Python package
CompositeProblem
ParMappingDict
ParMappingDictQuadruple
ParMappingDictTuple
Problem
ScaleMappingDict
ScaleMappingDictTuple
Simulator
assert_all_parameters_present_in_parameter_df()
assert_measured_observables_defined()
assert_measurement_conditions_present_in_condition_table()
assert_measurements_not_null()
assert_measurements_numeric()
assert_model_parameters_in_condition_or_parameter_table()
assert_no_leading_trailing_whitespace()
assert_noise_distributions_valid()
assert_overrides_match_parameter_count()
assert_parameter_bounds_are_numeric()
assert_parameter_estimate_is_boolean()
assert_parameter_id_is_string()
assert_parameter_prior_parameters_are_valid()
assert_parameter_prior_type_is_valid()
assert_parameter_scale_is_valid()
assert_single_condition_and_sbml_file()
assert_unique_observable_ids()
assert_unique_parameter_ids()
calculate_chi2()
calculate_chi2_for_table_from_residuals()
calculate_llh()
calculate_llh_for_table()
calculate_residuals()
calculate_residuals_for_table()
calculate_single_llh()
check_condition_df()
check_ids()
check_mapping_df()
check_measurement_df()
check_observable_df()
check_parameter_bounds()
check_parameter_df()
concat_tables()
condition_table_is_parameter_free()
create_combine_archive()
create_condition_df()
create_measurement_df()
create_observable_df()
create_parameter_df()
create_problem_yaml()
evaluate_noise_formula()
flatten_timepoint_specific_output_overrides()
get_condition_df()
get_formula_placeholders()
get_mapping_df()
get_measurement_df()
get_measurement_parameter_ids()
get_model_for_condition()
get_model_parameters()
get_notnull_columns()
get_observable_df()
get_optimization_parameter_scaling()
get_optimization_parameters()
get_optimization_to_simulation_parameter_mapping()
get_output_parameters()
get_parameter_df()
get_parameter_mapping_for_condition()
get_parametric_overrides()
get_path_prefix()
get_placeholders()
get_priors_from_df()
get_rows_for_condition()
get_sbml_model()
get_simulation_conditions()
get_simulation_df()
get_symbolic_noise_formulas()
get_valid_parameters_for_parameter_table()
get_visualization_df()
globalize_parameters()
handle_missing_overrides()
is_composite_problem()
is_empty()
is_sbml_consistent()
is_scalar_float()
is_valid_identifier()
lint_problem()
load_sbml_from_file()
load_sbml_from_string()
load_yaml()
log_sbml_errors()
map_scale()
map_unscale()
measurement_is_at_steady_state()
measurement_table_has_observable_parameter_numeric_overrides()
measurement_table_has_timepoint_specific_mappings()
measurements_have_replicates()
merge_preeq_and_sim_pars()
merge_preeq_and_sim_pars_condition()
normalize_parameter_df()
observable_table_has_nontrivial_noise_formula()
resolve_mapping()
sample_from_prior()
sample_noise()
sample_parameter_startpoints()
scale()
split_parameter_replacement_list()
to_float_if_float()
unflatten_simulation_df()
unique_preserve_order()
unscale()
validate()
validate_yaml_semantics()
validate_yaml_syntax()
write_condition_df()
write_mapping_df()
write_measurement_df()
write_observable_df()
write_parameter_df()
write_sbml()
write_simulation_df()
write_visualization_df()
write_yaml()
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Examples
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