rEMM: Extensible Markov Model for Modelling Temporal Relationships Between Clusters

Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN data stream clustering). Development of this package was supported in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute.

Author
Michael Hahsler [aut, cre, cph], Margaret H. Dunham [aut, cph]
Date of publication
2015-07-24 07:54:05
Maintainer
Michael Hahsler <mhahsler@lyle.smu.edu>
License
GPL-2
Version
1.0-11
URLs

View on CRAN

Man pages

16S
Count Data for 16S rRNA Sequences
build
Building an EMM using New Data
cluster
Data stream clustering with tNN
combine
Combining EMM Objects
conversion
TRAC: Creating an EMM from a Regular Clustering
Derwent
Derwent Catchment Data
EMM
Creator for Class "EMM"
EMM-class
Class "EMM"
EMMsim
Synthetic Data to Demonstrate EMMs
EMMTraffic
Hypothetical Traffic Data Set for EMM
fade
Fading Cluster Structure and EMM Layer
find_clusters
Find the EMM State/Cluster for an Observation
merge
Merge States of an EMM
plot.EMM
Visualize EMM Objects
predict
Predict a Future State
prune
Prune States and/or Transitions
recluster
Reclustering EMM states
remove
Remove States/Clusters or Transitions from an EMM
score
Score a New Sequence Given an EMM
smooth_transitions
Smooths transition counts between neighboring states/clusters
synthetic_stream
Create a Synthetic Data Stream
tNN-class
Class "tNN"
TRACDS-class
Class "TRACDS"
transition
Access Transition Probabilities/Counts in an EMM
transition_table
Extract a Transition Table for a New Sequence Given an EMM
update
Update a TRACDS temporal structure with new state...

Files in this package

rEMM
rEMM/inst
rEMM/inst/CITATION
rEMM/inst/tests
rEMM/inst/tests/test-EMM.R
rEMM/inst/tests/test-remove.R
rEMM/inst/NEWS
rEMM/inst/doc
rEMM/inst/doc/rEMM.R
rEMM/inst/doc/rEMM.pdf
rEMM/inst/doc/rEMM.Rnw
rEMM/tests
rEMM/tests/testthat.R
rEMM/src
rEMM/src/matrix.c
rEMM/src/matrix_pos.h
rEMM/NAMESPACE
rEMM/data
rEMM/data/EMMTraffic.rda
rEMM/data/16S.rda
rEMM/data/Derwent.rda
rEMM/data/EMMsim.rda
rEMM/R
rEMM/R/AllClasses.R
rEMM/R/TRACDS.R
rEMM/R/reset.R
rEMM/R/AllGenerics.R
rEMM/R/onload.R
rEMM/R/combine.R
rEMM/R/tNN.R
rEMM/R/plot.R
rEMM/R/smooth_transitions.R
rEMM/R/fade.R
rEMM/R/SimpleMC.R
rEMM/R/predict.R
rEMM/R/score.R
rEMM/R/synthetic_stream.R
rEMM/R/recluster.R
rEMM/R/update.R
rEMM/R/map.R
rEMM/R/remove.R
rEMM/R/ellipse.R
rEMM/R/graph.R
rEMM/R/conversion.R
rEMM/R/cluster.R
rEMM/R/compact.R
rEMM/R/merge.R
rEMM/R/prune.R
rEMM/R/EMM.R
rEMM/R/transition.R
rEMM/R/AAA.R
rEMM/R/build.R
rEMM/R/object.size.R
rEMM/vignettes
rEMM/vignettes/rna_sequences.bib
rEMM/vignettes/misc.bib
rEMM/vignettes/rEMM_class.pdf
rEMM/vignettes/stream_clust.bib
rEMM/vignettes/rEMM_class.odg
rEMM/vignettes/rEMM.bib
rEMM/vignettes/rEMM.Rnw
rEMM/vignettes/emm.bib
rEMM/MD5
rEMM/build
rEMM/build/vignette.rds
rEMM/DESCRIPTION
rEMM/man
rEMM/man/remove.Rd
rEMM/man/fade.Rd
rEMM/man/synthetic_stream.Rd
rEMM/man/16S.Rd
rEMM/man/score.Rd
rEMM/man/combine.Rd
rEMM/man/smooth_transitions.Rd
rEMM/man/transition_table.Rd
rEMM/man/EMM-class.Rd
rEMM/man/cluster.Rd
rEMM/man/EMMTraffic.Rd
rEMM/man/update.Rd
rEMM/man/merge.Rd
rEMM/man/predict.Rd
rEMM/man/plot.EMM.Rd
rEMM/man/Derwent.Rd
rEMM/man/find_clusters.Rd
rEMM/man/prune.Rd
rEMM/man/tNN-class.Rd
rEMM/man/build.Rd
rEMM/man/EMM.Rd
rEMM/man/transition.Rd
rEMM/man/recluster.Rd
rEMM/man/EMMsim.Rd
rEMM/man/conversion.Rd
rEMM/man/TRACDS-class.Rd