Index

Symbols

--ambiguous-as-missing teiphy command line option --ancestral-logger teiphy command line option --calibrate-dates teiphy command line option --clock teiphy command line option --dates-file teiphy command line option --drop-constant teiphy command line option --fill-correctors teiphy command line option --format teiphy command line option --fragmentary-threshold teiphy command line option --frequency teiphy command line option --install-completion teiphy command line option --labels teiphy command line option --mrbayes teiphy command line option --no-ambiguous-as-missing teiphy command line option --no-calibrate-dates teiphy command line option --no-drop-constant teiphy command line option --no-fill-correctors teiphy command line option --no-frequency teiphy command line option

--no-labels teiphy command line option --no-mrbayes teiphy command line option --no-proportion teiphy command line option --no-show-ext teiphy command line option --no-split-missing teiphy command line option --no-verbose teiphy command line option --no-version teiphy command line option --proportion teiphy command line option --seed teiphy command line option --show-completion teiphy command line option --show-ext teiphy command line option --split-missing teiphy command line option --table teiphy command line option --verbose teiphy command line option --version teiphy command line option -m teiphy command line option -s teiphy command line option -t teiphy command line option

C

certainties (teiphy.Reading attribute)

Collation (class in teiphy)

D

date_range (teiphy.Witness attribute)

F

fill_corrector_lacunae (teiphy.Collation attribute)

filter_fragmentary_witnesses() (teiphy.Collation method) fragmentary_threshold (teiphy.Collation attribute)

G

get_base_wit() (teiphy.Collation method) get_beast_code_map_for_unit() (teiphy.Collation method) get_beast_date_map() (teiphy.Collation method) get_beast_equilibrium_frequencies_for_unit() (teiphy.Collation method) get_beast_origin_span() (teiphy.Collation method) get_beast_root_frequencies_for_unit() (teiphy.Collation method) get_beast_symbols() (teiphy.Collation method)

get_fasta_symbols() (teiphy.Collation method) get_hennig86_symbols() (teiphy.Collation method) get_nexus_symbols() (teiphy.Collation method) get_phylip_symbols() (teiphy.Collation method) get_readings_by_witness_for_unit() (teiphy.Collation method) get_stemma_symbols() (teiphy.Collation method) get_tip_date_range() (teiphy.Collation method)

I

id (teiphy.Reading attribute) (teiphy.VariationUnit attribute) (teiphy.Witness attribute)

INPUT teiphy command line option intrinsic_relations (teiphy.VariationUnit attribute)

M

manuscript_suffixes (teiphy.Collation attribute)

missing_reading_types (teiphy.Collation attribute)

O

OUTPUT teiphy command line option

P

parse() (teiphy.Reading method) (teiphy.VariationUnit method) parse_apps() (teiphy.Collation method) parse_intrinsic_odds() (teiphy.Collation method)

parse_list_wit() (teiphy.Collation method) parse_origin_date_range() (teiphy.Collation method) parse_readings_by_witness() (teiphy.Collation method) parse_transcriptional_rates() (teiphy.Collation method)

R

Reading (class in teiphy)

readings (teiphy.VariationUnit attribute) readings_by_witness (teiphy.Collation attribute)

S

substantive_variation_unit_ids (teiphy.Collation attribute)

substantive_variation_unit_reading_tuples (teiphy.Collation attribute)

T

targets (teiphy.Reading attribute) teiphy command line option --ambiguous-as-missing --ancestral-logger --calibrate-dates --clock --dates-file --drop-constant --fill-correctors --format --fragmentary-threshold --frequency --install-completion --labels --mrbayes --no-ambiguous-as-missing --no-calibrate-dates --no-drop-constant --no-fill-correctors --no-frequency --no-labels --no-mrbayes --no-proportion --no-show-ext --no-split-missing --no-verbose --no-version --proportion --seed --show-completion --show-ext --split-missing --table --verbose --version -m -s -t INPUT OUTPUT

text (teiphy.Reading attribute) to_beast() (teiphy.Collation method) to_csv() (teiphy.Collation method) to_dataframe() (teiphy.Collation method) to_distance_matrix() (teiphy.Collation method) to_excel() (teiphy.Collation method) to_fasta() (teiphy.Collation method) to_file() (teiphy.Collation method) to_hennig86() (teiphy.Collation method) to_long_table() (teiphy.Collation method) to_nexus() (teiphy.Collation method) to_nexus_table() (teiphy.Collation method) to_numpy() (teiphy.Collation method) to_phylip() (teiphy.Collation method) to_similarity_matrix() (teiphy.Collation method) to_stemma() (teiphy.Collation method) transcriptional_relations (teiphy.VariationUnit attribute) trivial_reading_types (teiphy.Collation attribute) type (teiphy.Reading attribute) (teiphy.Witness attribute)

U

update_origin_date_range_from_witness_date_ranges() (teiphy.Collation method)

update_witness_date_ranges_from_dates_file() (teiphy.Collation method) update_witness_date_ranges_from_origin_date_range() (teiphy.Collation method)

V

validate_intrinsic_relations() (teiphy.Collation method) validate_wits() (teiphy.Collation method)

variation_units (teiphy.Collation attribute) VariationUnit (class in teiphy) verbose (teiphy.Collation attribute)

W

Witness (class in teiphy) witness_index_by_id (teiphy.Collation attribute)

witnesses (teiphy.Collation attribute) wits (teiphy.Reading attribute)