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stan_code_insertion.py
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#!/usr/bin/env python
# coding: utf-8
import numpy as np
import pandas as pd
import re
# 離散変数
def insert_disc_to_stan_file(template_stan_text,
x_disc
):
output_stan_text = template_stan_text
output_stan_text = _insert_disc_text_to_data_section(
output_stan_text, x_disc)
output_stan_text = _insert_disc_text_to_parameters_section(
output_stan_text, x_disc)
output_stan_text = _insert_disc_text_to_model_section_prior(
output_stan_text, x_disc)
output_stan_text = _insert_disc_text_to_model_section_likelihood(
output_stan_text, x_disc)
output_stan_text = _insert_disc_text_to_generated_quantities_section(
output_stan_text, x_disc)
return output_stan_text
def _insert_disc_text_to_data_section(template_stan_text, x_disc):
output_stan_text = template_stan_text
list_text = []
for var_index in x_disc.index:
list_text.append(' int<lower=1> X_disc_{}[N];'.format(var_index))
list_text.append(' int<lower=1> n_cat_{};'.format(var_index))
list_text.append(' vector<lower=0>[n_cat_{}] alpha_disc_{};'.format(var_index, var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// discrete data start //\s*// discrete data end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_disc_text_to_parameters_section(template_stan_text, x_disc):
output_stan_text = template_stan_text
list_text = []
for var_index in x_disc.index:
list_text.append(' simplex[n_cat_{}] phi_X_disc_{}[K];'.format(var_index, var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// discrete parameters start //\s*// discrete parameters end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_disc_text_to_model_section_prior(template_stan_text, x_disc):
output_stan_text = template_stan_text
list_text = []
for var_index in x_disc.index:
list_text.append(' phi_X_disc_{}[k] ~ dirichlet(alpha_disc_{});'.format(var_index, var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// discrete model prior start //\s*// discrete model prior end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_disc_text_to_model_section_likelihood(template_stan_text, x_disc):
output_stan_text = template_stan_text
list_text = []
for var_index in x_disc.index:
list_text.append(' eta[k] += categorical_lpmf(X_disc_{}[n] | phi_X_disc_{}[k]);'.format(var_index, var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// discrete model likelihood start //\s*// discrete model likelihood end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_disc_text_to_generated_quantities_section(template_stan_text, x_disc):
output_stan_text = template_stan_text
list_text = []
for var_index in x_disc.index:
list_text.append(' eta += categorical_lpmf(X_disc_{}[n] | phi_X_disc_{}[k]);'.format(var_index, var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// discrete generated quantities start //\s*// discrete generated quantities end //',
additional_text, output_stan_text)
return output_stan_text
def insert_zero_poi_to_stan_file(template_stan_text,
x_zero_poi
):
output_stan_text = template_stan_text
output_stan_text = _insert_zero_poi_text_to_data_section(
output_stan_text, x_zero_poi)
output_stan_text = _insert_zero_poi_text_to_parameters_section(
output_stan_text, x_zero_poi)
output_stan_text = _insert_zero_poi_text_to_model_section_prior(
output_stan_text, x_zero_poi)
output_stan_text = _insert_zero_poi_text_to_model_section_likelihood(
output_stan_text, x_zero_poi)
output_stan_text = _insert_zero_poi_text_to_generated_quantities_section(
output_stan_text, x_zero_poi)
return output_stan_text
def _insert_zero_poi_text_to_data_section(template_stan_text, x_zero_poi):
output_stan_text = template_stan_text
list_text = []
for var_index in x_zero_poi.index:
list_text.append(' int<lower=0> X_zero_poi_{}[N];'.format(var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// zero poi data start //\s*// zero poi data end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_zero_poi_text_to_parameters_section(template_stan_text, x_zero_poi):
output_stan_text = template_stan_text
list_text = []
for var_index in x_zero_poi.index:
list_text.append(' real<lower=0> lambda_X_zero_poi_{}[K];'.format(var_index))
list_text.append(' simplex[2] phi_X_zero_poi_{}[K];'.format(var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// zero poi parameters start //\s*// zero poi parameters end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_zero_poi_text_to_model_section_prior(template_stan_text, x_zero_poi):
output_stan_text = template_stan_text
list_text = []
for var_index in x_zero_poi.index:
list_text.append(' phi_X_zero_poi_{}[k] ~ dirichlet(alpha_bern);'.format(var_index))
list_text.append(' lambda_X_zero_poi_{}[k] ~ cauchy(0, 5);'.format(var_index))
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// zero poi model prior start //\s*// zero poi model prior end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_zero_poi_text_to_model_section_likelihood(template_stan_text, x_zero_poi):
output_stan_text = template_stan_text
list_text = []
for var_index in x_zero_poi.index:
list_text.append(' if (X_zero_poi_{}[n]==0)'.format(var_index) + '{')
list_text.append(' eta[k] += log_sum_exp(')
list_text.append(' bernoulli_lpmf(0 | phi_X_zero_poi_{}[k][2]),'.format(var_index))
list_text.append(' bernoulli_lpmf(1 | phi_X_zero_poi_{}[k][2]) + poisson_lpmf(0 | lambda_X_zero_poi_{})'.format(var_index, var_index))
list_text.append(' );')
list_text.append(' } else {')
list_text.append(' eta[k] += bernoulli_lpmf(1 | phi_X_zero_poi_{}[k][2]) + poisson_lpmf(X_zero_poi_{}[n] | lambda_X_zero_poi_{}[k]);'.format(var_index, var_index, var_index))
list_text.append(' }')
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// zero poi model likelihood start //\s*// zero poi model likelihood end //',
additional_text, output_stan_text)
return output_stan_text
def _insert_zero_poi_text_to_generated_quantities_section(template_stan_text, x_zero_poi):
output_stan_text = template_stan_text
list_text = []
for var_index in x_zero_poi.index:
list_text.append(' if (X_zero_poi_{}[n]==0)'.format(var_index) + '{')
list_text.append(' eta += log_sum_exp(')
list_text.append(' bernoulli_lpmf(0 | phi_X_zero_poi_{}[k][2]),'.format(var_index))
list_text.append(' bernoulli_lpmf(1 | phi_X_zero_poi_{}[k][2]) + poisson_lpmf(0 | lambda_X_zero_poi_{})'.format(var_index, var_index))
list_text.append(' );')
list_text.append(' } else {')
list_text.append(' eta += bernoulli_lpmf(1 | phi_X_zero_poi_{}[k][2]) + poisson_lpmf(X_zero_poi_{}[n] | lambda_X_zero_poi_{}[k]);'.format(var_index, var_index, var_index))
list_text.append(' }')
additional_text = "\n".join(list_text)
output_stan_text = re.sub(r'// zero poi generated quantities start //\s*// zero poi generated quantities end //',
additional_text, output_stan_text)
return output_stan_text