rEMM: Extensible Markov Model for Modelling Temporal Relationships Between Clusters
Version 1.0-11

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.

AuthorMichael Hahsler [aut, cre, cph], Margaret H. Dunham [aut, cph]
Date of publication2015-07-24 07:54:05
MaintainerMichael Hahsler <mhahsler@lyle.smu.edu>
LicenseGPL-2
Version1.0-11
URL http://lyle.smu.edu/IDA/TRACDS/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rEMM")

Popular man pages

16S: Count Data for 16S rRNA Sequences
build: Building an EMM using New Data
combine: Combining EMM Objects
EMMsim: Synthetic Data to Demonstrate EMMs
fade: Fading Cluster Structure and EMM Layer
merge: Merge States of an EMM
TRACDS-class: Class "TRACDS"
See all...

All man pages Function index File listing

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...

Functions

16S Man page
Alphaproteobacteria16S Man page
Derwent Man page
EMM Man page Source code
EMM-class Man page
EMMTraffic Man page
EMMsim Man page
EMMsim_sequence_test Man page
EMMsim_sequence_train Man page
EMMsim_test Man page
EMMsim_train Man page
Mollicutes16S Man page
SimpleMC Source code
StreamClustering-class Man page
TRAC Man page Source code
TRACDS Man page Source code
TRACDS-class Man page
as.graph Man page Source code
as.graph.TRACDS Man page Source code
as.igraph Man page Source code
as.igraph.TRACDS Man page Source code
build Man page
build,EMM,data.frame-method Man page Man page
build,EMM,matrix-method Man page Man page
build,EMM,numeric-method Man page Man page
c Man page
c,EMM-method Man page
cluster Man page
cluster,tNN,data.frame-method Man page
cluster,tNN,matrix-method Man page
cluster,tNN,numeric-method Man page
cluster_centers Man page
cluster_centers,tNN-method Man page
cluster_counts Man page
cluster_counts,tNN-method Man page
clusters Man page
clusters,tNN-method Man page
compact Man page
compact,TRACDS-method Man page
copy Man page
copy,EMM-method Man page
copy,TRACDS-method Man page
copy,tNN-method Man page
current_state Man page
current_state,TRACDS-method Man page
ellipsePoints Source code
fade Man page Source code
fade,EMM,missing,missing-method Man page
fade,EMM,missing,numeric-method Man page
fade,EMM,numeric,missing-method Man page
fade,EMM,numeric,numeric-method Man page
fade,EMM,numeric-method Man page
find_clusters Man page
find_clusters,tNN,data.frame-method Man page
find_clusters,tNN,matrix-method Man page Man page
find_clusters,tNN,numeric-method Man page Man page
find_medoids Source code
get_parameters Source code
initial_transition Man page
initial_transition,TRACDS-method Man page Man page
last_clustering Man page
last_clustering,tNN-method Man page
map Source code
merge_clusters Man page
merge_clusters,EMM,character-method Man page Man page
merge_clusters,EMM,integer-method Man page
nclusters Man page
nclusters,tNN-method Man page
nstalled Source code
nstates Man page
nstates,TRACDS-method Man page
ntransitions Man page
ntransitions,TRACDS-method Man page
object.size,EMM-method Man page
object.size,TRACDS-method Man page
object.size,tNN-method Man page
onLoad Source code
plot Man page
plot,EMM,missing-method Man page Man page
plot,TRACDS,missing-method Man page
plot,tNN,missing-method Man page
predict Man page
predict,TRACDS-method Man page Man page
prune Man page
prune,EMM,numeric-method Man page
prune,EMM-method Man page
rare_clusters Man page
rare_clusters,EMM,numeric-method Man page
rare_clusters,tNN-method Man page
rare_transitions Man page
rare_transitions,EMM,numeric-method Man page
rare_transitions,TRACDS-method Man page
recluster Man page
recluster_hclust Man page
recluster_hclust,EMM-method Man page Man page
recluster_kmeans Man page
recluster_kmeans,EMM-method Man page Man page
recluster_pam Man page
recluster_pam,EMM-method Man page Man page
recluster_reachability Man page
recluster_reachability,EMM-method Man page
recluster_tNN Man page
recluster_tNN,EMM-method Man page
recluster_transitions Man page
recluster_transitions,EMM-method Man page
remove_clusters Man page
remove_clusters,EMM,character-method Man page Man page
remove_selftransitions Man page
remove_selftransitions,EMM-method Man page Man page
remove_transitions Man page
remove_transitions,EMM,character,character-method Man page Man page
remove_transitions,EMM,data.frame,missing-method Man page
remove_transitions,EMM,matrix,missing-method Man page
reset Man page
reset,TRACDS-method Man page
score Man page
score,EMM,EMM-method Man page
score,EMM,data.frame-method Man page Man page
score,EMM,matrix-method Man page Man page
score,EMM,numeric-method Man page Man page
show,EMM-method Man page
show,TRACDS-method Man page
simil_weight Source code
size Man page
size,EMM-method Man page
smc_addState Source code
smc_addTransition Source code
smc_as.graph Source code
smc_as.igraph Source code
smc_compact Source code
smc_containsState Source code
smc_countMatrix Source code
smc_expand Source code
smc_fade Source code
smc_initialCounts Source code
smc_mergeStates Source code
smc_names2index Source code
smc_removeSelfTransition Source code
smc_removeState Source code
smc_removeTransition Source code
smc_setTransitions Source code
smc_size Source code
smc_states Source code
smooth_transitions Man page
smooth_transitions,EMM-method Man page
states Man page
states,TRACDS-method Man page
synthetic_stream Man page Source code
tNN Man page Source code
tNN-class Man page
transition Man page
transition,TRACDS,character,character-method Man page Man page
transition,TRACDS,data.frame,missing-method Man page Man page
transition,TRACDS,matrix,missing-method Man page
transition_matrix Man page
transition_matrix,TRACDS-method Man page Man page
transition_table Man page
transition_table,EMM,data.frame-method Man page
transition_table,EMM,matrix-method Man page
transition_table,EMM,numeric-method Man page
transitions Man page
transitions,TRACDS-method Man page
update Man page
update,TRACDS-method Man page

Files

inst
inst/CITATION
inst/tests
inst/tests/test-EMM.R
inst/tests/test-remove.R
inst/NEWS
inst/doc
inst/doc/rEMM.R
inst/doc/rEMM.pdf
inst/doc/rEMM.Rnw
tests
tests/testthat.R
src
src/matrix.c
src/matrix_pos.h
NAMESPACE
data
data/EMMTraffic.rda
data/16S.rda
data/Derwent.rda
data/EMMsim.rda
R
R/AllClasses.R
R/TRACDS.R
R/reset.R
R/AllGenerics.R
R/onload.R
R/combine.R
R/tNN.R
R/plot.R
R/smooth_transitions.R
R/fade.R
R/SimpleMC.R
R/predict.R
R/score.R
R/synthetic_stream.R
R/recluster.R
R/update.R
R/map.R
R/remove.R
R/ellipse.R
R/graph.R
R/conversion.R
R/cluster.R
R/compact.R
R/merge.R
R/prune.R
R/EMM.R
R/transition.R
R/AAA.R
R/build.R
R/object.size.R
vignettes
vignettes/rna_sequences.bib
vignettes/misc.bib
vignettes/rEMM_class.pdf
vignettes/stream_clust.bib
vignettes/rEMM_class.odg
vignettes/rEMM.bib
vignettes/rEMM.Rnw
vignettes/emm.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/remove.Rd
man/fade.Rd
man/synthetic_stream.Rd
man/16S.Rd
man/score.Rd
man/combine.Rd
man/smooth_transitions.Rd
man/transition_table.Rd
man/EMM-class.Rd
man/cluster.Rd
man/EMMTraffic.Rd
man/update.Rd
man/merge.Rd
man/predict.Rd
man/plot.EMM.Rd
man/Derwent.Rd
man/find_clusters.Rd
man/prune.Rd
man/tNN-class.Rd
man/build.Rd
man/EMM.Rd
man/transition.Rd
man/recluster.Rd
man/EMMsim.Rd
man/conversion.Rd
man/TRACDS-class.Rd
rEMM documentation built on May 19, 2017, 10:56 p.m.

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