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Functions | |
| std::string | format_simulator_input (const Epsilon &epsilon, const Parameter ¶meter) |
| bool | parse_simulator_output (const std::string &simulator_output) |
| Parameter | parse_prior_sampler_output (const std::string &prior_sampler_output) |
| std::string | format_perturber_input (int t, const Parameter &source_parameter) |
| Parameter | parse_perturber_output (const std::string &perturber_output) |
| std::string | format_prior_pdf_input (const Parameter ¶meter) |
| double | parse_prior_pdf_output (const std::string &prior_pdf_output) |
| std::string | format_perturbation_pdf_input (int t, const Parameter &perturbed_parameter, const std::vector< Parameter > ¶meter_population) |
| std::vector< double > | parse_perturbation_pdf_output (const std::string &perturbation_pdf_output) |
| std::vector< Parameter > | parse_generator_output (const std::string &generator_output) |
| Parameter | sample_from_prior (const Command &prior_sampler) |
| Parameter | perturb_parameter (const Command &perturber, int t, Parameter source_parameter) |
| double | get_prior_pdf (const Command &prior_pdf, Parameter parameter) |
| std::vector< double > | get_perturbation_pdf (const Command &perturbation_pdf, int t, const Parameter &perturbed_parameter, const std::vector< Parameter > ¶meter_population) |
Detailed Description
This file defines functions to format input to user executables and parse output from user executables according to the Pakman user executable API.
In addition, this file contains convenience functions that combine formatting and parsing.
Definition in file protocols.h.
Function Documentation
◆ format_perturbation_pdf_input()
| std::string format_perturbation_pdf_input | ( | int | t, |
| const Parameter & | perturbed_parameter, | ||
| const std::vector< Parameter > & | parameter_population | ||
| ) |
Format input to perturbation_pdf.
- Parameters
-
t current generation. perturbed_parameter perturbed parameter. parameter_population parameter population.
- Returns
- input string to perturbation_pdf.
Definition at line 182 of file protocols.cc.
◆ format_perturber_input()
| std::string format_perturber_input | ( | int | t, |
| const Parameter & | source_parameter | ||
| ) |
Format input to perturber.
- Parameters
-
t current generation. source_parameter source parameter to be perturbed.
- Returns
- input string to perturber.
Definition at line 99 of file protocols.cc.
◆ format_prior_pdf_input()
| std::string format_prior_pdf_input | ( | const Parameter & | parameter | ) |
Format input to prior_pdf.
- Parameters
-
parameter parameter to evaluate.
- Returns
- input string to prior_pdf.
Definition at line 128 of file protocols.cc.
◆ format_simulator_input()
Format input to simulator.
- Parameters
-
epsilon distance tolerance. parameter parameter to simulate.
- Returns
- input string to simulator.
Definition at line 11 of file protocols.cc.
◆ get_perturbation_pdf()
| std::vector<double> get_perturbation_pdf | ( | const Command & | perturbation_pdf, |
| int | t, | ||
| const Parameter & | perturbed_parameter, | ||
| const std::vector< Parameter > & | parameter_population | ||
| ) |
Get perturbation probability density function.
- Parameters
-
perturbation_pdf command to get perturbation pdf. t current generation. perturbed_parameter perturbed parameter. parameter_population parameter population.
- Returns
- perturbation kernel probability densities for perturbed parameter and parameter population.
Definition at line 319 of file protocols.cc.
◆ get_prior_pdf()
Get prior probability density function.
- Parameters
-
prior_pdf command to get prior pdf. parameter parameter to evaluate.
- Returns
- prior probability density of parameter.
Definition at line 311 of file protocols.cc.
◆ parse_generator_output()
| std::vector<Parameter> parse_generator_output | ( | const std::string & | generator_output | ) |
Parse output from generator.
- Parameters
-
generator_output output string from generator.
- Returns
- list of parameters to simulate.
Definition at line 253 of file protocols.cc.
◆ parse_perturbation_pdf_output()
| std::vector<double> parse_perturbation_pdf_output | ( | const std::string & | perturbation_pdf_output | ) |
Parse output from perturbation_pdf.
- Parameters
-
perturbation_pdf_output output string from perturbation_pdf.
- Returns
- perturbation kernel probability densities for perturbed parameter and parameter population.
Definition at line 202 of file protocols.cc.
◆ parse_perturber_output()
| Parameter parse_perturber_output | ( | const std::string & | perturber_output | ) |
Parse output from perturber.
- Parameters
-
perturber_output output string from perturber.
- Returns
- perturbed parameter.
Definition at line 110 of file protocols.cc.
◆ parse_prior_pdf_output()
| double parse_prior_pdf_output | ( | const std::string & | prior_pdf_output | ) |
Parse output from prior_pdf.
- Parameters
-
prior_pdf_output output string from prior_pdf.
- Returns
- prior probability density of parameter.
Definition at line 137 of file protocols.cc.
◆ parse_prior_sampler_output()
| Parameter parse_prior_sampler_output | ( | const std::string & | prior_sampler_output | ) |
Parse output from prior_sampler.
- Parameters
-
prior_sampler_output output string from prior_sampler.
- Returns
- parameter sampled from prior.
Definition at line 65 of file protocols.cc.
◆ parse_simulator_output()
| bool parse_simulator_output | ( | const std::string & | simulator_output | ) |
Parse output from simulator.
- Parameters
-
simulator_output output string from simulator.
- Returns
- whether parameter was accepted.
Definition at line 24 of file protocols.cc.
◆ perturb_parameter()
Perturb parameter.
- Parameters
-
perturber command to perturb parameter. t current generation. source_parameter source parameter to be perturbed.
- Returns
- perturbed parameter.
Definition at line 301 of file protocols.cc.
◆ sample_from_prior()
Sample from prior.
- Parameters
-
prior_sampler command to sample from prior.
- Returns
- parameter sampled from prior.
Definition at line 294 of file protocols.cc.
