Package: drimmR 1.0.1

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

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drimmR/json (API)

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

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

1.00 score 160 downloads 18 exports 125 dependencies

Last updated 3 years agofrom:788501c2cd. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winOKOct 10 2024
R-4.5-linuxOKOct 10 2024
R-4.4-winOKOct 10 2024
R-4.4-macOKOct 10 2024
R-4.3-winOKOct 10 2024
R-4.3-macOKOct 10 2024

Exports:aicavailabilitybicdistributionsfailureRatefitdmmgetDistributiongetStationaryLawgetTransitionMatrixlengthWord_probabilitiesloglikmaintainabilityreliabilitysimulatestationary_distributionsword_probabilitiesword_probabilitywords_probabilities

Dependencies:ade4askpassbackportsbase64encbitbit64blobbroombslibcachemcallrcellrangerclicliprcodetoolscolorspaceconflictedcpp11crayoncurldata.tableDBIdbplyrdigestdoParalleldplyrdtplyrevaluatefansifarverfastmapfontawesomeforcatsforeachfsfuturegarglegenericsggplot2globalsgluegoogledrivegooglesheets4gtablehavenhighrhmshtmltoolshttridsisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlubridatemagrittrMASSMatrixmemoisemgcvmimemodelrmunsellnlmeopensslparallellypillarpixmappkgconfigplyrprettyunitsprocessxprogresspspurrrR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRdpackreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownrstudioapirvestsassscalessegmentedselectrseqinrspstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdbutf8uuidvctrsviridisLitevroomwithrxfunxml2yaml

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