setModel4M: Create or extract a 'SetModel4M' object.

In lawlerem/markmodmover: Analyze animal movement data using the Markov-modulated movement model.

Description

Creates or extracts an object used to hold a model definition.

Usage

setModel4M(x, ...)

## S4 method for signature 'SetModel4M'
initialize(.Object, N.States = 2,
  Use.HMM = FALSE, Distribution = "gamma",
  Zero.Inflation = c(Step.Length = FALSE, Deflection.Angle = FALSE),
  Starting.Values = list(), Parameter.Mapping = list())

## S4 method for signature 'missing'
setModel4M(N.States = 2, Use.HMM = FALSE,
  Distribution = "gamma", Zero.Inflation = c(Step.Length = FALSE,
  Deflection.Angle = FALSE), Starting.Values = list(),
  Parameter.Mapping = list())

## S4 method for signature 'Model4M'
setModel4M(x)

## S4 method for signature 'missing'
setSim4M(Sim.Length = 100, N.States = 2,
  Use.HMM = FALSE, Distribution = "gamma", Parameters = list())

Arguments

x	An object to coerce to class SetModel4M. Missing in calls to create a new object.
N.States	An integer giving number of states to use in the model.
Use.HMM	A logical value which flags use of an HMM. If true, sets all step length autocorrelation parameters to 0.
Distribution	Which distribution should be used for step length? Currently available options are gamma and log-normal.
Zero.Inflation	A logical vector with names Step.Length and Deflection.Angle. TRUE entries enable zero inflation.
Starting.Values	A list holding starting values. All starting values default to randomly picked values, see details and the SetModel4M class documentation.
Parameter.Mapping	A list holding parameter mapping with the same structure as Starting.Values. See the TMB documentation for MakeADFun.
Sim.Length	An integer giving the length of the simulated data.
Parameters	A list holding parameter values to simulate from.
N.States	An integer giving number of states to use in the model.
Use.HMM	A logical value which flags use of an HMM. If true, sets all step length autocorrelation parameters to 0.
Distribution	Which distribution should be used for step length? Currently available options are gamma and log-normal.
Zero.Inflation	A logical vector with names Step.Length and Deflection.Angle. TRUE entries enable zero inflation.

Details

The initialize function is not meant to be used by the user, use setModel4M instead.

See Also

Other Construct4M: data4M, model4M, setSim4M, simulate4M

lawlerem/markmodmover documentation built on Feb. 12, 2020, 8:30 p.m.