PEtab
v0.0.2
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_
_apply_dynamic_parameter_overrides() (in module petab.parameter_mapping)
_apply_output_parameter_overrides() (in module petab.parameter_mapping)
_apply_overrides_for_observable() (in module petab.parameter_mapping)
_check_df() (in module petab.lint)
_perform_mapping_checks() (in module petab.parameter_mapping)
A
add_global_parameter() (in module petab.sbml)
add_model_output() (in module petab.sbml)
add_model_output_sigma() (in module petab.sbml)
add_model_output_with_sigma() (in module petab.sbml)
assert_all_parameters_present_in_parameter_df() (in module petab.lint)
assert_measured_observables_present_in_model() (in module petab.lint)
assert_model_parameters_in_condition_or_parameter_table() (in module petab.lint)
assert_no_leading_trailing_whitespace() (in module petab.lint)
assert_noise_distributions_valid() (in module petab.lint)
assert_overrides_match_parameter_count() (in module petab.measurements)
assert_parameter_bounds_are_numeric() (in module petab.lint)
assert_parameter_estimate_is_boolean() (in module petab.lint)
assert_parameter_id_is_string() (in module petab.lint)
assert_parameter_id_is_unique() (in module petab.lint)
assert_parameter_scale_is_valid() (in module petab.lint)
assert_single_condition_and_sbml_file() (in module petab.yaml)
assignment_rules_to_dict() (in module petab.sbml)
C
check_condition_df() (in module petab.lint)
check_measurement_df() (in module petab.lint)
check_parameter_bounds() (in module petab.lint)
check_parameter_df() (in module petab.lint)
check_vis_spec_consistency() (in module petab.visualize.helper_functions)
CompositeProblem (class in petab.composite_problem)
concat_measurements() (in module petab.measurements)
condition_df (petab.problem.Problem attribute)
condition_table_is_parameter_free() (in module petab.lint)
create_assigment_rule() (in module petab.sbml)
create_condition_df() (in module petab.conditions)
create_figure() (in module petab.visualize.helper_functions)
create_measurement_df() (in module petab.measurements)
create_parameter_df() (in module petab.parameters)
(petab.problem.Problem method)
create_report() (in module petab.visualize.data_overview)
F
fill_in_nominal_values() (in module petab.parameter_mapping)
flatten_timepoint_specific_output_overrides() (in module petab.core)
from_files() (petab.problem.Problem static method)
from_folder() (petab.problem.Problem static method)
from_yaml() (petab.composite_problem.CompositeProblem static method)
(petab.problem.Problem static method)
G
get_condition_df() (in module petab.conditions)
get_data_per_observable() (in module petab.visualize.data_overview)
get_data_to_plot() (in module petab.visualize.helper_functions)
get_default_condition_file_name() (in module petab.problem)
get_default_measurement_file_name() (in module petab.problem)
get_default_parameter_file_name() (in module petab.problem)
get_default_sbml_file_name() (in module petab.problem)
get_default_vis_specs() (in module petab.visualize.helper_functions)
get_dynamic_simulation_parameters() (petab.problem.Problem method)
get_measurement_df() (in module petab.measurements)
get_measurement_parameter_ids() (in module petab.measurements)
get_model_parameters() (in module petab.sbml)
get_noise_distributions() (in module petab.measurements)
(petab.problem.Problem method)
get_notnull_columns() (in module petab.core)
get_observable_id() (in module petab.core)
get_observables() (in module petab.sbml)
(petab.problem.Problem method)
get_optimization_parameters() (in module petab.parameters)
(petab.problem.Problem method)
get_optimization_to_simulation_parameter_mapping() (in module petab.parameter_mapping)
(petab.problem.Problem method)
get_optimization_to_simulation_scale_mapping() (in module petab.parameter_mapping)
get_parameter_df() (in module petab.parameters)
get_parameter_mapping_for_condition() (in module petab.parameter_mapping)
get_placeholders() (in module petab.measurements)
get_priors_from_df() (in module petab.parameters)
get_required_parameters_for_parameter_table() (in module petab.parameters)
get_rows_for_condition() (in module petab.measurements)
get_scale_mapping_for_condition() (in module petab.parameter_mapping)
get_sigmas() (in module petab.sbml)
(petab.problem.Problem method)
get_simulation_conditions() (in module petab.measurements)
get_simulation_conditions_from_measurement_df() (petab.problem.Problem method)
globalize_parameters() (in module petab.sbml)
H
handle_missing_overrides() (in module petab.parameter_mapping)
I
import_from_files() (in module petab.visualize.helper_functions)
is_composite_problem() (in module petab.yaml)
is_sbml_consistent() (in module petab.sbml)
L
lb (petab.problem.Problem attribute)
lb_scaled (petab.problem.Problem attribute)
lint_problem() (in module petab.lint)
load_yaml() (in module petab.yaml)
log_sbml_errors() (in module petab.sbml)
M
map_scale() (in module petab.parameters)
measurement_df (petab.problem.Problem attribute)
measurement_table_has_observable_parameter_numeric_overrides() (in module petab.lint)
measurement_table_has_timepoint_specific_mappings() (in module petab.lint)
measurements_have_replicates() (in module petab.measurements)
merge_preeq_and_sim_pars() (in module petab.parameter_mapping)
merge_preeq_and_sim_pars_condition() (in module petab.parameter_mapping)
P
parameter_df (petab.composite_problem.CompositeProblem attribute)
(petab.problem.Problem attribute)
parameter_id_is_valid() (in module petab.parameters)
parameter_is_offset_parameter() (in module petab.core)
parameter_is_scaling_parameter() (in module petab.core)
petab (module)
petab.composite_problem (module)
petab.conditions (module)
petab.core (module)
petab.lint (module)
petab.measurements (module)
petab.parameter_mapping (module)
petab.parameters (module)
petab.problem (module)
petab.sampling (module)
petab.sbml (module)
petab.visualize.data_overview (module)
petab.visualize.helper_functions (module)
petab.visualize.plotting_config (module)
petab.yaml (module)
plot_data_and_simulation() (in module petab.visualize)
plot_lowlevel() (in module petab.visualize.plotting_config)
Problem (class in petab.problem)
problems (petab.composite_problem.CompositeProblem attribute)
S
sample_from_prior() (in module petab.sampling)
sample_parameter_startpoints() (in module petab.sampling)
(petab.problem.Problem method)
sbml_document (petab.problem.Problem attribute)
sbml_model (petab.problem.Problem attribute)
sbml_parameter_is_observable() (in module petab.sbml)
sbml_parameter_is_sigma() (in module petab.sbml)
sbml_reader (petab.problem.Problem attribute)
scale() (in module petab.parameters)
split_parameter_replacement_list() (in module petab.measurements)
U
ub (petab.problem.Problem attribute)
ub_scaled (petab.problem.Problem attribute)
V
validate() (in module petab.yaml)
validate_yaml_semantics() (in module petab.yaml)
validate_yaml_syntax() (in module petab.yaml)
X
x_fixed_indices (petab.problem.Problem attribute)
x_fixed_vals (petab.problem.Problem attribute)
x_ids (petab.problem.Problem attribute)
x_nominal (petab.problem.Problem attribute)
x_nominal_scaled (petab.problem.Problem attribute)
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