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 |