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| 16S | Count Data for 16S rRNA Sequences |
| Alphaproteobacteria16S | Count Data for 16S rRNA Sequences |
| build | Building an EMM using New Data |
| build-method | Building an EMM using New Data |
| current_state | Class "EMMLayer" |
| current_state-method | Class "EMMLayer" |
| Derwent | Derwent Catchment Data |
| EMM | Class "EMM" |
| EMM-class | Class "EMM" |
| EMMLayer-class | Class "EMMLayer" |
| 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_states | Find the EMM State/Cluster for an Observation |
| find_states-method | Find the EMM State/Cluster for an Observation |
| initial_transition | Access Transition Probabilities/Counts in an EMM |
| initial_transition-method | Access Transition Probabilities/Counts in an EMM |
| merge_states | Merge States of an EMM |
| merge_states-method | Merge States of an EMM |
| Mollicutes16S | Count Data for 16S rRNA Sequences |
| plot | Visualize EMM Objects |
| plot-method | Visualize EMM Objects |
| 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_states | Prune States and/or Transitions |
| rare_states-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 |
| remove_selftransitions | Remove States/Clusters or Transitions from an EMM |
| remove_selftransitions-method | Remove States/Clusters or Transitions from an EMM |
| remove_states | Remove States/Clusters or Transitions from an EMM |
| remove_states-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 | Building an EMM using New Data |
| reset-method | Building an EMM using New Data |
| score | Score a New Sequence Given an EMM |
| score-method | Score a New Sequence Given an EMM |
| show,EMM | Class "EMM" |
| size | Class "EMMLayer" |
| size-method | Class "EMMLayer" |
| states | Class "EMMLayer" |
| states-method | Class "EMMLayer" |
| state_centers | Class "tNN" |
| state_centers-method | Class "tNN" |
| state_counts | Class "tNN" |
| state_counts-method | Class "tNN" |
| synthetic_stream | Create a Synthetic Data Stream |
| tNN-class | Class "tNN" |
| transition | Access Transition Probabilities/Counts in an EMM |
| transition-method | Access Transition Probabilities/Counts in an EMM |
| transitions | Class "EMMLayer" |
| transitions-method | Class "EMMLayer" |
| 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 |