Dist {hmmTMB}

R6 class for probability distribution

Description

Contains the probability density/mass function, and the link and inverse link functions for a probability distribution.

Methods

Public methods

• Dist$new()

• Dist$name()

• Dist$pdf()

• Dist$cdf()

• Dist$rng()

• Dist$link()

• Dist$invlink()

• Dist$npar()

• Dist$parnames()

• Dist$parapprox()

• Dist$fixed()

• Dist$code()

• Dist$name_long()

• Dist$set_npar()

• Dist$set_parnames()

• Dist$set_code()

• Dist$pdf_apply()

• Dist$rng_apply()

• Dist$n2w()

• Dist$w2n()

• Dist$clone()

Method new()

Create a Dist object

Usage

Dist$new(
  name,
  pdf,
  rng,
  cdf = NULL,
  link,
  invlink,
  npar,
  parnames,
  parapprox = NULL,
  fixed = NULL,
  name_long = name
)

Arguments

name

Name of distribution

pdf

Probability density/mass function of the distribution (e.g. dnorm for normal distribution).

rng

Random generator function of the distribution (e.g. rnorm for normal distribution).

cdf

Cumulative distribution function of the distribution (e.g., pnorm for normal distribution). This is used to compute pseudo-residuals.

link

Named list of link functions for distribution parameters

invlink

Named list of inverse link functions for distribution parameters

npar

Number of parameters of the distribution

parnames

Character vector with name of each parameter

parapprox

Function that takes a sample and produces approximate values for the unknown parameters

fixed

Vector with element for each parameter which is TRUE if parameter is fixed

name_long

Long version of the name of the distribution, possibly more user-readable than name.

Returns

A new Dist object

Method name()

Return name of Dist object

Usage

Dist$name()

Method pdf()

Return pdf of Dist object

Usage

Dist$pdf()

Method cdf()

Return cdf of Dist object

Usage

Dist$cdf()

Method rng()

Return random generator function of Dist object

Usage

Dist$rng()

Method link()

Return link function of Dist object

Usage

Dist$link()

Method invlink()

Return inverse link function of Dist object

Usage

Dist$invlink()

Method npar()

Return number of parameters of Dist object

Usage

Dist$npar()

Method parnames()

Return names of parameters

Usage

Dist$parnames()

Method parapprox()

Return function that approximates parameters

Usage

Dist$parapprox()

Method fixed()

Return which parameters are fixed

Usage

Dist$fixed()

Method code()

Return code of Dist object

Usage

Dist$code()

Method name_long()

Human-readable name of Dist object

Usage

Dist$name_long()

Method set_npar()

Set number of parameters this distribution has

Usage

Dist$set_npar(new_npar)

Arguments

new_npar

Number of parameters

Method set_parnames()

Set parameter names

Usage

Dist$set_parnames(new_parnames)

Arguments

new_parnames

Parameter names

Method set_code()

Set distribution code

Usage

Dist$set_code(new_code)

Arguments

new_code

Distribution code

Method pdf_apply()

Evaluate probability density/mass function

This method is used in the Dist$obs_probs() method. It is a wrapper around Dist$pdf(), which prepares the parameters and passes them to the function.

Usage

Dist$pdf_apply(x, par, log = FALSE)

Arguments

x

Value at which the function should be evaluated

par

Vector of parameters. The entries should be named if they are not in the same order as expected by the R function. (E.g. shape/scale rather than shape/rate for gamma distribution.)

log

Logical. If TRUE, the log-density is returned. Default: FALSE.

Returns

Probability density/mass function evaluated at x for parameters par

Method rng_apply()

Random number generator

This method is a wrapper around Dist$rng(), which prepares the parameters and passes them to the function.

Usage

Dist$rng_apply(n, par)

Arguments

n

Number of realisations to generate

par

Vector of parameters. The entries should be named if they are not in the same order as expected by the R function. (E.g. shape/scale rather than shape/rate for gamma distribution.)

Returns

Vector of n realisations of this distribution

Method n2w()

Natural to working parameter transformation

This method transforms parameters from the natural scale (i.e., their domain of definition) to the "working" or "linear predictor" scale (i.e., the real line). It is a wrapper for Dist$link().

Usage

Dist$n2w(par)

Arguments

par

List of parameters

Returns

Vector of parameters on the working scale

Method w2n()

Working to natural parameter transformation

This method transforms parameters from the "working" or "linear predictor" scale (i.e., the real line) to the natural scale (i.e., their domain of definition). It is a wrapper for Dist$invlink().

Usage

Dist$w2n(wpar, as_matrix = FALSE)

Arguments

wpar

Vector of working parameters

as_matrix

Logical. If TRUE, the natural parameters are returned as a matrix with one row for each state and one column for each parameter. If FALSE, the natural parameters are returned as a list (default).

Returns

List or matrix of parameters on natural scale

Method clone()

The objects of this class are cloneable with this method.

Usage

Dist$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.