pyPESTO
v0.2.12
User's guide
Install and upgrade
Examples
Storage
API reference
Developer's guide
Contribute
Deploy
About
Release notes
Authors
Contact
License
Logo
pyPESTO
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
X
_
__call__() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciCalculator method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.predict.AmiciPredictor method)
(pypesto.problem.ObjectiveBase method)
(pypesto.startpoint.CheckedStartpoints method)
(pypesto.startpoint.NoStartpoints method)
(pypesto.startpoint.StartpointMethod method)
__init__() (pypesto.AmiciObjective method)
(pypesto.CsvHistory method)
(pypesto.engine.Engine method)
(pypesto.engine.MultiProcessEngine method)
(pypesto.engine.MultiThreadEngine method)
(pypesto.engine.SingleCoreEngine method)
(pypesto.engine.Task method)
(pypesto.ensemble.Ensemble method)
(pypesto.ensemble.EnsemblePrediction method)
(pypesto.FD method)
(pypesto.FDDelta method)
(pypesto.Hdf5History method)
(pypesto.History method)
(pypesto.HistoryOptions method)
(pypesto.McmcPtResult method)
(pypesto.MemoryHistory method)
(pypesto.Objective method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciCalculator method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.FD method)
(pypesto.objective.FDDelta method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.History method)
(pypesto.objective.HistoryOptions method)
(pypesto.objective.MemoryHistory method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.objective.OptimizerHistory method)
(pypesto.ObjectiveBase method)
(pypesto.optimize.CmaesOptimizer method)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.FidesOptimizer method)
(pypesto.optimize.IpoptOptimizer method)
(pypesto.optimize.NLoptOptimizer method)
(pypesto.optimize.OptimizeOptions method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.PyswarmOptimizer method)
(pypesto.optimize.PyswarmsOptimizer method)
(pypesto.optimize.ScipyDifferentialEvolutionOptimizer method)
(pypesto.optimize.ScipyOptimizer method)
(pypesto.OptimizeResult method)
(pypesto.OptimizerHistory method)
(pypesto.OptimizerResult method)
(pypesto.petab.PetabImporter method)
(pypesto.petab.PetabImporterPysb method)
(pypesto.predict.AmiciPredictor method)
(pypesto.predict.PredictorTask method)
(pypesto.PredictionConditionResult method)
(pypesto.PredictionResult method)
(pypesto.Problem method)
(pypesto.problem.ObjectiveBase method)
(pypesto.problem.Problem method)
(pypesto.problem.SupportsFloat method)
(pypesto.problem.SupportsInt method)
(pypesto.profile.ProfileOptions method)
(pypesto.ProfileResult method)
(pypesto.ProfilerResult method)
(pypesto.Result method)
(pypesto.result.McmcPtResult method)
(pypesto.result.OptimizeResult method)
(pypesto.result.OptimizerResult method)
(pypesto.result.PredictionConditionResult method)
(pypesto.result.PredictionResult method)
(pypesto.result.ProfileResult method)
(pypesto.result.ProfilerResult method)
(pypesto.result.Result method)
(pypesto.result.SampleResult method)
(pypesto.sample.AdaptiveMetropolisSampler method)
(pypesto.sample.EmceeSampler method)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Sampler method)
(pypesto.SampleResult method)
(pypesto.select.Problem method)
(pypesto.startpoint.CheckedStartpoints method)
(pypesto.startpoint.FunctionStartpoints method)
(pypesto.startpoint.LatinHypercubeStartpoints method)
(pypesto.startpoint.UniformStartpoints method)
(pypesto.store.OptimizationResultHDF5Reader method)
(pypesto.store.OptimizationResultHDF5Writer method)
(pypesto.store.ProblemHDF5Reader method)
(pypesto.store.ProblemHDF5Writer method)
(pypesto.store.ProfileResultHDF5Reader method)
(pypesto.store.ProfileResultHDF5Writer method)
(pypesto.store.SamplingResultHDF5Reader method)
(pypesto.store.SamplingResultHDF5Writer method)
(pypesto.visualize.ReferencePoint method)
A
AdaptiveMetropolisSampler (class in pypesto.sample)
AdaptiveParallelTemperingSampler (class in pypesto.sample)
adjust_betas() (pypesto.sample.AdaptiveParallelTemperingSampler method)
(pypesto.sample.ParallelTemperingSampler method)
AggregatedObjective (class in pypesto.objective)
ALWAYS (pypesto.FDDelta attribute)
(pypesto.objective.FDDelta attribute)
AmiciCalculator (class in pypesto.objective)
AmiciObjectBuilder (class in pypesto.objective)
AmiciObjective (class in pypesto)
(class in pypesto.objective)
AmiciPredictor (class in pypesto.predict)
append() (pypesto.OptimizeResult method)
(pypesto.result.OptimizeResult method)
append_empty_profile_list() (pypesto.ProfileResult method)
(pypesto.result.ProfileResult method)
append_profile_point() (pypesto.ProfilerResult method)
(pypesto.result.ProfilerResult method)
append_profiler_result() (pypesto.ProfileResult method)
(pypesto.result.ProfileResult method)
apply_custom_timepoints() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
apply_steadystate_guess() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
approximate_parameter_profile() (in module pypesto.profile)
as_dataframe() (pypesto.OptimizeResult method)
(pypesto.result.OptimizeResult method)
as_list() (pypesto.OptimizeResult method)
(pypesto.result.OptimizeResult method)
assert_instance() (pypesto.HistoryOptions static method)
(pypesto.objective.HistoryOptions static method)
(pypesto.optimize.OptimizeOptions static method)
assign_clustered_colors() (in module pypesto.visualize)
assign_clusters() (in module pypesto.visualize)
assign_colors() (in module pypesto.visualize)
auto_color (pypesto.visualize.ReferencePoint attribute)
auto_correlation() (in module pypesto.sample)
autosave() (in module pypesto.store)
B
BACKWARD (pypesto.FD attribute)
(pypesto.objective.FD attribute)
C
calculate_approximate_ci() (in module pypesto.profile)
calculate_ci_mcmc_sample() (in module pypesto.sample)
calculate_ci_mcmc_sample_prediction() (in module pypesto.sample)
call_unprocessed() (pypesto.AmiciObjective method)
(pypesto.FD method)
(pypesto.Objective method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.FD method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
CENTRAL (pypesto.FD attribute)
(pypesto.objective.FD attribute)
check_and_resample() (pypesto.startpoint.CheckedStartpoints method)
check_grad() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_grad_multi_eps() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_gradients() (pypesto.petab.PetabImporter method)
check_gradients_match_finite_differences() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_identifiability() (pypesto.ensemble.Ensemble method)
check_mode() (pypesto.AmiciObjective method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_sensi_orders() (pypesto.AmiciObjective method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
CheckedStartpoints (class in pypesto.startpoint)
chi2_quantile_to_ratio() (in module pypesto.profile)
CmaesOptimizer (class in pypesto.optimize)
color (pypesto.visualize.ReferencePoint attribute)
compile_model() (pypesto.petab.PetabImporter method)
(pypesto.petab.PetabImporterPysb method)
compute_chi2() (pypesto.ensemble.EnsemblePrediction method)
compute_summary() (pypesto.ensemble.Ensemble method)
(pypesto.ensemble.EnsemblePrediction method)
condense_to_arrays() (pypesto.ensemble.EnsemblePrediction method)
CONSTANT (pypesto.FDDelta attribute)
(pypesto.objective.FDDelta attribute)
create_edatas() (pypesto.objective.AmiciObjectBuilder method)
(pypesto.petab.PetabImporter method)
create_history() (pypesto.HistoryOptions method)
(pypesto.objective.HistoryOptions method)
create_instance() (pypesto.profile.ProfileOptions static method)
create_method_caller() (pypesto.select.Problem method)
create_model() (pypesto.objective.AmiciObjectBuilder method)
(pypesto.petab.PetabImporter method)
create_objective() (pypesto.petab.PetabImporter method)
create_predictor() (pypesto.petab.PetabImporter method)
create_prior() (pypesto.petab.PetabImporter method)
create_problem() (pypesto.petab.PetabImporter method)
create_references() (in module pypesto.visualize)
create_solver() (pypesto.objective.AmiciObjectBuilder method)
(pypesto.petab.PetabImporter method)
create_startpoint_method() (pypesto.petab.PetabImporter method)
CsvHistory (class in pypesto)
(class in pypesto.objective)
D
default_options() (pypesto.sample.AdaptiveMetropolisSampler class method)
(pypesto.sample.AdaptiveParallelTemperingSampler class method)
(pypesto.sample.MetropolisSampler class method)
(pypesto.sample.ParallelTemperingSampler class method)
(pypesto.sample.Sampler class method)
delete_nan_inf() (in module pypesto.visualize)
delta (pypesto.objective.FDDelta attribute)
delta_fun (pypesto.objective.FD attribute)
delta_grad (pypesto.objective.FD attribute)
delta_res (pypesto.objective.FD attribute)
dim() (pypesto.Problem property)
(pypesto.problem.Problem property)
DISTANCE (pypesto.FDDelta attribute)
(pypesto.objective.FDDelta attribute)
DlibOptimizer (class in pypesto.optimize)
E
effective_sample_size() (in module pypesto.sample)
EmceeSampler (class in pypesto.sample)
Engine (class in pypesto.engine)
Ensemble (class in pypesto.ensemble)
ensemble_crosstab_scatter_lowlevel() (in module pypesto.visualize)
ensemble_identifiability() (in module pypesto.visualize)
ensemble_scatter_lowlevel() (in module pypesto.visualize)
EnsemblePrediction (class in pypesto.ensemble)
execute() (pypesto.engine.Engine method)
(pypesto.engine.MultiProcessEngine method)
(pypesto.engine.MultiThreadEngine method)
(pypesto.engine.SingleCoreEngine method)
(pypesto.engine.Task method)
(pypesto.predict.PredictorTask method)
exitflag (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
exitflag_path (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
extract_from_history() (pypesto.objective.OptimizerHistory method)
(pypesto.OptimizerHistory method)
F
f (in module pypesto.store)
FD (class in pypesto)
(class in pypesto.objective)
FDDelta (class in pypesto)
(class in pypesto.objective)
FidesOptimizer (class in pypesto.optimize)
fill_result_from_history() (in module pypesto.optimize)
finalize() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.History method)
(pypesto.HistoryBase method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.OptimizerHistory method)
(pypesto.OptimizerHistory method)
fix_parameters() (pypesto.Problem method)
(pypesto.problem.Problem method)
flip_profile() (pypesto.ProfilerResult method)
(pypesto.result.ProfilerResult method)
FORWARD (pypesto.FD attribute)
(pypesto.objective.FD attribute)
from_optimization_endpoints() (pypesto.ensemble.Ensemble static method)
from_optimization_history() (pypesto.ensemble.Ensemble static method)
from_sample() (pypesto.ensemble.Ensemble static method)
from_yaml() (pypesto.petab.PetabImporter static method)
full_index_to_free_index() (pypesto.Problem method)
(pypesto.problem.Problem method)
FunctionStartpoints (class in pypesto.startpoint)
fval (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
fval0 (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
fval_path (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
G
get() (pypesto.FDDelta method)
(pypesto.objective.FDDelta method)
get_chi2_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_config() (pypesto.AmiciObjective method)
(pypesto.Objective method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_covariance_matrix_parameters() (in module pypesto.ensemble)
get_covariance_matrix_predictions() (in module pypesto.ensemble)
get_default_options() (pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.ScipyOptimizer method)
get_for_key() (pypesto.OptimizeResult method)
(pypesto.result.OptimizeResult method)
get_full_matrix() (pypesto.Problem method)
(pypesto.problem.Problem method)
get_full_vector() (pypesto.Problem method)
(pypesto.problem.Problem method)
get_fval() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_fval_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_grad() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_grad_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_hess() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_hess_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_history_directory() (pypesto.Hdf5History method)
(pypesto.objective.Hdf5History method)
get_last_sample() (pypesto.sample.InternalSampler method)
(pypesto.sample.MetropolisSampler method)
get_or_create_group() (in module pypesto.store)
get_parameter_prior_dict() (in module pypesto.objective)
get_pca_representation_parameters() (in module pypesto.ensemble)
get_pca_representation_predictions() (in module pypesto.ensemble)
get_percentile_label() (in module pypesto.ensemble)
get_profiler_result() (pypesto.ProfileResult method)
(pypesto.result.ProfileResult method)
get_reduced_matrix() (pypesto.Problem method)
(pypesto.problem.Problem method)
get_reduced_vector() (pypesto.Problem method)
(pypesto.problem.Problem method)
get_res() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_res_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_samples() (pypesto.sample.EmceeSampler method)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Sampler method)
get_schi2_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_spectral_decomposition_lowlevel() (in module pypesto.ensemble)
get_spectral_decomposition_parameters() (in module pypesto.ensemble)
get_spectral_decomposition_predictions() (in module pypesto.ensemble)
get_sres() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_sres_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_time_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_trimmed_indices() (pypesto.HistoryBase method)
(pypesto.objective.HistoryBase method)
get_umap_representation_parameters() (in module pypesto.ensemble)
get_umap_representation_predictions() (in module pypesto.ensemble)
get_x_trace() (pypesto.CsvHistory method)
(pypesto.Hdf5History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
geweke_test() (in module pypesto.sample)
grad (pypesto.objective.FD attribute)
(pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
grad_min (pypesto.objective.OptimizerHistory attribute)
(pypesto.OptimizerHistory attribute)
gradient_neg_log_density() (pypesto.objective.NegLogParameterPriors method)
gradnorm_path (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
group_path (in module pypesto.store)
H
has_fun() (pypesto.FD property)
(pypesto.Objective property)
(pypesto.objective.FD property)
(pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_grad() (pypesto.FD property)
(pypesto.Objective property)
(pypesto.objective.FD property)
(pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_hess() (pypesto.FD property)
(pypesto.Objective property)
(pypesto.objective.FD property)
(pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_hessp() (pypesto.Objective property)
(pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_res() (pypesto.FD property)
(pypesto.Objective property)
(pypesto.objective.FD property)
(pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_sres() (pypesto.FD property)
(pypesto.Objective property)
(pypesto.objective.FD property)
(pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
Hdf5History (class in pypesto)
(class in pypesto.objective)
hess (pypesto.objective.FD attribute)
(pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
hess_min (pypesto.objective.OptimizerHistory attribute)
(pypesto.OptimizerHistory attribute)
hess_via_fval (pypesto.objective.FD attribute)
hessian_neg_log_density() (pypesto.objective.NegLogParameterPriors method)
hessian_vp_neg_log_density() (pypesto.objective.NegLogParameterPriors method)
History (class in pypesto)
(class in pypesto.objective)
history (pypesto.objective.ObjectiveBase attribute)
(pypesto.ObjectiveBase attribute)
(pypesto.OptimizerResult attribute)
(pypesto.problem.ObjectiveBase attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.select.Problem attribute)
HistoryBase (class in pypesto)
(class in pypesto.objective)
HistoryOptions (class in pypesto)
(class in pypesto.objective)
I
id (pypesto.OptimizerResult attribute)
(pypesto.predict.PredictorTask attribute)
(pypesto.result.OptimizerResult attribute)
initialize() (pypesto.AmiciObjective method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciCalculator method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
(pypesto.sample.AdaptiveMetropolisSampler method)
(pypesto.sample.EmceeSampler method)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Sampler method)
InternalSampler (class in pypesto.sample)
IpoptOptimizer (class in pypesto.optimize)
is_least_squares() (pypesto.optimize.CmaesOptimizer method)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.FidesOptimizer method)
(pypesto.optimize.IpoptOptimizer method)
(pypesto.optimize.NLoptOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.PyswarmOptimizer method)
(pypesto.optimize.PyswarmsOptimizer method)
(pypesto.optimize.ScipyDifferentialEvolutionOptimizer method)
(pypesto.optimize.ScipyOptimizer method)
L
latin_hypercube() (in module pypesto.startpoint)
LatinHypercubeStartpoints (class in pypesto.startpoint)
lb() (pypesto.Problem property)
(pypesto.problem.Problem property)
lb_init() (pypesto.Problem property)
(pypesto.problem.Problem property)
legend (pypesto.visualize.ReferencePoint attribute)
load() (pypesto.Hdf5History static method)
(pypesto.objective.Hdf5History static method)
load_objective_config() (in module pypesto.store)
log() (in module pypesto.logging)
log_level_active() (in module pypesto.logging)
log_to_console() (in module pypesto.logging)
log_to_file() (in module pypesto.logging)
M
make_internal() (pypesto.sample.InternalSampler method)
(pypesto.sample.MetropolisSampler method)
max_distance (pypesto.objective.FDDelta attribute)
max_steps (pypesto.objective.FDDelta attribute)
McmcPtResult (class in pypesto)
(class in pypesto.result)
MemoryHistory (class in pypesto)
(class in pypesto.objective)
message (pypesto.OptimizerResult attribute)
(pypesto.ProfilerResult attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.result.ProfilerResult attribute)
method (pypesto.objective.FD attribute)
method_caller (pypesto.select.Problem attribute)
METHODS (pypesto.FD attribute)
(pypesto.objective.FD attribute)
MetropolisSampler (class in pypesto.sample)
minimize() (in module pypesto.optimize)
(pypesto.optimize.CmaesOptimizer method)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.FidesOptimizer method)
(pypesto.optimize.IpoptOptimizer method)
(pypesto.optimize.NLoptOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.PyswarmOptimizer method)
(pypesto.optimize.PyswarmsOptimizer method)
(pypesto.optimize.ScipyDifferentialEvolutionOptimizer method)
(pypesto.optimize.ScipyOptimizer method)
mode (pypesto.predict.PredictorTask attribute)
MODEL_BASE_DIR (pypesto.petab.PetabImporter attribute)
model_postprocessor (pypesto.select.Problem attribute)
model_to_pypesto_problem() (in module pypesto.select)
module
pypesto
pypesto.engine
pypesto.ensemble
pypesto.logging
pypesto.objective
pypesto.optimize
pypesto.petab
pypesto.predict
pypesto.problem
pypesto.profile
pypesto.result
pypesto.sample
pypesto.select
pypesto.startpoint
pypesto.store
pypesto.visualize
MultiProcessEngine (class in pypesto.engine)
multistart_select() (pypesto.select.Problem method)
MultiThreadEngine (class in pypesto.engine)
N
n_fval (pypesto.OptimizerResult attribute)
(pypesto.ProfilerResult attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.result.ProfilerResult attribute)
n_fval() (pypesto.Hdf5History property)
(pypesto.History property)
(pypesto.HistoryBase property)
(pypesto.objective.Hdf5History property)
(pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_grad (pypesto.OptimizerResult attribute)
(pypesto.ProfilerResult attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.result.ProfilerResult attribute)
n_grad() (pypesto.Hdf5History property)
(pypesto.History property)
(pypesto.HistoryBase property)
(pypesto.objective.Hdf5History property)
(pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_hess (pypesto.OptimizerResult attribute)
(pypesto.ProfilerResult attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.result.ProfilerResult attribute)
n_hess() (pypesto.Hdf5History property)
(pypesto.History property)
(pypesto.HistoryBase property)
(pypesto.objective.Hdf5History property)
(pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_res (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
n_res() (pypesto.Hdf5History property)
(pypesto.History property)
(pypesto.HistoryBase property)
(pypesto.objective.Hdf5History property)
(pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_sres (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
n_sres() (pypesto.Hdf5History property)
(pypesto.History property)
(pypesto.HistoryBase property)
(pypesto.objective.Hdf5History property)
(pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
neg_log_density() (pypesto.objective.NegLogParameterPriors method)
NegLogParameterPriors (class in pypesto.objective)
NegLogPriors (class in pypesto)
(class in pypesto.objective)
(class in pypesto.problem)
NLoptOptimizer (class in pypesto.optimize)
normalize() (pypesto.Problem method)
(pypesto.problem.Problem method)
NoStartpoints (class in pypesto.startpoint)
O
obj (pypesto.objective.FD attribute)
Objective (class in pypesto)
(class in pypesto.objective)
ObjectiveBase (class in pypesto)
(class in pypesto.objective)
(class in pypesto.problem)
optimization_result_from_history() (in module pypesto.optimize)
optimization_run_properties_one_plot() (in module pypesto.visualize)
optimization_run_properties_per_multistart() (in module pypesto.visualize)
optimization_run_property_per_multistart() (in module pypesto.visualize)
OptimizationResultHDF5Reader (class in pypesto.store)
OptimizationResultHDF5Writer (class in pypesto.store)
optimize_result (pypesto.Result attribute)
(pypesto.result.Result attribute)
OptimizeOptions (class in pypesto.optimize)
Optimizer (class in pypesto.optimize)
optimizer (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
optimizer_convergence() (in module pypesto.visualize)
optimizer_history() (in module pypesto.visualize)
optimizer_history_lowlevel() (in module pypesto.visualize)
OptimizeResult (class in pypesto)
(class in pypesto.result)
OptimizerHistory (class in pypesto)
(class in pypesto.objective)
OptimizerResult (class in pypesto)
(class in pypesto.result)
output_to_tuple() (pypesto.objective.ObjectiveBase static method)
(pypesto.ObjectiveBase static method)
(pypesto.problem.ObjectiveBase static method)
P
par_arr_to_dct() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
ParallelTemperingSampler (class in pypesto.sample)
parameter_hist() (in module pypesto.visualize)
parameter_profile() (in module pypesto.profile)
parameters() (in module pypesto.visualize)
parameters_lowlevel() (in module pypesto.visualize)
petab_select_problem (pypesto.select.Problem attribute)
PetabImporter (class in pypesto.petab)
PetabImporterPysb (class in pypesto.petab)
pre_post_processor (pypesto.objective.ObjectiveBase attribute)
(pypesto.ObjectiveBase attribute)
(pypesto.problem.ObjectiveBase attribute)
predict() (pypesto.ensemble.Ensemble method)
prediction_to_petab_measurement_df() (pypesto.petab.PetabImporter method)
prediction_to_petab_simulation_df() (pypesto.petab.PetabImporter method)
PredictionConditionResult (class in pypesto)
(class in pypesto.result)
PredictionResult (class in pypesto)
(class in pypesto.result)
predictor (pypesto.predict.PredictorTask attribute)
PredictorTask (class in pypesto.predict)
print_parameter_summary() (pypesto.Problem method)
(pypesto.problem.Problem method)
Problem (class in pypesto)
(class in pypesto.problem)
(class in pypesto.select)
problem (pypesto.Result attribute)
(pypesto.result.Result attribute)
ProblemHDF5Reader (class in pypesto.store)
ProblemHDF5Writer (class in pypesto.store)
process_offset_y() (in module pypesto.visualize)
process_result_list() (in module pypesto.visualize)
process_y_limits() (in module pypesto.visualize)
profile_cis() (in module pypesto.visualize)
profile_lowlevel() (in module pypesto.visualize)
profile_result (pypesto.Result attribute)
(pypesto.result.Result attribute)
ProfileOptions (class in pypesto.profile)
ProfileResult (class in pypesto)
(class in pypesto.result)
ProfileResultHDF5Reader (class in pypesto.store)
ProfileResultHDF5Writer (class in pypesto.store)
ProfilerResult (class in pypesto)
(class in pypesto.result)
profiles() (in module pypesto.visualize)
profiles_lowlevel() (in module pypesto.visualize)
projection_scatter_pca() (in module pypesto.visualize)
projection_scatter_umap() (in module pypesto.visualize)
projection_scatter_umap_original() (in module pypesto.visualize)
pypesto
module
pypesto.engine
module
pypesto.ensemble
module
pypesto.logging
module
pypesto.objective
module
pypesto.optimize
module
pypesto.petab
module
pypesto.predict
module
pypesto.problem
module
pypesto.profile
module
pypesto.result
module
pypesto.sample
module
pypesto.select
module
pypesto.startpoint
module
pypesto.store
module
pypesto.visualize
module
PyswarmOptimizer (class in pypesto.optimize)
PyswarmsOptimizer (class in pypesto.optimize)
R
ratio_path (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
rdatas_to_measurement_df() (pypesto.petab.PetabImporter method)
rdatas_to_simulation_df() (pypesto.petab.PetabImporter method)
read() (pypesto.store.OptimizationResultHDF5Reader method)
(pypesto.store.ProblemHDF5Reader method)
(pypesto.store.ProfileResultHDF5Reader method)
(pypesto.store.SamplingResultHDF5Reader method)
read_ensemble_prediction_from_h5() (in module pypesto.ensemble)
read_from_csv() (in module pypesto.ensemble)
read_from_df() (in module pypesto.ensemble)
read_result() (in module pypesto.store)
read_result_from_file() (in module pypesto.optimize)
read_results_from_file() (in module pypesto.optimize)
recover_options() (pypesto.Hdf5History method)
(pypesto.objective.Hdf5History method)
ReferencePoint (class in pypesto.visualize)
res (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
res_min (pypesto.objective.OptimizerHistory attribute)
(pypesto.OptimizerHistory attribute)
res_to_chi2() (in module pypesto.objective)
reset_steadystate_guesses() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
residual() (pypesto.objective.NegLogParameterPriors method)
residual_jacobian() (pypesto.objective.NegLogParameterPriors method)
Result (class in pypesto)
(class in pypesto.result)
S
sample() (in module pypesto.sample)
(pypesto.sample.EmceeSampler method)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Sampler method)
(pypesto.startpoint.CheckedStartpoints method)
(pypesto.startpoint.FunctionStartpoints method)
(pypesto.startpoint.LatinHypercubeStartpoints method)
sample_result (pypesto.Result attribute)
(pypesto.result.Result attribute)
Sampler (class in pypesto.sample)
SampleResult (class in pypesto)
(class in pypesto.result)
sampling_1d_marginals() (in module pypesto.visualize)
sampling_fval_traces() (in module pypesto.visualize)
sampling_parameter_cis() (in module pypesto.visualize)
sampling_parameter_traces() (in module pypesto.visualize)
sampling_prediction_trajectories() (in module pypesto.visualize)
sampling_scatter() (in module pypesto.visualize)
SamplingResultHDF5Reader (class in pypesto.store)
SamplingResultHDF5Writer (class in pypesto.store)
ScipyDifferentialEvolutionOptimizer (class in pypesto.optimize)
ScipyOptimizer (class in pypesto.optimize)
select() (pypesto.select.Problem method)
select_to_completion() (pypesto.select.Problem method)
sensi_orders (pypesto.predict.PredictorTask attribute)
set_custom_timepoints() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
set_last_sample() (pypesto.sample.InternalSampler method)
(pypesto.sample.MetropolisSampler method)
set_profiler_result() (pypesto.ProfileResult method)
(pypesto.result.ProfileResult method)
set_x_guesses() (pypesto.Problem method)
(pypesto.problem.Problem method)
SingleCoreEngine (class in pypesto.engine)
sort() (pypesto.OptimizeResult method)
(pypesto.result.OptimizeResult method)
sres (pypesto.objective.FD attribute)
(pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
sres_min (pypesto.objective.OptimizerHistory attribute)
(pypesto.OptimizerHistory attribute)
sres_to_schi2() (in module pypesto.objective)
start_time() (pypesto.History property)
(pypesto.HistoryBase property)
(pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
StartpointMethod (class in pypesto.startpoint)
STEPS (pypesto.FDDelta attribute)
(pypesto.objective.FDDelta attribute)
steps (pypesto.objective.FDDelta attribute)
storage_filename (pypesto.store.OptimizationResultHDF5Reader attribute)
(pypesto.store.OptimizationResultHDF5Writer attribute)
(pypesto.store.ProblemHDF5Reader attribute)
(pypesto.store.ProblemHDF5Writer attribute)
(pypesto.store.ProfileResultHDF5Reader attribute)
(pypesto.store.ProfileResultHDF5Writer attribute)
(pypesto.store.SamplingResultHDF5Reader attribute)
(pypesto.store.SamplingResultHDF5Writer attribute)
store_steadystate_guess() (pypesto.AmiciObjective method)
(pypesto.objective.AmiciObjective method)
summary() (pypesto.OptimizeResult method)
(pypesto.OptimizerResult method)
(pypesto.result.OptimizeResult method)
(pypesto.result.OptimizerResult method)
SupportsFloat (class in pypesto.problem)
SupportsInt (class in pypesto.problem)
swap_samples() (pypesto.sample.ParallelTemperingSampler method)
T
Task (class in pypesto.engine)
test_deltas (pypesto.objective.FDDelta attribute)
time (pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
time_path (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
time_total (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
to_startpoint_method() (in module pypesto.startpoint)
trace_save_iter() (pypesto.Hdf5History property)
(pypesto.objective.Hdf5History property)
translate_options() (pypesto.sample.Sampler class method)
U
ub() (pypesto.Problem property)
(pypesto.problem.Problem property)
ub_init() (pypesto.Problem property)
(pypesto.problem.Problem property)
unfix_parameters() (pypesto.Problem method)
(pypesto.problem.Problem method)
uniform() (in module pypesto.startpoint)
UniformStartpoints (class in pypesto.startpoint)
update() (pypesto.CsvHistory method)
(pypesto.FDDelta method)
(pypesto.Hdf5History method)
(pypesto.History method)
(pypesto.HistoryBase method)
(pypesto.MemoryHistory method)
(pypesto.objective.CsvHistory method)
(pypesto.objective.FDDelta method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
(pypesto.objective.OptimizerHistory method)
(pypesto.OptimizerHistory method)
update_condition (pypesto.objective.FDDelta attribute)
UPDATE_CONDITIONS (pypesto.FDDelta attribute)
(pypesto.objective.FDDelta attribute)
update_from_problem() (pypesto.objective.ObjectiveBase method)
(pypesto.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
update_to_full() (pypesto.OptimizerResult method)
(pypesto.result.OptimizerResult method)
updates (pypesto.objective.FDDelta attribute)
V
validation_profile_significance() (in module pypesto.profile)
W
waterfall() (in module pypesto.visualize)
waterfall_lowlevel() (in module pypesto.visualize)
write() (pypesto.store.OptimizationResultHDF5Writer method)
(pypesto.store.ProblemHDF5Writer method)
(pypesto.store.ProfileResultHDF5Writer method)
(pypesto.store.SamplingResultHDF5Writer method)
write_array() (in module pypesto.store)
write_ensemble_prediction_to_h5() (in module pypesto.ensemble)
write_result() (in module pypesto.store)
write_to_csv() (pypesto.PredictionResult method)
(pypesto.result.PredictionResult method)
write_to_h5() (pypesto.PredictionResult method)
(pypesto.result.PredictionResult method)
X
x (pypesto.OptimizerResult attribute)
(pypesto.predict.PredictorTask attribute)
(pypesto.result.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
x0 (pypesto.objective.FDDelta attribute)
(pypesto.OptimizerResult attribute)
(pypesto.result.OptimizerResult attribute)
x_free_indices() (pypesto.Problem property)
(pypesto.problem.Problem property)
x_guesses() (pypesto.Problem property)
(pypesto.problem.Problem property)
x_names() (pypesto.objective.ObjectiveBase property)
(pypesto.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
x_path (pypesto.ProfilerResult attribute)
(pypesto.result.ProfilerResult attribute)
Read the Docs
v: v0.2.12
Versions
latest
stable
v0.2.12
v0.2.11
v0.2.10
v0.2.9
v0.2.8
v0.2.7
v0.2.6
v0.2.5
v0.2.4
v0.2.3
v0.2.2
v0.2.1
v0.2.0
v0.1.0
develop
v0.0.13
v0.0.12
v0.0.11
v0.0.10
v0.0.9
v0.0.8
v0.0.7
v0.0.6
v0.0.5
v0.0.4
v0.0.3
v0.0.2
v0.0.1
Downloads
On Read the Docs
Project Home
Builds