Package: drimmR 1.0.3

drimmR: Estimation, Simulation and Reliability of Drifting Markov Models

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), <doi:10.2202/1544-6115.1326> and Barbu, V.S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8> .

Authors:Nicolas Vergne [aut, cre], Corentin Lothodé [aut], Alexandre Seiller [aut], Victor Mataigne [ctb], Arnaud Lefebvre [ctb], Annthomy Gilles [ctb], Vlad Stefan Barbu [aut]

drimmR_1.0.3.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
drimmR/json (API)
NEWS

# Install 'drimmR' in R:
install.packages('drimmR', repos = c('https://nicolasv-dev.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 211 downloads 18 exports 46 dependencies

Last updated from:3aa3241ea3. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK162
source / vignettesOK216
linux-release-x86_64OK142
macos-release-arm64OK170
macos-oldrel-arm64OK201
windows-develOK130
windows-releaseOK109
windows-oldrelOK120
wasm-releaseOK100

Exports:aicavailabilitybicdistributionsfailureRatefitdmmgetDistributiongetStationaryLawgetTransitionMatrixlengthWord_probabilitiesloglikmaintainabilityreliabilitysimulatestationary_distributionsword_probabilitiesword_probabilitywords_probabilities

Dependencies:ade4clicodetoolscpp11doParalleldplyrfarverforeachgenericsggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSnlmeparallellypillarpixmappkgconfigplyrR6rbibutilsRColorBrewerRcppRcppArmadilloRdpackreshape2rlangS7scalessegmentedseqinrspstringistringrtibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
drimmR-packagedrimmR-package drimmR
Akaike Information Criterion (AIC)aic
Evaluate the AIC of a drifting Markov Modelaic.dmm
Availability functionavailability
Bayesian Information Criterion (BIC)bic
Evaluate the BIC of a drifting Markov Modelbic.dmm
Distributions for a range of positions between <start> and <end>distributions
Failure rates functionfailureRate
Point by point estimates of a k-th order drifting Markov Modelfitdmm
Distributions of the drifting Markov ModelgetDistribution
Get the distributions of the DMMgetDistribution.dmm
Stationary laws of the drifting Markov ModelgetStationaryLaw
Get the stationary laws of the DMMgetStationaryLaw.dmm
Transition matrix of the drifting Markov ModelgetTransitionMatrix
Get transition matrix of the drifting Markov ModelgetTransitionMatrix.dmm
lambda genomelambda
Probability of occurrence of the observed word of size m in a sequence at several positionslengthWord_probabilities
Log-likelihood of the drifting Markov Modelloglik
Evaluate the log-likelihood of a drifting Markov Modelloglik.dmm
Maintainability functionmaintainability
Reliability functionreliability
Simulate a sequence under a drifting Markov modelsimulate
Simulate a sequence under a drifting Markov modelsimulate.dmm
Stationary laws for a range of positions between <start> and <end>stationary_distributions
Probabilities of a word at several positions of a DMMword_probabilities
Probability of a word at a position t of a DMMword_probability
Probability of appearance of several words at several positions of a DMMwords_probabilities