rEMM v1.0-11
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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.
Functions in rEMM
| Name | Description | |
| find_clusters | Find the EMM State/Cluster for an Observation | |
| EMMTraffic | Hypothetical Traffic Data Set for EMM | |
| EMM | Creator for Class "EMM" | |
| predict | Predict a Future State | |
| EMM-class | Class "EMM" | |
| score | Score a New Sequence Given an EMM | |
| prune | Prune States and/or Transitions | |
| fade | Fading Cluster Structure and EMM Layer | |
| transition | Access Transition Probabilities/Counts in an EMM | |
| Derwent | Derwent Catchment Data | |
| build | Building an EMM using New Data | |
| remove | Remove States/Clusters or Transitions from an EMM | |
| tNN-class | Class "tNN" | |
| smooth_transitions | Smooths transition counts between neighboring states/clusters | |
| cluster | Data stream clustering with tNN | |
| merge_clusters | Merge States of an EMM | |
| 16S | Count Data for 16S rRNA Sequences | |
| transition_table | Extract a Transition Table for a New Sequence Given an EMM | |
| recluster | Reclustering EMM states | |
| combine | Combining EMM Objects | |
| update | Update a TRACDS temporal structure with new state assignements | |
| EMMsim | Synthetic Data to Demonstrate EMMs | |
| TRACDS-class | Class "TRACDS" | |
| synthetic_stream | Create a Synthetic Data Stream | |
| plot | Visualize EMM Objects | |
| TRAC | TRAC: Creating an EMM from a Regular Clustering | |
| No Results! | ||
Vignettes of rEMM
| Name | ||
| emm.bib | ||
| misc.bib | ||
| rEMM.Rnw | ||
| rEMM.bib | ||
| rEMM_class.odg | ||
| rEMM_class.pdf | ||
| rna_sequences.bib | ||
| stream_clust.bib | ||
| No Results! | ||
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Details
| Date | 2015-07-23 |
| Classification/ACM | G.4, H.2.8, I.5.1 |
| URL | http://lyle.smu.edu/IDA/TRACDS/ |
| License | GPL-2 |
| NeedsCompilation | yes |
| Packaged | 2015-07-23 22:02:39 UTC; hahsler |
| Repository | CRAN |
| Date/Publication | 2015-07-24 07:54:05 |
| depends | base (>= 2.10.0) , igraph , proxy (>= 0.4-7) , R (>= 2.10.0) |
| imports | cluster , clusterGeneration , MASS , methods , stats , utils |
| suggests | graph , Rgraphviz , testthat |
| Contributors | Michael Hahsler, Margaret H. Dunham |
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