A B C D E F G I L M N O P R S T U misc
| 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" |
| build | Building an EMM using New Data |
| build-method | Building an EMM using New Data |
| 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" |
| Derwent | Derwent Catchment Data |
| DSC_EMM | DSC Interface for EMM and tNN (package stream) |
| DSC_tNN | DSC Interface for EMM and tNN (package stream) |
| 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 |
| 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 |
| get_EMM | DSC Interface for EMM and tNN (package stream) |
| initial_transition | Access Transition Probabilities/Counts in an EMM |
| initial_transition-method | Access Transition Probabilities/Counts in an EMM |
| last_clustering | Class "tNN" |
| last_clustering-method | Class "tNN" |
| merge_clusters | Merge States of an EMM |
| merge_clusters-method | Merge States of an EMM |
| Mollicutes16S | Count Data for 16S rRNA Sequences |
| nclusters | Class "tNN" |
| nclusters-method | Class "tNN" |
| nstates | Class "TRACDS" |
| nstates-method | Class "TRACDS" |
| ntransitions | Class "TRACDS" |
| ntransitions-method | Class "TRACDS" |
| object.size-method | Creator for Class "EMM" |
| object.size-method | Class "TRACDS" |
| object.size-method | Class "tNN" |
| 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 |
| 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 |
| 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 |
| 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 |
| update | Update a TRACDS temporal structure with new state assignements |
| update-method | Update a TRACDS temporal structure with new state assignements |
| 16S | Count Data for 16S rRNA Sequences |