pyPESTO
v0.0.11
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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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_
__call__() (pypesto.objective.Objective method)
__init__() (pypesto.engine.Engine method)
(pypesto.engine.MultiProcessEngine method)
(pypesto.engine.OptimizerTask method)
(pypesto.engine.SingleCoreEngine method)
(pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
(pypesto.objective.Objective method)
(pypesto.objective.ObjectiveOptions method)
(pypesto.objective.PetabImporter method)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.GlobalOptimizer method)
(pypesto.optimize.OptimizeOptions method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.OptimizerResult method)
(pypesto.optimize.ScipyOptimizer method)
(pypesto.problem.Problem 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.visualize.ReferencePoint method)
A
add_profile() (pypesto.result.ProfileResult method)
aggregate_fun() (pypesto.objective.AggregatedObjective method)
aggregate_fun_sensi_orders() (pypesto.objective.AggregatedObjective method)
aggregate_grad() (pypesto.objective.AggregatedObjective method)
aggregate_hess() (pypesto.objective.AggregatedObjective method)
aggregate_hessp() (pypesto.objective.AggregatedObjective method)
aggregate_res() (pypesto.objective.AggregatedObjective method)
aggregate_res_sensi_orders() (pypesto.objective.AggregatedObjective method)
aggregate_sres() (pypesto.objective.AggregatedObjective method)
AggregatedObjective (class in pypesto.objective)
AmiciObjective (class in pypesto.objective)
append() (pypesto.result.OptimizeResult method)
append_profile_point() (pypesto.profile.ProfilerResult method)
apply_steadystate_guess() (pypesto.objective.AmiciObjective method)
as_dataframe() (pypesto.result.OptimizeResult method)
as_list() (pypesto.result.OptimizeResult method)
assert_instance() (pypesto.objective.ObjectiveOptions 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)
C
check_grad() (pypesto.objective.Objective method)
check_sensi_orders() (pypesto.objective.Objective method)
color (pypesto.visualize.ReferencePoint attribute)
compile_model() (pypesto.objective.PetabImporter method)
create_edatas() (pypesto.objective.PetabImporter method)
create_instance() (pypesto.profile.ProfileOptions static method)
create_model() (pypesto.objective.PetabImporter method)
create_new_profile() (pypesto.result.ProfileResult method)
create_new_profile_list() (pypesto.result.ProfileResult method)
create_objective() (pypesto.objective.PetabImporter method)
create_problem() (pypesto.objective.PetabImporter method)
create_references() (in module pypesto.visualize)
create_solver() (pypesto.objective.PetabImporter method)
D
dim (pypesto.problem.Problem attribute)
DlibOptimizer (class in pypesto.optimize)
E
Engine (class in pypesto.engine)
execute() (pypesto.engine.Engine method)
(pypesto.engine.MultiProcessEngine method)
(pypesto.engine.OptimizerTask method)
(pypesto.engine.SingleCoreEngine method)
exitflag (pypesto.optimize.OptimizerResult attribute)
exitflag_path (pypesto.profile.ProfilerResult attribute)
F
finalize_history() (pypesto.objective.Objective method)
fix_parameters() (pypesto.problem.Problem method)
flip_profile() (pypesto.profile.ProfilerResult method)
from_folder() (pypesto.objective.PetabImporter static method)
from_yaml() (pypesto.objective.PetabImporter static method)
fval (pypesto.optimize.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
fval_path (pypesto.profile.ProfilerResult attribute)
G
get_bound_fun() (pypesto.objective.AmiciObjective method)
get_bound_res() (pypesto.objective.AmiciObjective method)
get_current_profile() (pypesto.result.ProfileResult method)
get_default_options() (pypesto.optimize.DlibOptimizer static method)
(pypesto.optimize.Optimizer static method)
(pypesto.optimize.ScipyOptimizer static method)
get_error_output() (pypesto.objective.AmiciObjective 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.Objective method)
get_grad() (pypesto.objective.Objective method)
get_hess() (pypesto.objective.Objective method)
get_reduced_matrix() (pypesto.problem.Problem method)
get_reduced_vector() (pypesto.problem.Problem method)
get_res() (pypesto.objective.Objective method)
get_sres() (pypesto.objective.Objective method)
GlobalOptimizer (class in pypesto.optimize)
gradnorm_path (pypesto.profile.ProfilerResult attribute)
H
has_fun (pypesto.objective.Objective attribute)
has_grad (pypesto.objective.Objective attribute)
has_hess (pypesto.objective.Objective attribute)
has_hessp (pypesto.objective.Objective attribute)
has_res (pypesto.objective.Objective attribute)
has_sres (pypesto.objective.Objective attribute)
history (pypesto.objective.Objective attribute)
I
is_least_squares() (pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.GlobalOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.ScipyOptimizer method)
L
latin_hypercube() (in module pypesto.startpoint)
legend (pypesto.visualize.ReferencePoint attribute)
M
message (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
minimize() (in module pypesto.optimize)
(pypesto.optimize.DlibOptimizer method)
(pypesto.optimize.GlobalOptimizer method)
(pypesto.optimize.Optimizer method)
(pypesto.optimize.ScipyOptimizer method)
MODEL_BASE_DIR (pypesto.objective.PetabImporter attribute)
MultiProcessEngine (class in pypesto.engine)
N
n_fval (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_grad (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_hess (pypesto.optimize.OptimizerResult attribute)
(pypesto.profile.ProfilerResult attribute)
n_procs (pypesto.engine.MultiProcessEngine attribute)
normalize_input() (pypesto.problem.Problem method)
O
Objective (class in pypesto.objective)
ObjectiveOptions (class in pypesto.objective)
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)
OptimizerResult (class in pypesto.optimize)
OptimizerTask (class in pypesto.engine)
output_to_dict() (pypesto.objective.Objective static method)
output_to_tuple() (pypesto.objective.Objective static method)
P
par_arr_to_dct() (pypesto.objective.AmiciObjective method)
parameter_profile() (in module pypesto.profile)
parameters() (in module pypesto.visualize)
parameters_lowlevel() (in module pypesto.visualize)
PetabImporter (class in pypesto.objective)
postprocess (pypesto.objective.Objective attribute)
preprocess (pypesto.objective.Objective attribute)
print_parameter_summary() (pypesto.problem.Problem method)
Problem (class in pypesto.problem)
problem (pypesto.result.Result attribute)
process_offset_y() (in module pypesto.visualize)
process_result_list() (in module pypesto.visualize)
process_y_limits() (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)
pypesto.engine (module)
pypesto.objective (module)
pypesto.optimize (module)
pypesto.problem (module)
pypesto.profile (module)
pypesto.result (module)
pypesto.sample (module)
pypesto.startpoint (module)
pypesto.visualize (module)
R
ratio_path (pypesto.profile.ProfilerResult attribute)
rdatas_to_measurement_df() (pypesto.objective.PetabImporter method)
rebind_fun() (pypesto.objective.AmiciObjective method)
rebind_res() (pypesto.objective.AmiciObjective method)
ReferencePoint (class in pypesto.visualize)
res_to_chi2() (in module pypesto.objective)
reset() (pypesto.objective.AmiciObjective method)
(pypesto.objective.Objective method)
reset_history() (pypesto.objective.Objective method)
reset_steadystate_guesses() (pypesto.objective.AggregatedObjective method)
(pypesto.objective.AmiciObjective method)
Result (class in pypesto.result)
S
sample_result (pypesto.result.Result attribute)
SampleResult (class in pypesto.result)
ScipyOptimizer (class in pypesto.optimize)
sensitivity_orders (pypesto.objective.Objective attribute)
SingleCoreEngine (class in pypesto.engine)
sort() (pypesto.result.OptimizeResult method)
sres_to_schi2() (in module pypesto.objective)
store_steadystate_guess() (pypesto.objective.AmiciObjective method)
T
time_path (pypesto.profile.ProfilerResult attribute)
time_total (pypesto.profile.ProfilerResult attribute)
U
unfix_parameters() (pypesto.problem.Problem method)
uniform() (in module pypesto.startpoint)
update_from_problem() (pypesto.objective.Objective method)
W
waterfall() (in module pypesto.visualize)
waterfall_lowlevel() (in module pypesto.visualize)
X
x (pypesto.optimize.OptimizerResult attribute)
(pypesto.visualize.ReferencePoint attribute)
x_free_indices (pypesto.problem.Problem attribute)
x_path (pypesto.profile.ProfilerResult attribute)
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