PEtab
v0.1.14
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Index
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A
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C
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
_
_apply_condition_parameters() (in module petab.parameter_mapping)
_apply_mask() (petab.Problem method)
(petab.problem.Problem method)
_apply_output_parameter_overrides() (in module petab.parameter_mapping)
_apply_overrides_for_observable() (in module petab.parameter_mapping)
_apply_parameter_table() (in module petab.parameter_mapping)
_check_df() (in module petab.lint)
_keep_positive() (petab.Counter method)
(petab.lint.Counter method)
_map_condition() (in module petab.parameter_mapping)
_map_condition_arg_packer() (in module petab.parameter_mapping)
_output_parameters_to_nan() (in module petab.parameter_mapping)
_perform_mapping_checks() (in module petab.parameter_mapping)
A
add_global_parameter() (in module petab)
(in module petab.sbml)
add_model_output() (in module petab)
(in module petab.sbml)
add_model_output_sigma() (in module petab)
(in module petab.sbml)
add_model_output_with_sigma() (in module petab)
(in module petab.sbml)
add_noise() (petab.Simulator method)
assert_all_parameters_present_in_parameter_df() (in module petab)
(in module petab.lint)
assert_measured_observables_defined() (in module petab)
(in module petab.lint)
assert_measurement_conditions_present_in_condition_table() (in module petab)
(in module petab.lint)
assert_model_parameters_in_condition_or_parameter_table() (in module petab)
(in module petab.lint)
assert_no_leading_trailing_whitespace() (in module petab)
(in module petab.lint)
assert_noise_distributions_valid() (in module petab)
(in module petab.lint)
assert_overrides_match_parameter_count() (in module petab)
(in module petab.measurements)
assert_parameter_bounds_are_numeric() (in module petab)
(in module petab.lint)
assert_parameter_estimate_is_boolean() (in module petab)
(in module petab.lint)
assert_parameter_id_is_string() (in module petab)
(in module petab.lint)
assert_parameter_prior_parameters_are_valid() (in module petab)
(in module petab.lint)
assert_parameter_prior_type_is_valid() (in module petab)
(in module petab.lint)
assert_parameter_scale_is_valid() (in module petab)
(in module petab.lint)
assert_single_condition_and_sbml_file() (in module petab)
(in module petab.yaml)
assert_unique_observable_ids() (in module petab)
(in module petab.lint)
assert_unique_parameter_ids() (in module petab)
(in module petab.lint)
assignment_rules_to_dict() (in module petab)
(in module petab.sbml)
C
calculate_chi2() (in module petab)
calculate_chi2_for_table_from_residuals() (in module petab)
calculate_llh() (in module petab)
calculate_llh_for_table() (in module petab)
calculate_residuals() (in module petab)
calculate_residuals_for_table() (in module petab)
calculate_single_llh() (in module petab)
check_condition_df() (in module petab)
(in module petab.lint)
check_ex_exp_columns() (in module petab.visualize.helper_functions)
check_ex_visu_columns() (in module petab.visualize.helper_functions)
check_ids() (in module petab)
(in module petab.lint)
check_measurement_df() (in module petab)
(in module petab.lint)
check_observable_df() (in module petab)
(in module petab.lint)
check_parameter_bounds() (in module petab)
(in module petab.lint)
check_parameter_df() (in module petab)
(in module petab.lint)
check_vis_spec_consistency() (in module petab.visualize.helper_functions)
clear() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
CompositeProblem (class in petab)
(class in petab.composite_problem)
concat_tables() (in module petab)
(in module petab.core)
condition_df (petab.Problem attribute)
(petab.problem.Problem attribute)
condition_table_is_parameter_free() (in module petab)
(in module petab.lint)
copy() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
copyfile() (in module petab.visualize.data_overview)
Counter (class in petab)
(class in petab.lint)
create_assigment_rule() (in module petab)
(in module petab.sbml)
create_combine_archive() (in module petab)
(in module petab.core)
create_condition_df() (in module petab)
(in module petab.conditions)
create_dataset_id_list() (in module petab.visualize.helper_functions)
create_figure() (in module petab.visualize.helper_functions)
create_measurement_df() (in module petab)
(in module petab.measurements)
create_observable_df() (in module petab)
create_or_update_vis_spec() (in module petab.visualize.helper_functions)
create_parameter_df() (in module petab)
(in module petab.parameters)
(petab.Problem method)
(petab.problem.Problem method)
create_problem_yaml() (in module petab)
(in module petab.yaml)
create_report() (in module petab.visualize.data_overview)
E
elements() (petab.Counter method)
(petab.lint.Counter method)
ENV_NUM_THREADS (in module petab)
evaluate_noise_formula() (in module petab)
expand_vis_spec_settings() (in module petab.visualize.helper_functions)
F
flatten_timepoint_specific_output_overrides() (in module petab)
(in module petab.core)
from_combine() (petab.Problem static method)
(petab.problem.Problem static method)
from_files() (petab.Problem static method)
(petab.problem.Problem static method)
from_folder() (petab.Problem static method)
(petab.problem.Problem static method)
from_yaml() (petab.composite_problem.CompositeProblem static method)
(petab.CompositeProblem static method)
(petab.Problem static method)
(petab.problem.Problem static method)
fromkeys() (petab.Counter class method)
(petab.lint.Counter class method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
G
get() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
get_condition_df() (in module petab)
(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)
(in module petab.problem)
get_default_measurement_file_name() (in module petab)
(in module petab.problem)
get_default_parameter_file_name() (in module petab)
(in module petab.problem)
get_default_sbml_file_name() (in module petab)
(in module petab.problem)
get_default_vis_specs() (in module petab.visualize.helper_functions)
get_formula_placeholders() (in module petab)
get_handle() (in module petab)
(in module petab.sbml)
(in module petab.yaml)
get_lb() (petab.Problem method)
(petab.problem.Problem method)
get_measurement_df() (in module petab)
(in module petab.measurements)
get_measurement_parameter_ids() (in module petab)
(in module petab.measurements)
get_model_parameters() (in module petab)
(in module petab.sbml)
(petab.Problem method)
(petab.problem.Problem method)
get_noise_distributions() (in module petab)
(in module petab.measurements)
(petab.Problem method)
(petab.problem.Problem method)
get_notnull_columns() (in module petab)
(in module petab.core)
get_observable_df() (in module petab)
get_observable_id() (in module petab)
(in module petab.core)
get_observable_ids() (petab.Problem method)
(petab.problem.Problem method)
get_observables() (in module petab)
(in module petab.sbml)
(petab.Problem method)
(petab.problem.Problem method)
get_optimization_parameter_scales() (petab.Problem method)
(petab.problem.Problem method)
get_optimization_parameter_scaling() (in module petab)
(in module petab.parameters)
get_optimization_parameters() (in module petab)
(in module petab.parameters)
(petab.Problem method)
(petab.problem.Problem method)
get_optimization_to_simulation_parameter_mapping() (in module petab)
(in module petab.parameter_mapping)
(petab.Problem method)
(petab.problem.Problem method)
get_output_parameters() (in module petab)
get_parameter_df() (in module petab)
(in module petab.parameters)
get_parameter_mapping_for_condition() (in module petab)
(in module petab.parameter_mapping)
get_parametric_overrides() (in module petab)
(in module petab.conditions)
get_placeholders() (in module petab)
get_priors_from_df() (in module petab)
(in module petab.parameters)
get_required_parameters_for_parameter_table() (in module petab)
(in module petab.parameters)
get_rows_for_condition() (in module petab)
(in module petab.measurements)
get_sbml_model() (in module petab)
(in module petab.sbml)
get_sigmas() (in module petab)
(in module petab.sbml)
(petab.Problem method)
(petab.problem.Problem method)
get_simulation_conditions() (in module petab)
(in module petab.measurements)
get_simulation_conditions_from_measurement_df() (petab.Problem method)
(petab.problem.Problem method)
get_simulation_df() (in module petab)
(in module petab.core)
get_symbolic_noise_formulas() (in module petab)
get_ub() (petab.Problem method)
(petab.problem.Problem method)
get_valid_parameters_for_parameter_table() (in module petab)
(in module petab.parameters)
get_vis_spec_dependent_columns_dict() (in module petab.visualize.helper_functions)
get_visualization_df() (in module petab)
(in module petab.core)
get_x_ids() (petab.Problem method)
(petab.problem.Problem method)
get_x_nominal() (petab.Problem method)
(petab.problem.Problem method)
globalize_parameters() (in module petab)
(in module petab.sbml)
H
handle_dataset_plot() (in module petab.visualize.helper_functions)
handle_missing_overrides() (in module petab)
(in module petab.parameter_mapping)
I
import_from_files() (in module petab.visualize.helper_functions)
is_composite_problem() (in module petab)
(in module petab.yaml)
is_empty() (in module petab)
(in module petab.core)
is_file_like() (in module petab)
(in module petab.sbml)
is_sbml_consistent() (in module petab)
(in module petab.sbml)
is_url() (in module petab)
(in module petab.sbml)
is_valid_identifier() (in module petab)
(in module petab.lint)
items() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
K
keys() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
L
lb() (petab.Problem property)
(petab.problem.Problem property)
lb_scaled() (petab.Problem property)
(petab.problem.Problem property)
lint_problem() (in module petab)
(in module petab.lint)
load_sbml_from_file() (in module petab)
(in module petab.sbml)
load_sbml_from_string() (in module petab)
(in module petab.sbml)
load_yaml() (in module petab)
(in module petab.yaml)
log_sbml_errors() (in module petab)
(in module petab.sbml)
M
main() (in module petab.visualize.data_overview)
map_scale() (in module petab)
(in module petab.parameters)
matches_plot_spec() (in module petab.visualize.helper_functions)
measurement_df (petab.Problem attribute)
(petab.problem.Problem attribute)
measurement_table_has_observable_parameter_numeric_overrides() (in module petab)
(in module petab.lint)
measurement_table_has_timepoint_specific_mappings() (in module petab)
(in module petab.lint)
measurements_have_replicates() (in module petab)
(in module petab.measurements)
merge_preeq_and_sim_pars() (in module petab)
(in module petab.parameter_mapping)
merge_preeq_and_sim_pars_condition() (in module petab)
(in module petab.parameter_mapping)
module
petab
petab.C
petab.composite_problem
petab.conditions
petab.core
petab.lint
petab.measurements
petab.parameter_mapping
petab.parameters
petab.problem
petab.sampling
petab.sbml
petab.visualize.data_overview
petab.visualize.helper_functions
petab.visualize.plotting_config
petab.yaml
most_common() (petab.Counter method)
(petab.lint.Counter method)
move_to_end() (petab.OrderedDict method)
(petab.parameters.OrderedDict method)
N
noise_formulas (petab.Simulator attribute)
normalize_parameter_df() (in module petab)
(in module petab.parameters)
Number (class in petab.visualize.helper_functions)
O
observable_df (petab.Problem attribute)
(petab.problem.Problem attribute)
OrderedDict (class in petab)
(class in petab.parameters)
P
parameter_df (petab.composite_problem.CompositeProblem attribute)
(petab.CompositeProblem attribute)
(petab.Problem attribute)
(petab.problem.Problem attribute)
petab
module
petab.C
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
petab_problem (petab.Simulator attribute)
plot_data_and_simulation() (in module petab.visualize)
plot_lowlevel() (in module petab.visualize.helper_functions)
(in module petab.visualize.plotting_config)
pop() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
popitem() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
Problem (class in petab)
(class in petab.problem)
problems (petab.composite_problem.CompositeProblem attribute)
(petab.CompositeProblem attribute)
R
reduce() (in module petab)
remove_working_dir() (petab.Simulator method)
rng (petab.Simulator attribute)
S
sample_from_prior() (in module petab)
(in module petab.sampling)
sample_noise() (in module petab)
sample_parameter_startpoints() (in module petab)
(in module petab.sampling)
(petab.Problem method)
(petab.problem.Problem method)
sbml_document (petab.Problem attribute)
(petab.problem.Problem attribute)
sbml_model (petab.Problem attribute)
(petab.problem.Problem attribute)
sbml_parameter_is_observable() (in module petab)
(in module petab.sbml)
sbml_parameter_is_sigma() (in module petab)
(in module petab.sbml)
sbml_reader (petab.Problem attribute)
(petab.problem.Problem attribute)
scale() (in module petab)
(in module petab.parameters)
setdefault() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
simulate() (petab.Simulator method)
simulate_without_noise() (petab.Simulator method)
Simulator (class in petab)
split_parameter_replacement_list() (in module petab)
(in module petab.measurements)
square_plot_equal_ranges() (in module petab.visualize.plotting_config)
subtract() (petab.Counter method)
(petab.lint.Counter method)
T
temporary_working_dir (petab.Simulator attribute)
to_files() (petab.Problem method)
(petab.problem.Problem method)
to_float_if_float() (in module petab)
(in module petab.core)
U
ub() (petab.Problem property)
(petab.problem.Problem property)
ub_scaled() (petab.Problem property)
(petab.problem.Problem property)
unique_preserve_order() (in module petab)
(in module petab.core)
unscale() (in module petab)
(in module petab.parameters)
update() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
V
validate() (in module petab)
(in module petab.yaml)
validate_yaml_semantics() (in module petab)
(in module petab.yaml)
validate_yaml_syntax() (in module petab)
(in module petab.yaml)
values() (petab.Counter method)
(petab.lint.Counter method)
(petab.OrderedDict method)
(petab.parameters.OrderedDict method)
visualization_df (petab.Problem attribute)
(petab.problem.Problem attribute)
W
warn() (in module petab)
(in module petab.core)
(in module petab.measurements)
(in module petab.problem)
(in module petab.sbml)
working_dir (petab.Simulator attribute)
write_condition_df() (in module petab)
(in module petab.conditions)
write_measurement_df() (in module petab)
(in module petab.measurements)
write_observable_df() (in module petab)
write_parameter_df() (in module petab)
(in module petab.parameters)
write_sbml() (in module petab)
(in module petab.sbml)
write_simulation_df() (in module petab)
(in module petab.core)
write_visualization_df() (in module petab)
(in module petab.core)
write_yaml() (in module petab)
(in module petab.yaml)
X
x_fixed_ids() (petab.Problem property)
(petab.problem.Problem property)
x_fixed_indices() (petab.Problem property)
(petab.problem.Problem property)
x_free_ids() (petab.Problem property)
(petab.problem.Problem property)
x_free_indices() (petab.Problem property)
(petab.problem.Problem property)
x_ids() (petab.Problem property)
(petab.problem.Problem property)
x_nominal() (petab.Problem property)
(petab.problem.Problem property)
x_nominal_fixed() (petab.Problem property)
(petab.problem.Problem property)
x_nominal_fixed_scaled() (petab.Problem property)
(petab.problem.Problem property)
x_nominal_free() (petab.Problem property)
(petab.problem.Problem property)
x_nominal_free_scaled() (petab.Problem property)
(petab.problem.Problem property)
x_nominal_scaled() (petab.Problem property)
(petab.problem.Problem property)
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