Index

A

abspath() (in module gadma.utils.utils) add_epoch() (gadma.models.demographic_model.EpochDemographicModel method) add_inbreeding() (gadma.models.demographic_model.EpochDemographicModel method) add_p_misid() (gadma.models.demographic_model.EpochDemographicModel method) add_split() (gadma.models.demographic_model.EpochDemographicModel method) add_variable() (gadma.models.model.Model method) add_variables() (gadma.models.model.Model method) Addition (class in gadma.models.variables_combinations)

all_engines() (in module gadma.engines.engine) append() (gadma.utils.variable_pool.VariablePool method) apply_logarithm() (gadma.utils.variables.ContinuousVariable method) (gadma.utils.variables.Variable method) apply_transform() (in module gadma.utils.utils) as_custom_string() (gadma.models.demographic_model.EpochDemographicModel method) (gadma.models.event.Epoch method) (gadma.models.event.Event method) (gadma.models.event.Split method)

B

base_module (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) bcolors (class in gadma.utils.utils)

BinaryOperation (class in gadma.models.variables_combinations) BOLD (gadma.utils.utils.bcolors attribute)

C

cache_func() (in module gadma.utils.utils) CacheInfo (class in gadma.utils.utils) can_draw_comp (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute) can_draw_model (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute) (gadma.engines.moments_engine.MomentsEngine attribute) can_evaluate (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute) can_simulate (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute)

check_dir_existence() (in module gadma.utils.utils) check_file_existence() (in module gadma.utils.utils) check_type() (gadma.utils.variable_pool.VariablePool method) choose_by_weight() (in module gadma.utils.utils) ContinuousVariable (class in gadma.utils.variables) correct_value() (gadma.utils.variables.ContinuousVariable method) (gadma.utils.variables.DiscreteVariable method) (gadma.utils.variables.Variable method) create_from() (gadma.models.demographic_model.EpochDemographicModel class method) custom_generator() (in module gadma.utils.distributions) CustomDemographicModel (class in gadma.models.custom_demographic_model)

D

DadiEngine (class in gadma.engines.dadi_engine) DadiOrMomentsEngine (class in gadma.engines.dadi_moments_common) data (gadma.engines.engine.Engine property) DataHolder (class in gadma.data.data) default_domain (gadma.utils.variables.ContinuousVariable attribute) (gadma.utils.variables.DiscreteVariable attribute) (gadma.utils.variables.DynamicVariable attribute) (gadma.utils.variables.FractionVariable attribute) (gadma.utils.variables.MigrationVariable attribute) (gadma.utils.variables.PopulationSizeVariable attribute) (gadma.utils.variables.SelectionVariable attribute) (gadma.utils.variables.TimeVariable attribute) (gadma.utils.variables.Variable attribute) default_dt_fac (gadma.engines.moments_engine.MomentsEngine attribute) default_rand_gen (gadma.utils.variables.Variable attribute) default_rand_gen() (gadma.utils.variables.ContinuousVariable method) (gadma.utils.variables.DiscreteVariable method) (gadma.utils.variables.DynamicVariable method) (gadma.utils.variables.FractionVariable method) (gadma.utils.variables.MigrationVariable method) (gadma.utils.variables.PopulationSizeVariable method) (gadma.utils.variables.SelectionVariable method) (gadma.utils.variables.TimeVariable method)

DemographicGenerator (class in gadma.utils.distributions) deserialize_meta_array() (in module gadma.utils.utils) DiscreteVariable (class in gadma.utils.variables) Division (class in gadma.models.variables_combinations) domain (gadma.utils.variables.DiscreteVariable property) draw_data_comp_plot() (gadma.engines.dadi_engine.DadiEngine method) (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) (gadma.engines.moments_engine.MomentsEngine method) draw_schematic_model_plot() (gadma.engines.moments_engine.MomentsEngine method) Dynamic (class in gadma.utils.variables) DynamicVariable (class in gadma.utils.variables)

E

ENDC (gadma.utils.utils.bcolors attribute) Engine (class in gadma.engines.engine) ensure_dir_existence() (in module gadma.utils.utils) ensure_file_existence() (in module gadma.utils.utils) Epoch (class in gadma.models.event) EpochDemographicModel (class in gadma.models.demographic_model) eval_wrapper() (in module gadma.utils.utils) evaluate() (gadma.engines.dadi_engine.DadiEngine method) (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) (gadma.engines.engine.Engine method) (gadma.engines.moments_engine.MomentsEngine method)

Event (class in gadma.models.event) Exp (class in gadma.utils.variables) exponent_transform() (in module gadma.utils.utils) extend() (gadma.utils.variable_pool.VariablePool method) extrapolation (gadma.engines.dadi_engine.DadiEngine attribute)

F

FAIL (gadma.utils.utils.bcolors attribute) fix_args() (in module gadma.utils.utils) fix_dynamics() (gadma.models.demographic_model.EpochDemographicModel method) fix_pickling() (gadma.utils.variable_pool.VariablePool method) fix_variable() (gadma.models.demographic_model.EpochDemographicModel method) (gadma.models.model.Model method) float_repr() (in module gadma.utils.utils)

flush() (gadma.utils.utils.StdAndFileLogger method) format_str (gadma.utils.variables.Dynamic attribute) (gadma.utils.variables.Exp attribute) (gadma.utils.variables.Lin attribute) (gadma.utils.variables.Sud attribute) FractionVariable (class in gadma.utils.variables) from_structure() (gadma.models.structure_demographic_model.StructureDemographicModel method) func_str() (gadma.utils.variables.Dynamic class method)

G

gadma.code_generator.dadi_generator module gadma.code_generator.moments_generator module gadma.data.data module gadma.engines.dadi_engine module gadma.engines.dadi_moments_common module gadma.engines.engine module gadma.engines.moments_engine module gadma.models.custom_demographic_model module gadma.models.demographic_model module gadma.models.event module gadma.models.model module gadma.models.structure_demographic_model module gadma.models.variables_combinations module gadma.utils.distributions module gadma.utils.utils module gadma.utils.variable_pool module gadma.utils.variables module generate_code() (gadma.engines.dadi_engine.DadiEngine method) (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) (gadma.engines.engine.Engine method) (gadma.engines.moments_engine.MomentsEngine method)

generator_for_Nanc() (in module gadma.utils.distributions) get_aic_score() (in module gadma.utils.utils) get_best_kernel() (in module gadma.utils.utils) get_bounds() (gadma.utils.variables.ContinuousVariable method) (gadma.utils.variables.DiscreteVariable method) (gadma.utils.variables.DynamicVariable method) (gadma.utils.variables.Variable method) get_claic_component() (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) get_claic_score() (in module gadma.utils.utils) get_correct_dtype() (in module gadma.utils.utils) get_engine() (in module gadma.engines.engine) get_func_from_value() (gadma.utils.variables.DynamicVariable static method) get_involved_for_split_time_vars() (gadma.models.demographic_model.EpochDemographicModel method) get_LOO_score() (in module gadma.utils.utils) get_loo_score_for_optimizer() (in module gadma.utils.utils) get_loo_scores_for_kernels() (in module gadma.utils.utils) get_mu_and_sigma_rassmusen() (in module gadma.utils.utils) get_N_ancestral() (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) (gadma.engines.engine.Engine method) (gadma.engines.moments_engine.MomentsEngine method) get_N_ancestral_from_theta() (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) get_number_of_parameters() (gadma.models.demographic_model.EpochDemographicModel method) get_one_score() (in module gadma.utils.utils) get_possible_values() (gadma.utils.variables.ContinuousVariable method) (gadma.utils.variables.DiscreteVariable method) (gadma.utils.variables.Variable method) get_structure() (gadma.models.structure_demographic_model.StructureDemographicModel method) get_theta() (gadma.engines.dadi_engine.DadiEngine method) (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) (gadma.engines.moments_engine.MomentsEngine method) get_total_sequence_length() (gadma.data.data.DataHolder method) get_value() (gadma.models.variables_combinations.BinaryOperation method) get_value_from_var2value() (gadma.engines.engine.Engine static method) (gadma.models.model.Model static method) get_variable() (gadma.models.model.Model method) get_vars_not_in_init_args() (gadma.models.event.Epoch method)

H

has_inbreeding (gadma.models.demographic_model.EpochDemographicModel property)

has_p_misid (gadma.models.demographic_model.EpochDemographicModel property) HEADER (gadma.utils.utils.bcolors attribute)

I

id (gadma.engines.dadi_engine.DadiEngine attribute) (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute) (gadma.engines.moments_engine.MomentsEngine attribute) ident_transform() (in module gadma.utils.utils) increase_structure() (gadma.models.structure_demographic_model.StructureDemographicModel method) inner_data_type (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute)

is_commutative() (gadma.models.variables_combinations.Addition method) (gadma.models.variables_combinations.BinaryOperation method) (gadma.models.variables_combinations.Division method) (gadma.models.variables_combinations.Multiplication method) (gadma.models.variables_combinations.Subtraction method) is_pickleable() (in module gadma.utils.utils)

L

Lin (class in gadma.utils.variables) log_transformed (gadma.utils.variables.Variable property)

logarithm_transform() (in module gadma.utils.utils) lru_cache() (in module gadma.utils.utils)

M

MigrationVariable (class in gadma.utils.variables) Model (class in gadma.models.model) model (gadma.engines.engine.Engine property) module gadma.code_generator.dadi_generator gadma.code_generator.moments_generator gadma.data.data gadma.engines.dadi_engine gadma.engines.dadi_moments_common gadma.engines.engine gadma.engines.moments_engine gadma.models.custom_demographic_model gadma.models.demographic_model gadma.models.event gadma.models.model gadma.models.structure_demographic_model gadma.models.variables_combinations gadma.utils.distributions gadma.utils.utils gadma.utils.variable_pool gadma.utils.variables

module_name_from_path() (in module gadma.utils.utils) MomentsEngine (class in gadma.engines.moments_engine) multinom (gadma.engines.dadi_moments_common.DadiOrMomentsEngine property) Multiplication (class in gadma.models.variables_combinations)

N

name (gadma.models.variables_combinations.BinaryOperation property) Nanc_size (gadma.models.demographic_model.EpochDemographicModel property)

normalize() (in module gadma.utils.utils) number_of_populations() (gadma.models.demographic_model.EpochDemographicModel method)

O

OKBLUE (gadma.utils.utils.bcolors attribute) OKGREEN (gadma.utils.utils.bcolors attribute) operation() (gadma.models.variables_combinations.Addition static method) (gadma.models.variables_combinations.BinaryOperation static method) (gadma.models.variables_combinations.Division static method) (gadma.models.variables_combinations.Multiplication static method) (gadma.models.variables_combinations.Subtraction static method)

operation_str() (gadma.models.variables_combinations.Addition static method) (gadma.models.variables_combinations.BinaryOperation static method) (gadma.models.variables_combinations.Division static method) (gadma.models.variables_combinations.Multiplication static method) (gadma.models.variables_combinations.Subtraction static method)

P

PopulationSizeVariable (class in gadma.utils.variables)

print_dadi_code() (in module gadma.code_generator.dadi_generator) print_moments_code() (in module gadma.code_generator.moments_generator)

R

read_data() (gadma.engines.engine.Engine class method) read_sfs_data() (in module gadma.engines.dadi_moments_common) read_vcf_data() (in module gadma.engines.dadi_moments_common)

register_engine() (in module gadma.engines.engine) resample() (gadma.utils.variables.Variable method) rescale_generator() (in module gadma.utils.distributions) run_f_and_save_result_into_queue() (in module gadma.utils.utils)

S

SelectionVariable (class in gadma.utils.variables) serialize_meta_array() (in module gadma.utils.utils) set_and_evaluate() (gadma.engines.engine.Engine method) set_data() (gadma.engines.engine.Engine method) set_model() (gadma.engines.engine.Engine method) SFSDataHolder (class in gadma.data.data) simulate() (gadma.engines.dadi_engine.DadiEngine method) (gadma.engines.moments_engine.MomentsEngine method) sort_by_other_list() (in module gadma.utils.utils) Split (class in gadma.models.event)

StdAndFileLogger (class in gadma.utils.utils) str_as_list() (gadma.utils.utils.WeightedMetaArray method) string_repr() (gadma.models.model.Model method) (gadma.models.variables_combinations.BinaryOperation method) StructureDemographicModel (class in gadma.models.structure_demographic_model) Subtraction (class in gadma.models.variables_combinations) Sud (class in gadma.utils.variables) supported_data (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute) supported_models (gadma.engines.dadi_moments_common.DadiOrMomentsEngine attribute) (gadma.engines.engine.Engine attribute)

T

timeout() (in module gadma.utils.utils) TimeVariable (class in gadma.utils.variables) transform_smac() (in module gadma.utils.utils) transform_values_from_other_model() (gadma.models.structure_demographic_model.StructureDemographicModel method) translate_to() (gadma.models.demographic_model.EpochDemographicModel method) translate_units_to() (gadma.utils.variables.PopulationSizeVariable method)

translate_values() (gadma.models.custom_demographic_model.CustomDemographicModel method) trunc_lognormal() (in module gadma.utils.distributions) trunc_lognormal_3_sigma_rule() (in module gadma.utils.distributions) trunc_lognormal_sigma_generator() (in module gadma.utils.distributions) trunc_normal() (in module gadma.utils.distributions) trunc_normal_3_sigma_rule() (in module gadma.utils.distributions) trunc_normal_sigma_generator() (in module gadma.utils.distributions)

U

UNDERLINE (gadma.utils.utils.bcolors attribute) unfix_dynamics() (gadma.models.demographic_model.EpochDemographicModel method) unfix_if_fixed() (gadma.models.model.Model method) unfix_variable() (gadma.models.demographic_model.EpochDemographicModel method) (gadma.models.model.Model method)

uniform_generator() (in module gadma.utils.distributions) units (gadma.utils.variables.FractionVariable attribute) update_by_one_fifth_rule() (in module gadma.utils.utils) update_data_holder_with_inner_data() (gadma.engines.dadi_moments_common.DadiOrMomentsEngine method) (gadma.engines.engine.Engine method)

V

var2value() (gadma.models.model.Model method) Variable (class in gadma.utils.variables) VariablePool (class in gadma.utils.variable_pool)

variables (gadma.models.model.Model property) variables_values_repr() (in module gadma.utils.utils) VariablesCombination (class in gadma.models.variables_combinations) VCFDataHolder (class in gadma.data.data)

W

WARNING (gadma.utils.utils.bcolors attribute) warning_format() (in module gadma.utils.utils)

WeightedMetaArray (class in gadma.utils.utils) write() (gadma.utils.utils.StdAndFileLogger method)