Learn R Programming

drimmR (version 1.0.1)

Estimation, Simulation and Reliability of Drifting Markov Models

Description

Performs the drifting Markov models (DMM) which are non-homogeneous Markov models designed for modeling the heterogeneities of sequences in a more flexible way than homogeneous Markov chains or even hidden Markov models. In this context, we developed an R package dedicated to the estimation, simulation and the exact computation of associated reliability of drifting Markov models. The implemented methods are described in Vergne, N. (2008), and Barbu, V.S., Vergne, N. (2019) .

Copy Link

Version

Install

install.packages('drimmR')

Monthly Downloads

201

Version

1.0.1

License

GPL-3

Maintainer

Nicolas Vergne

Last Published

May 10th, 2021

Functions in drimmR (1.0.1)

lambda

lambda genome
loglik

Log-likelihood of the drifting Markov Model
lengthWord_probabilities

Probability of occurrence of the observed word of size m in a sequence at several positions
simulate.dmm

Simulate a sequence under a drifting Markov model
stationary_distributions

Stationary laws for a range of positions between <start> and <end>
bic.dmm

Evaluate the BIC of a drifting Markov Model
reliability

Reliability function
getDistribution.dmm

Get the distributions of the DMM
getStationaryLaw

Stationary laws of the drifting Markov Model
simulate

Simulate a sequence under a drifting Markov model
getStationaryLaw.dmm

Get the stationary laws of the DMM
distributions

Distributions for a range of positions between <start> and <end>
getTransitionMatrix

Transition matrix of the drifting Markov Model
words_probabilities

Probability of appearance of several words at several positions of a DMM
loglik.dmm

Evaluate the log-likelihood of a drifting Markov Model
fitdmm

Point by point estimates of a k-th order drifting Markov Model
getDistribution

Distributions of the drifting Markov Model
aic

Akaike Information Criterion (AIC)
maintainability

Maintainability function
aic.dmm

Evaluate the AIC of a drifting Markov Model
word_probability

Probability of a word at a position t of a DMM
word_probabilities

Probabilities of a word at several positions of a DMM
failureRate

Failure rates function
drimmR-package

drimmR-package
availability

Availability function
bic

Bayesian Information Criterion (BIC)
getTransitionMatrix.dmm

Get transition matrix of the drifting Markov Model