plotDw: Plot of the estimated HSMM dwell-time distributions.

In JenniferPohle/PHSMM: Penalised maximum likelihood estimation for hidden semi-Markov models

Description

Plots the HSMM dwell-time distributions estimated using plmeHSMM.

Usage

plotDw(mod,R_max,state='all',mfrow=NULL)

Arguments

mod	model object as returned by pmleHSMM.
R_max	integer, maximum dwell time which the dwell-time probabilities are plotted for.
state	value determining the states which the distributions are plotted for. Either "all" (default) for plotting the dwell-time distributions of all states, or positive integer in 1,..,N.
mfrow	If NULL (default) and state="all", the probability mass functions are plotted one below the other. Otherwise, a vector of length 2 which determines the number of rows (first element) and the number of columns (second argument) of the matrix of plots.

Value

plot of the estimated HSMM dwell-time distributions.

Examples

# fit 3-state HSMM to hourly muskox step length
# initial values
p_list0<-list()
p_list0[[1]]<-c(dgeom(0:9,0.2),1-pgeom(9,0.2))
p_list0[[2]]<-c(dgeom(0:9,0.2),1-pgeom(9,0.2))
p_list0[[3]]<-c(dgeom(0:9,0.2),1-pgeom(9,0.2))
omega0<-matrix(0.5,3,3)
diag(omega0)<-0
mu0<-c(5,100,350)
sigma0<-c(3,90,300)
# fit HSMM with state-dependent gamma distributions, lambda=c(1000,1000)
# and difference order of 3
PHSMM<-pmleHSMM(y=muskox$step,N=3,p_list=p_list0,mu=mu0,sigma=sigma0,
  omega=omega0,lambda=c(1000,1000,1000),order_diff=3,y_dist='gamma')
# plot the estimated distributions for dwell-times up to 15.
plotDw(mod=PHSMM,R_max=15)
plotDw(mod=PHSMM,R_max=15,state=1)
plotDw(mod=PHSMM,R_max=15,mfrow=c(1,3))

JenniferPohle/PHSMM documentation built on Jan. 27, 2021, 7:07 p.m.