16S	16S
Alphaproteobacteria16S	16S
build	build
build,EMM,data.frame-method	build
build,EMM,matrix-method	build
build,EMM,numeric-method	build
current_state	EMMLayer-class
current_state,EMMLayer-method	EMMLayer-class
Derwent	Derwent
EMM	EMM-class
EMM-class	EMM-class
EMMLayer-class	EMMLayer-class
EMMsim	EMMsim
EMMsim_sequence_test	EMMsim
EMMsim_sequence_train	EMMsim
EMMsim_test	EMMsim
EMMsim_train	EMMsim
EMMTraffic	EMMTraffic
fade	fade
fade,EMM,missing,missing-method	fade
fade,EMM,numeric,missing-method	fade
fade,EMM,numeric,numeric-method	fade
find_states	find_states
find_states,tNN,data.frame-method	find_states
find_states,tNN,matrix-method	find_states
find_states,tNN,numeric-method	find_states
initial_transition	transition
initial_transition,EMMLayer-method	transition
merge_states	merge_states
merge_states,EMM,character-method	merge_states
merge_states,EMM,integer-method	merge_states
Mollicutes16S	16S
plot	plot.EMM
plot,EMM,missing-method	plot.EMM
predict	predict
predict,EMMLayer-method	predict
prune	prune
prune,EMM-method	prune
rare_states	prune
rare_states,EMM-method	prune
rare_transitions	prune
rare_transitions,EMM-method	prune
recluster	recluster
recluster_hclust	recluster
recluster_hclust,EMM-method	recluster
recluster_kmeans	recluster
recluster_kmeans,EMM-method	recluster
recluster_pam	recluster
recluster_pam,EMM-method	recluster
remove_selftransitions	remove
remove_selftransitions,EMM-method	remove
remove_states	remove
remove_states,EMM,character-method	remove
remove_transitions	remove
remove_transitions,EMM,character,character-method	remove
remove_transitions,EMM,matrix,missing-method	remove
reset	build
reset,EMMLayer-method	build
score	score
score,EMM,data.frame-method	score
score,EMM,matrix-method	score
score,EMM,numeric-method	score
show,EMM	EMM-class
size	EMMLayer-class
size,EMMLayer-method	EMMLayer-class
states	EMMLayer-class
states,EMMLayer-method	EMMLayer-class
state_centers	tNN-class
state_centers,tNN-method	tNN-class
state_counts	tNN-class
state_counts,tNN-method	tNN-class
synthetic_stream	synthetic_stream
tNN-class	tNN-class
transition	transition
transition,EMMLayer,character,character-method	transition
transition,EMMLayer,matrix,missing-method	transition
transitions	EMMLayer-class
transitions,EMMLayer-method	EMMLayer-class
transition_matrix	transition
transition_matrix,EMMLayer-method	transition
transition_table	transition_table
transition_table,EMM,data.frame-method	transition_table
transition_table,EMM,matrix-method	transition_table
transition_table,EMM,numeric-method	transition_table
