pyPESTO
v0.2.1
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Index
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A
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C
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D
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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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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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W
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X
_
__call__() (pypesto.objective.AmiciCalculator method)
(pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
__init__() (pypesto.engine.Engine method)
(pypesto.engine.MultiProcessEngine method)
(pypesto.engine.MultiThreadEngine method)
(pypesto.engine.SingleCoreEngine method)
(pypesto.engine.Task method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciCalculator method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.CsvHistory 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.optimize.DlibOptimizer method)
(pypesto.optimize.IpoptOptimizer method)
(pypesto.optimize.OptimizeOptions method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.OptimizerResult method)
(pypesto.optimize.PyswarmOptimizer method)
(pypesto.optimize.ScipyOptimizer method)
(pypesto.petab.PetabImporter method)
(pypesto.problem.ObjectiveBase method)
(pypesto.problem.Problem method)
(pypesto.problem.SupportsFloat method)
(pypesto.problem.SupportsInt method)
(pypesto.profile.ProfileOptions method)
(pypesto.profile.ProfilerResult method)
(pypesto.result.OptimizeResult method)
(pypesto.result.ProfileResult method)
(pypesto.result.Result method)
(pypesto.result.SampleResult method)
(pypesto.sample.AdaptiveMetropolisSampler method)
(pypesto.sample.McmcPtResult method)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Pymc3Sampler method)
(pypesto.sample.Sampler method)
(pypesto.store.OptimizationResultHDF5Reader method)
(pypesto.store.OptimizationResultHDF5Writer method)
(pypesto.store.ProblemHDF5Reader method)
(pypesto.store.ProblemHDF5Writer 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)
AmiciCalculator (class in pypesto.objective)
AmiciObjectBuilder (class in pypesto.objective)
AmiciObjective (class in pypesto.objective)
append() (pypesto.result.OptimizeResult method)
append_empty_profile_list() (pypesto.result.ProfileResult method)
append_profile_point() (pypesto.profile.ProfilerResult method)
append_profiler_result() (pypesto.result.ProfileResult method)
apply_steadystate_guess() (pypesto.objective.AmiciObjective method)
approximate_parameter_profile() (in module pypesto.profile)
as_dataframe() (pypesto.result.OptimizeResult method)
as_list() (pypesto.result.OptimizeResult method)
assert_instance() (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)
assign_startpoints() (in module pypesto.startpoint)
auto_color (pypesto.visualize.ReferencePoint attribute)
auto_correlation() (in module pypesto.sample)
C
calculate_approximate_ci() (in module pypesto.profile)
call_unprocessed() (pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_grad() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_mode() (pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
check_sensi_orders() (pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.NegLogParameterPriors method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
chi2_quantile_to_ratio() (in module pypesto.profile)
color (pypesto.visualize.ReferencePoint attribute)
compile_model() (pypesto.petab.PetabImporter method)
create_edatas() (pypesto.objective.AmiciObjectBuilder method)
(pypesto.petab.PetabImporter method)
create_history() (pypesto.objective.HistoryOptions method)
create_instance() (pypesto.profile.ProfileOptions static method)
create_model() (pypesto.objective.AmiciObjectBuilder method)
(pypesto.petab.PetabImporter method)
create_objective() (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)
CsvHistory (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)
dim() (pypesto.problem.Problem property)
DlibOptimizer (class in pypesto.optimize)
E
effective_sample_size() (in module pypesto.sample)
Engine (class in pypesto.engine)
execute() (pypesto.engine.Engine method)
(pypesto.engine.MultiProcessEngine method)
(pypesto.engine.MultiThreadEngine method)
(pypesto.engine.SingleCoreEngine method)
(pypesto.engine.Task method)
exitflag (pypesto.optimize.OptimizerResult attribute)
exitflag_path (pypesto.profile.ProfilerResult attribute)
extract_from_history() (pypesto.objective.OptimizerHistory method)
F
finalize() (pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.OptimizerHistory method)
fix_parameters() (pypesto.problem.Problem method)
flip_profile() (pypesto.profile.ProfilerResult method)
from_yaml() (pypesto.petab.PetabImporter static method)
full_index_to_free_index() (pypesto.problem.Problem method)
fval (pypesto.optimize.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
fval0 (pypesto.optimize.OptimizerResult attribute)
fval_path (pypesto.profile.ProfilerResult attribute)
G
get_chi2_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_default_options() (pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.ScipyOptimizer method)
get_for_key() (pypesto.result.OptimizeResult method)
get_full_matrix() (pypesto.problem.Problem method)
get_full_vector() (pypesto.problem.Problem method)
get_fval() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_fval_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_grad() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_grad_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_hess() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_hess_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_last_sample() (pypesto.sample.InternalSampler method)
(pypesto.sample.MetropolisSampler method)
get_profiler_result() (pypesto.result.ProfileResult method)
get_reduced_matrix() (pypesto.problem.Problem method)
get_reduced_vector() (pypesto.problem.Problem method)
get_res() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_res_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_samples() (pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Pymc3Sampler method)
(pypesto.sample.Sampler method)
get_schi2_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_sres() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
get_sres_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_time_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
get_x_trace() (pypesto.objective.CsvHistory method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
geweke_test() (in module pypesto.sample)
grad (pypesto.optimize.OptimizerResult attribute)
grad_min (pypesto.objective.OptimizerHistory attribute)
gradient_neg_log_density() (pypesto.objective.NegLogParameterPriors method)
gradnorm_path (pypesto.profile.ProfilerResult attribute)
H
has_fun() (pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_grad() (pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_hess() (pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_hessp() (pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_res() (pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
has_sres() (pypesto.objective.Objective property)
(pypesto.objective.ObjectiveBase property)
(pypesto.problem.ObjectiveBase property)
Hdf5History (class in pypesto.objective)
hess (pypesto.optimize.OptimizerResult attribute)
hess_min (pypesto.objective.OptimizerHistory attribute)
hessian_neg_log_density() (pypesto.objective.NegLogParameterPriors method)
hessian_vp_neg_log_density() (pypesto.objective.NegLogParameterPriors method)
History (class in pypesto.objective)
history (pypesto.objective.ObjectiveBase attribute)
(pypesto.optimize.OptimizerResult attribute)
(pypesto.problem.ObjectiveBase attribute)
HistoryBase (class in pypesto.objective)
HistoryOptions (class in pypesto.objective)
I
id (pypesto.optimize.OptimizerResult attribute)
initialize() (pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciCalculator method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
(pypesto.sample.AdaptiveMetropolisSampler method)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Pymc3Sampler method)
(pypesto.sample.Sampler method)
InternalSampler (class in pypesto.sample)
IpoptOptimizer (class in pypesto.optimize)
is_least_squares() (pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.IpoptOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.PyswarmOptimizer method)
(pypesto.optimize.ScipyOptimizer method)
Iterable (in module pypesto.problem)
L
latin_hypercube() (in module pypesto.startpoint)
lb() (pypesto.problem.Problem property)
legend (pypesto.visualize.ReferencePoint attribute)
List (in module pypesto.problem)
log() (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)
McmcPtResult (class in pypesto.sample)
MemoryHistory (class in pypesto.objective)
message (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
MetropolisSampler (class in pypesto.sample)
minimize() (in module pypesto.optimize)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.IpoptOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.PyswarmOptimizer method)
(pypesto.optimize.ScipyOptimizer method)
MODEL_BASE_DIR (pypesto.petab.PetabImporter attribute)
module
pypesto.engine
pypesto.logging
pypesto.objective
pypesto.optimize
pypesto.petab
pypesto.problem
pypesto.profile
pypesto.result
pypesto.sample
pypesto.startpoint
pypesto.store
pypesto.visualize
MultiProcessEngine (class in pypesto.engine)
MultiThreadEngine (class in pypesto.engine)
N
n_fval (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_fval() (pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_grad (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_grad() (pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_hess (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_hess() (pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_res (pypesto.optimize.OptimizerResult attribute)
n_res() (pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
n_sres (pypesto.optimize.OptimizerResult attribute)
n_sres() (pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
neg_log_density() (pypesto.objective.NegLogParameterPriors method)
NegLogParameterPriors (class in pypesto.objective)
NegLogPriors (class in pypesto.objective)
(class in pypesto.problem)
normalize() (pypesto.problem.Problem method)
O
Objective (class in pypesto.objective)
ObjectiveBase (class in pypesto.objective)
(class in pypesto.problem)
OptimizationResultHDF5Reader (class in pypesto.store)
OptimizationResultHDF5Writer (class in pypesto.store)
optimize_result (pypesto.result.Result attribute)
OptimizeOptions (class in pypesto.optimize)
Optimizer (class in pypesto.optimize)
optimizer_history() (in module pypesto.visualize)
optimizer_history_lowlevel() (in module pypesto.visualize)
OptimizeResult (class in pypesto.result)
OptimizerHistory (class in pypesto.objective)
OptimizerResult (class in pypesto.optimize)
output_to_tuple() (pypesto.objective.ObjectiveBase static method)
(pypesto.problem.ObjectiveBase static method)
P
par_arr_to_dct() (pypesto.objective.AmiciObjective method)
ParallelTemperingSampler (class in pypesto.sample)
parameter_profile() (in module pypesto.profile)
parameters() (in module pypesto.visualize)
parameters_lowlevel() (in module pypesto.visualize)
PetabImporter (class in pypesto.petab)
pre_post_processor (pypesto.objective.ObjectiveBase attribute)
(pypesto.problem.ObjectiveBase attribute)
print_parameter_summary() (pypesto.problem.Problem method)
Problem (class in pypesto.problem)
problem (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.Result attribute)
ProfileOptions (class in pypesto.profile)
ProfileResult (class in pypesto.result)
ProfilerResult (class in pypesto.profile)
profiles() (in module pypesto.visualize)
profiles_lowlevel() (in module pypesto.visualize)
Pymc3Sampler (class in pypesto.sample)
pypesto.engine
module
pypesto.logging
module
pypesto.objective
module
pypesto.optimize
module
pypesto.petab
module
pypesto.problem
module
pypesto.profile
module
pypesto.result
module
pypesto.sample
module
pypesto.startpoint
module
pypesto.store
module
pypesto.visualize
module
PyswarmOptimizer (class in pypesto.optimize)
R
ratio_path (pypesto.profile.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)
ReferencePoint (class in pypesto.visualize)
res (pypesto.optimize.OptimizerResult attribute)
res_min (pypesto.objective.OptimizerHistory attribute)
res_to_chi2() (in module pypesto.objective)
reset_steadystate_guesses() (pypesto.objective.AmiciObjective method)
Result (class in pypesto.result)
S
sample() (in module pypesto.sample)
(pypesto.sample.MetropolisSampler method)
(pypesto.sample.ParallelTemperingSampler method)
(pypesto.sample.Pymc3Sampler method)
(pypesto.sample.Sampler method)
sample_result (pypesto.result.Result attribute)
Sampler (class in pypesto.sample)
SampleResult (class in pypesto.result)
sampling_1d_marginals() (in module pypesto.visualize)
sampling_fval_trace() (in module pypesto.visualize)
sampling_parameters_trace() (in module pypesto.visualize)
sampling_scatter() (in module pypesto.visualize)
ScipyOptimizer (class in pypesto.optimize)
Sequence (in module pypesto.result)
set_last_sample() (pypesto.sample.InternalSampler method)
(pypesto.sample.MetropolisSampler method)
set_profiler_result() (pypesto.result.ProfileResult method)
SingleCoreEngine (class in pypesto.engine)
sort() (pypesto.result.OptimizeResult method)
sres (pypesto.optimize.OptimizerResult attribute)
sres_min (pypesto.objective.OptimizerHistory attribute)
sres_to_schi2() (in module pypesto.objective)
start_time() (pypesto.objective.History property)
(pypesto.objective.HistoryBase property)
storage_filename (pypesto.store.OptimizationResultHDF5Reader attribute)
(pypesto.store.OptimizationResultHDF5Writer attribute)
(pypesto.store.ProblemHDF5Reader attribute)
(pypesto.store.ProblemHDF5Writer attribute)
store_steadystate_guess() (pypesto.objective.AmiciObjective method)
SupportsFloat (class in pypesto.problem)
SupportsFloatIterableOrValue (in module pypesto.problem)
SupportsInt (class in pypesto.problem)
SupportsIntIterableOrValue (in module pypesto.problem)
swap_samples() (pypesto.sample.ParallelTemperingSampler method)
T
Task (class in pypesto.engine)
time (pypesto.optimize.OptimizerResult attribute)
time_path (pypesto.profile.ProfilerResult attribute)
time_total (pypesto.profile.ProfilerResult attribute)
translate_options() (pypesto.sample.Pymc3Sampler class method)
(pypesto.sample.Sampler class method)
U
ub() (pypesto.problem.Problem property)
unfix_parameters() (pypesto.problem.Problem method)
uniform() (in module pypesto.startpoint)
update() (pypesto.objective.CsvHistory method)
(pypesto.objective.Hdf5History method)
(pypesto.objective.History method)
(pypesto.objective.HistoryBase method)
(pypesto.objective.MemoryHistory method)
(pypesto.objective.OptimizerHistory method)
update_from_problem() (pypesto.objective.ObjectiveBase method)
(pypesto.problem.ObjectiveBase method)
update_to_full() (pypesto.optimize.OptimizerResult method)
W
waterfall() (in module pypesto.visualize)
waterfall_lowlevel() (in module pypesto.visualize)
write() (pypesto.store.OptimizationResultHDF5Writer method)
(pypesto.store.ProblemHDF5Writer method)
X
x (pypesto.optimize.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
x0 (pypesto.optimize.OptimizerResult attribute)
x_free_indices() (pypesto.problem.Problem property)
x_guesses() (pypesto.problem.Problem property)
x_path (pypesto.profile.ProfilerResult attribute)
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