w2n: Scaling function: working to natural parameters

Description Usage Arguments Value Examples

View source: R/w2n.R

Description

Scales each parameter from the set of real numbers, back to its natural interval. Used during the optimization of the log-likelihood.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
w2n(
  wpar,
  bounds,
  parSize,
  nbStates,
  nbCovs,
  estAngleMean,
  circularAngleMean,
  consensus,
  stationary,
  fullDM,
  DMind,
  nbObs,
  dist,
  Bndind,
  nc,
  meanind,
  covsDelta,
  workBounds,
  covsPi
)

Arguments

wpar

Vector of working parameters.

bounds

Named list of 2-column matrices specifying bounds on the natural (i.e, real) scale of the probability distribution parameters for each data stream.

parSize

Named list indicating the number of natural parameters of the data stream probability distributions

nbStates

The number of states of the HMM.

nbCovs

The number of beta covariates.

estAngleMean

Named list indicating whether or not to estimate the angle mean for data streams with angular distributions ('vm' and 'wrpcauchy').

circularAngleMean

Named list indicating whether to use circular-linear or circular-circular regression on the mean of circular distributions ('vm' and 'wrpcauchy') for turning angles. See fitHMM.

consensus

Named list indicating whether to use the circular-circular regression consensus model

stationary

FALSE if there are time-varying covariates in formula or any covariates in formulaDelta. If TRUE, the initial distribution is considered equal to the stationary distribution. Default: FALSE.

fullDM

Named list containing the full (i.e. not shorthand) design matrix for each data stream.

DMind

Named list indicating whether fullDM includes individual- and/or temporal-covariates for each data stream specifies (-1,1) bounds for the concentration parameters instead of the default [0,1) bounds.

nbObs

Number of observations in the data.

dist

Named list indicating the probability distributions of the data streams.

Bndind

Named list indicating whether DM is NULL with default parameter bounds for each data stream.

nc

indicator for zeros in fullDM

meanind

index for circular-circular regression mean angles with at least one non-zero entry in fullDM

covsDelta

data frame containing the delta model covariates

workBounds

named list of 2-column matrices specifying bounds on the working scale of the probability distribution, transition probability, and initial distribution parameters

covsPi

data frame containing the pi model covariates

Value

A list of:

...

Matrices containing the natural parameters for each data stream (e.g., 'step', 'angle', etc.)

beta

Matrix of regression coefficients of the transition probabilities

delta

Initial distribution

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
## Not run: 
m<-example$m
nbStates <- 2
nbCovs <- 2
parSize <- list(step=2,angle=2)
par <- list(step=c(t(m$mle$step)),angle=c(t(m$mle$angle)))
bounds <- m$conditions$bounds
beta <- matrix(rnorm(6),ncol=2,nrow=3)
delta <- c(0.6,0.4)

#working parameters
wpar <- momentuHMM:::n2w(par,bounds,list(beta=beta),log(delta[-1]/delta[1]),nbStates,
m$conditions$estAngleMean,NULL,m$conditions$Bndind,
m$conditions$dist)

#natural parameter
p <-   momentuHMM:::w2n(wpar,bounds,parSize,nbStates,nbCovs,m$conditions$estAngleMean,
m$conditions$circularAngleMean,lapply(m$conditions$dist,function(x) x=="vmConsensus"),
m$conditions$stationary,m$conditions$fullDM,
m$conditions$DMind,1,m$conditions$dist,m$conditions$Bndind,
matrix(1,nrow=length(unique(m$data$ID)),ncol=1),covsDelta=m$covsDelta,
workBounds=m$conditions$workBounds)

## End(Not run)

momentuHMM documentation built on Sept. 5, 2021, 5:17 p.m.