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.

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
http://lyle.smu.edu/IDA/TRACDS/

View on CRAN

Functions

16S Man page
Alphaproteobacteria16S Man page
as.graph Man page
as.graph.TRACDS Man page
as.igraph Man page
as.igraph.TRACDS Man page
build Man page
build,EMM,data.frame-method Man page
build,EMM,data.frame-method Man page
build,EMM,matrix-method Man page
build,EMM,matrix-method Man page
build,EMM,numeric-method Man page
build,EMM,numeric-method Man page
c Man page
c,EMM-method Man page
cluster 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
cluster,tNN,data.frame-method Man page
cluster,tNN,matrix-method Man page
cluster,tNN,numeric-method Man page
compact Man page
compact,TRACDS-method Man page
copy Man page
copy,EMM-method Man page
copy,tNN-method Man page
copy,TRACDS-method Man page
current_state Man page
current_state,TRACDS-method Man page
Derwent Man page
EMM Man page
EMM-class Man page
EMMsim Man page
EMMsim_sequence_test Man page
EMMsim_sequence_train Man page
EMMsim_test Man page
EMMsim_train Man page
EMMTraffic Man page
fade Man page
fade,EMM,missing,missing-method Man page
fade,EMM,missing,numeric-method Man page
fade,EMM,numeric-method Man page
fade,EMM,numeric,missing-method Man page
fade,EMM,numeric,numeric-method Man page
find_clusters Man page
find_clusters,tNN,data.frame-method Man page
find_clusters,tNN,matrix-method Man page
find_clusters,tNN,matrix-method Man page
find_clusters,tNN,numeric-method Man page
find_clusters,tNN,numeric-method Man page
initial_transition Man page
initial_transition,TRACDS-method Man page
initial_transition,TRACDS-method Man page
last_clustering Man page
last_clustering,tNN-method Man page
merge_clusters Man page
merge_clusters,EMM,character-method Man page
merge_clusters,EMM,character-method Man page
merge_clusters,EMM,integer-method Man page
Mollicutes16S Man page
nclusters Man page
nclusters,tNN-method Man page
nstates Man page
nstates,TRACDS-method Man page
ntransitions Man page
ntransitions,TRACDS-method Man page
object.size,EMM-method Man page
object.size,tNN-method Man page
object.size,TRACDS-method Man page
plot Man page
plot,EMM,missing-method Man page
plot,EMM,missing-method Man page
plot,tNN,missing-method Man page
plot,TRACDS,missing-method Man page
predict Man page
predict,TRACDS-method Man page
predict,TRACDS-method Man page
prune Man page
prune,EMM-method Man page
prune,EMM,numeric-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
recluster_hclust,EMM-method Man page
recluster_kmeans Man page
recluster_kmeans,EMM-method Man page
recluster_kmeans,EMM-method Man page
recluster_pam Man page
recluster_pam,EMM-method Man page
recluster_pam,EMM-method 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
remove_clusters,EMM,character-method Man page
remove_selftransitions Man page
remove_selftransitions,EMM-method Man page
remove_selftransitions,EMM-method Man page
remove_transitions Man page
remove_transitions,EMM,character,character-method Man page
remove_transitions,EMM,character,character-method 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,data.frame-method Man page
score,EMM,data.frame-method Man page
score,EMM,EMM-method Man page
score,EMM,matrix-method Man page
score,EMM,matrix-method Man page
score,EMM,numeric-method Man page
score,EMM,numeric-method Man page
show,EMM-method Man page
show,TRACDS-method Man page
size Man page
size,EMM-method Man page
smooth_transitions Man page
smooth_transitions,EMM-method Man page
states Man page
states,TRACDS-method Man page
StreamClustering-class Man page
synthetic_stream Man page
tNN Man page
tNN-class Man page
TRAC Man page
TRACDS Man page
TRACDS-class Man page
transition Man page
transition_matrix Man page
transition_matrix,TRACDS-method Man page
transition_matrix,TRACDS-method Man page
transitions Man page
transitions,TRACDS-method 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
transition,TRACDS,character,character-method Man page
transition,TRACDS,character,character-method Man page
transition,TRACDS,data.frame,missing-method Man page
transition,TRACDS,data.frame,missing-method Man page
transition,TRACDS,matrix,missing-method Man page
update Man page
update,TRACDS-method Man page

Files

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

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