barry: Your go-to motif accountant
0.0-1
Full enumeration of sample space and fast count of sufficient statistics for binary arrays
- a -
active :
Cell< Cell_Type >
annotations :
Node
Array :
ConstBArrayRowIter< Cell_Type, Data_Type >
array :
DEFMData
,
Node
arrays :
Node
arrays2support :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- b -
blengths :
NodeData
- c -
change_stats :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
column_major :
DEFMData
coordiantes_n_free :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
coordiantes_n_locked :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
coordinates_free :
PowerSet< Array_Type, Data_Rule_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
coordinates_locked :
PowerSet< Array_Type, Data_Rule_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
count_fun :
Counter< Array_Type, Data_Type >
counter_fun :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
counters :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
counts :
DEFMRuleDynData
,
PhyloRuleDynData
covar_sort :
DEFMData
covar_used :
DEFMData
covariates :
DEFMData
current_col :
ConstBArrayRowIter< Cell_Type, Data_Type >
current_row :
ConstBArrayRowIter< Cell_Type, Data_Type >
current_stats :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- d -
dat :
Flock
data :
Counter< Array_Type, Data_Type >
,
PowerSet< Array_Type, Data_Rule_Type >
delete_counters :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
delete_rengine :
Geese
,
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
delete_rules :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
delete_rules_dyn :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
delete_support :
Geese
desc :
Counter< Array_Type, Data_Type >
directed :
NetworkData
duplication :
Node
,
NodeData
,
PhyloRuleDynData
- e -
EmptyArray :
PowerSet< Array_Type, Data_Rule_Type >
etype_default :
Geese
etype_duplication :
Geese
etype_either :
Geese
etype_speciation :
Geese
- f -
first_calc_done :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- h -
has_leaf :
NodeData
hasher_fun :
Counter< Array_Type, Data_Type >
hashes :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
hashes_initialized :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- i -
id :
Node
indices :
DEFMCounterData
,
DEFMRuleData
,
NetCounterData
init :
DEFMRuleData
init_fun :
Counter< Array_Type, Data_Type >
initialized :
Flock
,
Geese
is_motif :
DEFMCounterData
iter :
ConstBArrayRowIter< Cell_Type, Data_Type >
- k -
keys2support :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- l -
lb :
DEFMRuleDynData
,
PhyloRuleDynData
logical :
DEFMCounterData
,
DEFMRuleData
- m -
M :
PowerSet< Array_Type, Data_Rule_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
map_to_state_id :
Geese
max_num_elements :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
model :
Flock
- n -
N :
PowerSet< Array_Type, Data_Rule_Type >
,
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
n_counters :
Support< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
n_free :
PowerSet< Array_Type, Data_Rule_Type >
n_locked :
PowerSet< Array_Type, Data_Rule_Type >
name :
Counter< Array_Type, Data_Type >
narray :
Node
nfunctions :
Flock
,
Geese
nodes :
Geese
normalizing_constants :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
numbers :
DEFMCounterData
,
DEFMRuleData
,
NetCounterData
- o -
obs_start :
DEFMData
offspring :
Node
ord :
Node
- p -
params_last :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
parent :
Node
pos :
DEFMRuleDynData
,
PhyloRuleDynData
probability :
Node
pset_arrays :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
pset_loc :
Geese
pset_locations :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
pset_probs :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
pset_sizes :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
pset_stats :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- r -
reduced_sequence :
Geese
rengine :
Flock
,
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
rules :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
,
PowerSet< Array_Type, Data_Rule_Type >
rules_deleted :
PowerSet< Array_Type, Data_Rule_Type >
rules_dyn :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- s -
sequence :
Geese
source :
Entries< Cell_Type >
states :
NodeData
stats_likelihood :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
stats_support :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
stats_support_n_arrays :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
stats_support_sizes :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
stats_support_sizes_acc :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
stats_target :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
subtree_prob :
Node
support_fun :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- t -
target :
Entries< Cell_Type >
transform_model_fun :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
transform_model_term_names :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- u -
ub :
DEFMRuleDynData
,
PhyloRuleDynData
- v -
val :
Entries< Cell_Type >
value :
Cell< Cell_Type >
vertex_attr :
NetworkData
visited :
BArray< Cell_Type, Data_Type >
,
BArrayDense< Cell_Type, Data_Type >
,
Cell< Cell_Type >
,
Node
- w -
with_pset :
Model< Array_Type, Data_Counter_Type, Data_Rule_Type, Data_Rule_Dyn_Type >
- x -
X_ncol :
DEFMData
X_nrow :
DEFMData
Generated on Thu Nov 16 2023 23:48:36 for barry: Your go-to motif accountant by
1.9.1