Extensible Markov Model for Modelling Temporal Relationships Between Clusters

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Documentation for package ‘rEMM’ version 1.2.1

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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