R: Extensible Markov Model for Modelling Temporal Relationships Between Clusters

# Extensible Markov Model for Modelling Temporal Relationships Between Clusters

## Documentation for package ‘rEMM’ version 1.2.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M N O P R S T U misc

## -- A --

Alphaproteobacteria16S | Count Data for 16S rRNA Sequences
as.graph | Class "TRACDS"
as.graph.TRACDS | Class "TRACDS"
as.igraph | Class "TRACDS"
as.igraph.TRACDS | Class "TRACDS"

## -- B --

build | Building an EMM using New Data
build-method | Building an EMM using New Data

## -- C --

c | Combining EMM Objects
c-method | Combining EMM Objects
cluster | Data stream clustering with tNN
cluster-method | Data stream clustering with tNN
clusters | Class "tNN"
clusters-method | Class "tNN"
cluster_centers | Class "tNN"
cluster_centers-method | Class "tNN"
cluster_counts | Class "tNN"
cluster_counts-method | Class "tNN"
compact | Update a TRACDS temporal structure with new state assignements
compact-method | Update a TRACDS temporal structure with new state assignements
copy | Class "EMM"
copy-method | Class "EMM"
copy-method | Class "TRACDS"
copy-method | Class "tNN"
current_state | Class "TRACDS"
current_state-method | Class "TRACDS"

## -- D --

Derwent | Derwent Catchment Data
DSC_EMM | DSC Interface for EMM and tNN (package stream)
DSC_tNN | DSC Interface for EMM and tNN (package stream)

## -- E --

EMM | Creator for Class "EMM"
EMM-class | Class "EMM"
EMMsim | Synthetic Data to Demonstrate EMMs
EMMsim_sequence_test | Synthetic Data to Demonstrate EMMs
EMMsim_sequence_train | Synthetic Data to Demonstrate EMMs
EMMsim_test | Synthetic Data to Demonstrate EMMs
EMMsim_train | Synthetic Data to Demonstrate EMMs
EMMTraffic | Hypothetical Traffic Data Set for EMM

## -- F --

fade | Fading Cluster Structure and EMM Layer
fade-method | Fading Cluster Structure and EMM Layer
find_clusters | Find the EMM State/Cluster for an Observation
find_clusters-method | Find the EMM State/Cluster for an Observation

## -- G --

get_EMM | DSC Interface for EMM and tNN (package stream)

## -- I --

initial_transition | Access Transition Probabilities/Counts in an EMM
initial_transition-method | Access Transition Probabilities/Counts in an EMM

## -- L --

last_clustering | Class "tNN"
last_clustering-method | Class "tNN"

## -- M --

merge_clusters | Merge States of an EMM
merge_clusters-method | Merge States of an EMM
Mollicutes16S | Count Data for 16S rRNA Sequences

## -- N --

nclusters | Class "tNN"
nclusters-method | Class "tNN"
nstates | Class "TRACDS"
nstates-method | Class "TRACDS"
ntransitions | Class "TRACDS"
ntransitions-method | Class "TRACDS"

## -- O --

object.size-method | Creator for Class "EMM"
object.size-method | Class "TRACDS"
object.size-method | Class "tNN"

## -- P --

plot | Visualize EMM Objects
plot-method | Class "TRACDS"
plot-method | Visualize EMM Objects
plot-method | Class "tNN"
predict | Predict a Future State
predict-method | Predict a Future State
prune | Prune States and/or Transitions
prune-method | Prune States and/or Transitions

## -- R --

rare_clusters | Prune States and/or Transitions
rare_clusters-method | Prune States and/or Transitions
rare_transitions | Prune States and/or Transitions
rare_transitions-method | Prune States and/or Transitions
recluster | Reclustering EMM states
recluster_hclust | Reclustering EMM states
recluster_hclust-method | Reclustering EMM states
recluster_kmeans | Reclustering EMM states
recluster_kmeans-method | Reclustering EMM states
recluster_pam | Reclustering EMM states
recluster_pam-method | Reclustering EMM states
recluster_reachability | Reclustering EMM states
recluster_reachability-method | Reclustering EMM states
recluster_tNN | Reclustering EMM states
recluster_tNN-method | Reclustering EMM states
recluster_transitions | Reclustering EMM states
recluster_transitions-method | Reclustering EMM states
remove_clusters | Remove States/Clusters or Transitions from an EMM
remove_clusters-method | Remove States/Clusters or Transitions from an EMM
remove_selftransitions | Remove States/Clusters or Transitions from an EMM
remove_selftransitions-method | Remove States/Clusters or Transitions from an EMM
remove_transitions | Remove States/Clusters or Transitions from an EMM
remove_transitions-method | Remove States/Clusters or Transitions from an EMM
reset | Update a TRACDS temporal structure with new state assignements
reset-method | Update a TRACDS temporal structure with new state assignements

## -- S --

score | Score a New Sequence Given an EMM
score-method | Score a New Sequence Given an EMM
set_EMM | DSC Interface for EMM and tNN (package stream)
show-method | Class "EMM"
show-method | Class "TRACDS"
size | Class "EMM"
size-method | Class "EMM"
smooth_transitions | Smooths transition counts between neighboring states/clusters
smooth_transitions-method | Smooths transition counts between neighboring states/clusters
states | Class "TRACDS"
states-method | Class "TRACDS"
StreamClustering-class | Class "tNN"
synthetic_stream | Create a Synthetic Data Stream

## -- T --

tNN | Class "tNN"
tNN-class | Class "tNN"
TRAC | TRAC: Creating a Markov Model from a Regular Clustering
TRACDS | Class "TRACDS"
TRACDS-class | Class "TRACDS"
transition | Access Transition Probabilities/Counts in an EMM
transition-method | Access Transition Probabilities/Counts in an EMM
transitions | Class "TRACDS"
transitions-method | Class "TRACDS"
transition_matrix | Access Transition Probabilities/Counts in an EMM
transition_matrix-method | Access Transition Probabilities/Counts in an EMM
transition_table | Extract a Transition Table for a New Sequence Given an EMM
transition_table-method | Extract a Transition Table for a New Sequence Given an EMM

## -- U --

update | Update a TRACDS temporal structure with new state assignements
update-method | Update a TRACDS temporal structure with new state assignements

## -- misc --

16S | Count Data for 16S rRNA Sequences