mhsmm: Inference for Hidden Markov and Semi-Markov Models

Parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. Suitable for equidistant time series data, with multivariate and/or missing data. Allows user defined emission distributions.

AuthorJared O'Connell <jaredoconnell@gmail.com>, Søren Højsgaard <sorenh@math.aau.dk>
Date of publication2017-01-15 17:21:14
MaintainerJared O'Connell <jaredoconnell@gmail.com>
LicenseGPL (>= 2)
Version0.4.16
https://github.com/jaredo/mhsmm

View on CRAN

Man pages

addStates: Adds a bar representing state sequence.

dmvnorm.hsmm: Emission ensity function for a multivariate normal emission...

dnorm.hsmm: Emission density function for normal emission distribution

dpois.hsmm: Emission density function for Poisson emission distribution

gammafit: Parameter estimation for the Gamma distribution

hmmfit: fit a hidden Markov model

hmmspec: Specificatin of HMMs

hsmmfit: fit a hidden semi-Markov model

hsmmspec: Hidden semi-Markov model specification

mstep.mvnorm: Performs re-estimation (the M-step) for a multivariate normal...

mstep.norm: Performs re-estimation (the M-step) for a normal emission...

mstep.pois: Performs re-estimation (the M-step) for a Poisson emission...

plot.hsmm: Plot function for hsmms

plot.hsmm.data: Plot function for hsmm data

predict.hmm: Prediction function for hmm

predict.hmmspec: Prediction function for hmmspec

predict.hsmm: Prediction for hsmms

predict.hsmmspec: Prediction for hsmmspec

print.hmm: Print method for hmm objects

print.hmmspec: Print function for hmmspec

print.hsmmspec: Print function for hsmmspec

reproai: Artificial insemination times for seven cows

reprocows: Reproductive data from seven dairy cows

rmvnorm.hsmm: Random number generation from a multivariate normal...

rnorm.hsmm: Random number generation from a normally distributed emission...

rpois.hsmm: Random number generation from a Poisson distributed emission...

sim.mc: Markov chain simulation

simulate.hmmspec: Simulation of hidden Markov models

simulate.hsmmspec: Simulation for HSMMs

smooth.discrete: Smoothing a discrete time series.

summary.hmm: Summary method for hmm objects

summary.hsmm: Summary function for hsmm

Functions

addStates Man page
createTransition Man page
dmvnorm.hsmm Man page
dnorm.hsmm Man page
dpois.hsmm Man page
gammafit Man page
hmmfit Man page
hmmspec Man page
hsmmfit Man page
hsmmspec Man page
mstep.mvnorm Man page
mstep.norm Man page
mstep.pois Man page
plot.hsmm Man page
plot.hsmm.data Man page
predict.hmm Man page
predict.hmmspec Man page
predict.hsmm Man page
predict.hsmmspec Man page
predict.smoothDiscrete Man page
print.hmm Man page
print.hmmspec Man page
print.hsmmspec Man page
print.smoothDiscrete Man page
reproai Man page
reprocows Man page
rmvnorm.hsmm Man page
rnorm.hsmm Man page
rpois.hsmm Man page
sim.mc Man page
simulate.hmmspec Man page
simulate.hsmmspec Man page
smooth.discrete Man page
summary.hmm Man page
summary.hsmm Man page
summary.smoothDiscrete Man page

Files

mhsmm
mhsmm/inst
mhsmm/inst/CITATION
mhsmm/inst/doc
mhsmm/inst/doc/DHMM2.Rnw
mhsmm/inst/doc/DHMM1.R
mhsmm/inst/doc/DHMM1.pdf
mhsmm/inst/doc/DHMM2.pdf
mhsmm/inst/doc/DHMM2.R
mhsmm/inst/doc/DHMM1.Rnw
mhsmm/src
mhsmm/src/hsmm.c
mhsmm/NAMESPACE
mhsmm/data
mhsmm/data/reproai.RData
mhsmm/data/reproppa.RData
mhsmm/data/reprocows.RData
mhsmm/R
mhsmm/R/smooth.discrete-src.R mhsmm/R/hsmm_functions.R mhsmm/R/spec_functions.R mhsmm/R/plotting_functions.R mhsmm/R/hmm_functions.R
mhsmm/vignettes
mhsmm/vignettes/DHMM2.Rnw
mhsmm/vignettes/fig
mhsmm/vignettes/fig/dhmm-011.pdf
mhsmm/vignettes/fig/dhmm-008.eps
mhsmm/vignettes/fig/dhmm-017.pdf
mhsmm/vignettes/fig/dhmm-clsfig1.eps
mhsmm/vignettes/fig/dhmm-014.pdf
mhsmm/vignettes/fig/dhmm-008.pdf
mhsmm/vignettes/fig/dhmm-clsfig2.pdf
mhsmm/vignettes/fig/dhmm-clsfig1.pdf
mhsmm/vignettes/fig/dhmm-009.pdf
mhsmm/vignettes/fig/dhmm-012.eps
mhsmm/vignettes/fig/dhmm-009.eps
mhsmm/vignettes/fig/dhmm-017.eps
mhsmm/vignettes/fig/smooth-smooth1.pdf
mhsmm/vignettes/fig/dhmm-012.pdf
mhsmm/vignettes/fig/dhmm-015.pdf
mhsmm/vignettes/fig/smooth-smooth1.eps
mhsmm/vignettes/fig/dhmm-018.eps
mhsmm/vignettes/fig/dhmm-014.eps
mhsmm/vignettes/fig/dhmm-011.eps
mhsmm/vignettes/fig/dhmm-018.pdf
mhsmm/vignettes/fig/dhmm-clsfig2.eps
mhsmm/vignettes/fig/dhmm-015.eps
mhsmm/vignettes/clsX.RData
mhsmm/vignettes/DHMM1.Rnw
mhsmm/MD5
mhsmm/README
mhsmm/build
mhsmm/build/vignette.rds
mhsmm/DESCRIPTION
mhsmm/ChangeLog
mhsmm/man
mhsmm/man/rpois.hsmm.Rd mhsmm/man/hsmmfit.Rd mhsmm/man/print.hsmmspec.Rd mhsmm/man/predict.hsmmspec.Rd mhsmm/man/print.hmm.Rd mhsmm/man/hmmspec.Rd mhsmm/man/dnorm.hsmm.Rd mhsmm/man/sim.mc.Rd mhsmm/man/mstep.norm.Rd mhsmm/man/gammafit.Rd mhsmm/man/plot.hsmm.data.Rd mhsmm/man/mstep.pois.Rd mhsmm/man/predict.hsmm.Rd mhsmm/man/predict.hmm.Rd mhsmm/man/smooth.discrete.Rd mhsmm/man/rmvnorm.hsmm.Rd mhsmm/man/predict.hmmspec.Rd mhsmm/man/rnorm.hsmm.Rd mhsmm/man/addStates.Rd mhsmm/man/mstep.mvnorm.Rd mhsmm/man/summary.hsmm.Rd mhsmm/man/reprocows.Rd mhsmm/man/print.hmmspec.Rd mhsmm/man/hsmmspec.Rd mhsmm/man/hmmfit.Rd mhsmm/man/dmvnorm.hsmm.Rd mhsmm/man/plot.hsmm.Rd mhsmm/man/simulate.hsmmspec.Rd mhsmm/man/simulate.hmmspec.Rd
mhsmm/man/reproppa.rd
mhsmm/man/summary.hmm.Rd mhsmm/man/reproai.Rd mhsmm/man/dpois.hsmm.Rd

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