted",
  model = c("jmpm", "mpm"),
  coords = 3:4,
  control = mpm_control(),
  inner.control = NULL,
  optim = NULL,
  optMeth = NULL,
  verbose = NULL
)

Arguments

x	a ssm_df fit object or a data frame of observations (see details)
what	if a ssm_df fit object is supplied then what determines whether fitted, predicted (default), or rerouted values are mapped; ignored if x is a data frame
model	mpm model to fit; either mpm with unpooled random walk variance parameters (sigma_(g,i)) or jmpm with a single, pooled random variance parameter (sigma_g)
coords	column numbers of the location coordinates (default = 3:4)
control	list of control settings for the outer optimizer (see mpm_control for details)
inner.control	list of control parameters for the inner optimization
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
verbose	is deprecated, use ssm_control(verbose = 1) instead, see ssm_control for details

Value

a list with components

• fitted a dataframe of fitted locations

• par model parameter summary

• data input data.frame

• tmb the TMB object

• opt the object returned by the optimizer

References

Jonsen ID, McMahon CR, Patterson TA, et al. (2019) Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model. Ecology. 100(1):e02566

Examples

## fit jmpm to two southern elephant seal tracks
xs <- fit_ssm(sese2, spdf=FALSE, model = "rw", time.step=72, control = ssm_control(verbose = 0))

fmpm <- fit_mpm(xs, model = "jmpm")

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