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svmcmc.cpp
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// svmcmc.cpp
#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::plugins("cpp11")]]
// [[Rcpp::export]]
arma::vec sample_s(arma::vec h,
double mu, double phi, double sigma_eta, double rho,
arma::vec p, arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star,
arma::vec d,
int T);
// [[Rcpp::export]]
Rcpp::List kalman_filter(arma::vec s,
double mu, double phi, double sigma_eta, double rho,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star,
arma::vec d,
int T);
// [[Rcpp::export]]
arma::vec sim_smoother(arma::vec s,
double mu, double phi, double sigma_eta, double rho,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star,
arma::vec d,
int T);
// [[Rcpp::export]]
double loglikelihood(arma::vec s,
double mu, double phi, double sigma_eta, double rho,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star,
arma::vec d,
double mu_0, double sigma_0,
double T);
double calc_posterior(arma::vec x, double mu,
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0);
// [[Rcpp::export]]
double calc_posterior_maximize(arma::vec x, double mu,
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0);
// [[Rcpp::export]]
arma::vec deriv1(arma::vec x, double mu,
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0);
// [[Rcpp::export]]
arma::mat deriv2(arma::vec x, double mu,
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0);
// [[Rcpp::export]]
arma::vec Opt(arma::vec x, double mu,
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0);
// [[Rcpp::export]]
arma::vec aug_kalman_filter(arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, int T,
double mu, double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0,
bool call_r_opt_func);
// [[Rcpp::export]]
Rcpp::List svmcmc(arma::vec Y, // 日次リターンを格納したベクトル
bool call_r_opt_func // Rの最大化関数を呼び出すか否か
){
/*---設定---*/
int nsim, nburn;
nsim = 5000; // サンプリングの個数
nburn = 0.1 * nsim; // 稼働検査期間
/*---初期値の設定---*/
double phi, sigma_eta, mu, rho;
arma::vec h;
mu = -8.0;
phi = 0.97;
sigma_eta = 0.1;
rho = 0;
h = arma::zeros(Y.n_elem) + mu;
/*---パラメータの事前分布---*/
double a_0, b_0, n_0, S_0, mu_0, sigma_0;
arma::vec p, m, v, a, b;
mu_0 = -8.0; // mu~N(mu_0,sigma_0)
sigma_0 = 1;
a_0 = 20; // phi~Beta(a_0,b_0)
b_0 = 1.5;
n_0 = 5; // sigma_eta^2~IG(n_0/2,S_0/2)
S_0 = 0.05;
// s
p = {0.00609, 0.04775, 0.13057, 0.20674, 0.22715,
0.18842, 0.12047, 0.05591, 0.01575, 0.00115};
m = {1.92677, 1.34744, 0.73504, 0.02266, -0.85173,
-1.97278, -3.46788, -5.55246, -8.68384, -14.65};
v = {0.11265, 0.17788, 0.26768, 0.40611, 0.62699,
0.98583, 1.57469, 2.54498, 4.16591, 7.33342};
v = sqrt(v); // 上のベクトルはv^2なのでsqrtを取る.
//v = {0.3356, 0.4218, 0.5174, 0.6373, 0.7918,
// 0.9929, 1.2549, 1.5953, 2.0411, 2.7080}
a = {1.01418, 1.02248, 1.03403, 1.05207, 1.08153,
1.13114, 1.21754, 1.37454, 1.68327, 2.50097};
b = {0.5071, 0.51124, 0.51701, 0.52604, 0.54076,
0.56557, 0.60877, 0.68728, 0.84163, 1.25049};
/*---変数の定義---*/
int T;
double dcst;
arma::vec Y_star, d, s, theta;
arma::vec mu_result, phi_result, sigma_eta_result, rho_result;
Rcpp::NumericVector Y_, d_;
Rcpp::List result;
T = Y.n_elem; // 全時間長
dcst = 0.0001; // 十分に小な定数
Y_ = Rcpp::wrap(Y); // YをRcppのNumericVector化
d_ = Rcpp::ifelse(Y_ > 0, 1.0, -1.0); // y_t>0なら1, y_t<0なら-1を要素にもつ長さTのベクトル
d = Rcpp::as<arma::vec>(d_); // d_をarma::vec化
Y_star = log(Y%Y + dcst); // log(y^2)
mu_result = arma::zeros(nsim);
phi_result = arma::zeros(nsim);
sigma_eta_result = arma::zeros(nsim);
rho_result = arma::zeros(nsim);
/*---イテレーション開始---*/
int k;
for(k = -nburn; k < nsim; k++){
/*---多項分布からのsのサンプリング---*/
s = sample_s(h,
mu, phi, sigma_eta, rho,
p, m, v, a, b,
Y_star, d, T);
/*---シミュレーションスムーザによるh_tのサンプリング---*/
h = sim_smoother(s,
mu, phi, sigma_eta, rho,
m, v, a, b,
Y_star, d, T);
/*---拡大カルマンフィルタによるvartheta, muのサンプリング---*/
theta = aug_kalman_filter(s,
m, v, a, b,
Y_star, d, T,
mu, mu_0, sigma_0, a_0, b_0, n_0, S_0, call_r_opt_func);
mu = theta[0];
phi = theta[1];
sigma_eta = theta[2];
rho = theta[3];
/*---保存---*/
if(0 <= k){
mu_result[k] = mu;
phi_result[k] = phi;
sigma_eta_result[k] = sigma_eta;
rho_result[k] = rho;
}
}
result = Rcpp::List::create(mu_result, phi_result, sigma_eta_result, rho_result, Y_star, h);
return(result);
}
arma::vec sample_s(arma::vec h, // h_t, t=1,...,T
double mu, double phi, double sigma_eta, double rho, // theta={mu, phi, sigma_eta, rho}
arma::vec p, arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, int T){
int t;
arma::vec eps_star, eta;
arma::vec result = arma::zeros(T);
for(t = 0; t < T; t++){
/*---事後分布を計算---*/
eps_star = arma::pow((Y_star[t]-h[t]-m), 2) / (2*v%v); // 指数部分の中身1 (epsilon_starの尤度)
if(t!=T-1){ // 指数部分の中身2 (etaの尤度)
eta = arma::pow((h[t+1]-mu)-phi*(h[t]-mu)-d[t]*rho*sigma_eta*arma::exp(m/2)%(a+b%(Y_star[t]-h[t]-m)), 2)
/ (2*sigma_eta*sigma_eta*(1-rho*rho));
}else{
eta = arma::pow(-phi*(h[t]-mu)-d[t]*rho*sigma_eta*arma::exp(m/2)%(a+b%(Y_star[t]-h[t]-m)), 2)
/ (2*sigma_eta*sigma_eta*(1-rho*rho));
}
arma::vec pi = p % (1/v) % (arma::exp(- (eps_star - arma::min(eps_star))
- (eta - arma::min(eta))));
pi = pi / arma::sum(pi);
Rcpp::NumericVector j = {0,1,2,3,4,5,6,7,8,9};
double s_t = Rcpp::sample(j, 1, true, Rcpp::wrap(pi))[0];
result[t] = s_t;
}
return(result);
}
Rcpp::List kalman_filter(arma::vec s, // s_t, t=1,...,T
double mu, double phi, double sigma_eta, double rho, // theta={mu, phi, sigma_eta, rho}
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, int T){
/*---カルマンフィルタの実行---*/
int t;
double h = mu;
double P = sigma_eta*sigma_eta / (1-phi*phi);
double h_star = 0;
double A_star = -1;
arma::vec e, D, K, L, f, F;
arma::mat J;
e = arma::zeros(T);
D = arma::zeros(T);
K = arma::zeros(T);
L = arma::zeros(T);
J = arma::zeros(T,2);
f = arma::zeros(T);
F = arma::zeros(T);
for(t = 0; t < T; t++){
arma::vec H = {d[t]*rho*sigma_eta*b[s[t]]*v[s[t]]*exp(m[s[t]]/2), sigma_eta*sqrt(1-rho*rho)};
arma::vec G = {v[s[t]], 0};
arma::vec W = {0, 1-phi, d[t]*rho*sigma_eta*a[s[t]]*exp(m[s[t]]/2)};
arma::vec beta = {1, mu, 1};
arma::vec B = {0, 1, 0};
e[t] = Y_star[t] - m[s[t]] - h;
D[t] = P + arma::dot(G,G);
K[t] = (phi*P + arma::dot(H,G)) / D[t];
L[t] = phi - K[t];
J(t, arma::span(0,1)) = (H - K[t]*G).t();
f[t] = Y_star[t] - m[s[t]] - h_star;
F[t] = - A_star;
h = arma::dot(W,beta) + phi*h + K[t]*e[t];
P = phi*P*L[t] + arma::dot(H, J(t,arma::span(0,1)).t());
h_star = W[2] + phi*h_star + K[t]*f[t];
A_star = phi - 1 + phi*A_star + K[t]*F[t];
}
Rcpp::List result = Rcpp::List::create(e, D, J, L, f, F);
return(result);
}
arma::vec sim_smoother(arma::vec s, // s_t, t=1,...,T
double mu, double phi, double sigma_eta, double rho, // theta={mu, phi, sigma_eta, rho}
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, int T){
/*---カルマンフィルタの実行---*/
int t;
Rcpp::List kalman_list;
kalman_list = kalman_filter(s, mu, phi, sigma_eta, rho, m, v, a, b, Y_star, d, T);
arma::vec e = kalman_list[0];
arma::vec D = kalman_list[1];
arma::mat J = kalman_list[2];
arma::vec L = kalman_list[3];
/*---平滑化の実行---*/
double r, U, C, kappa, V;
arma::vec eta, result;
r = 0;
U = 0;
eta = arma::zeros(T);
result = arma::ones(T) * mu;
for(t = T-1; t > -1; t--){
arma::mat H = {d[t]*rho*sigma_eta*b[s[t]]*v[s[t]]*exp(m[s[t]]/2), sigma_eta*sqrt(1-rho*rho)};
arma::mat G = {v[s[t]], 0};
arma::mat mJ = J(t,arma::span(0,1));
arma::mat I = arma::eye(2,2);
arma::mat matC = H * (I - G.t()*G/D[t] - mJ.t()*mJ*U) * H.t();
C = matC(0,0);
kappa = R::rnorm(0, sqrt(C));
arma::mat matV = H * (G.t()/D[t] + mJ.t()*U*L[t]);
V = matV(0,0);
arma::mat mateta = H * (G.t()*e[t]/D[t] + mJ.t()*r) + kappa;
eta[t] = mateta(0,0);
r = e[t]/D[t] + L[t]*r - kappa*V/C;
U = 1/D[t] + L[t]*U*L[t] + V*V/C;
}
arma::mat H_0 = {0, sigma_eta/sqrt(1-phi*phi)};
arma::mat mJ_0 = H_0;
arma::mat I = arma::eye(2,2);
arma::mat matC_0 = H_0 * (I - mJ_0.t()*mJ_0*U) * H_0.t();
double C_0 = matC_0(0,0);
double kappa_0 = R::rnorm(0, sqrt(C_0));
arma::mat mateta = H_0 * mJ_0.t()*r + kappa_0;
double eta_0 = mateta(0,0);
result[0] = mu + eta_0;
for(t = 1; t < T; t++){
result[t] = mu*(1-phi)+d[t-1]*rho*sigma_eta*a[s[t-1]]*exp(m[s[t-1]]/2)+phi*result[t-1]+eta[t-1];
}
return(result);
}
double loglikelihood(arma::vec s, // s_t, t=1,...,T
double mu, double phi, double sigma_eta, double rho, // theta={mu, phi, sigma_eta, rho}
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double mu_0, double sigma_0, double T){
/*---カルマンフィルタの実行---*/
Rcpp::List kalman_list;
kalman_list = kalman_filter(s, mu, phi, sigma_eta, rho, m, v, a, b, Y_star, d, T);
arma::vec D = kalman_list[1];
arma::mat f = kalman_list[4];
arma::vec F = kalman_list[5];
/*---対数尤度の計算---*/
double C_1, mu_1;
C_1 = 1 / ( 1/sigma_0 + arma::sum(F%(1/D)%F) );
mu_1 = C_1 * ( mu_0/sigma_0 + arma::sum(F%(1/D)%f) );
double result;
result = -T*log(2*arma::datum::pi)/2 - arma::sum(log(abs(D)))/2 -
log(abs(sigma_0))/2 + log(abs(C_1))/2 -
( arma::sum(f%(1/D)%f) + mu_0*(1/sigma_0)*mu_0 - mu_1*(1/C_1)*mu_1 )/2;
return(result);
}
double calc_posterior(arma::vec x, double mu, // x={phi, sigma_eta, rho}
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0){
double phi, sigma_eta, rho;
phi = x[0];
sigma_eta = x[1];
rho = x[2];
/*---事前分布の定義---*/
double log_prior_mu, log_prior_phi, log_prior_sigma_eta;
log_prior_mu = R::dnorm(mu, mu_0, sigma_0, true);
log_prior_phi = R::dbeta(phi, a_0, b_0, true); // phi~Beta(a_0,b_0)
log_prior_sigma_eta = R::dgamma(1/(sigma_eta*sigma_eta), n_0/2, 2/S_0, true)
- 2 * log(sigma_eta*sigma_eta); // sigma_eta^2~IG(n_0/2,S_0/2)
/*---対数尤度の計算---*/
double loglike = loglikelihood(s, mu, phi, sigma_eta, rho, m, v, a, b, Y_star, d, mu_0, sigma_0, T);
/*---事後分布の計算---*/
double result = loglike + log_prior_phi + log_prior_sigma_eta + log_prior_mu;
return(result);
}
double calc_posterior_maximize(arma::vec x, double mu, // x={phi_, sigma_eta_, rho_}
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0){
double phi_, sigma_eta_, rho_, phi, sigma_eta, rho;
phi_ = x[0];
phi = (exp(phi_)-1) / (exp(phi_)+1);
sigma_eta_ = x[1];
sigma_eta = exp(sigma_eta_);
rho_ = x[2];
rho = (exp(rho_)-1) / (exp(rho_)+1);
/*---事前分布の定義---*/
double log_prior_mu, log_prior_phi, log_prior_sigma_eta;
log_prior_mu = R::dnorm(mu, mu_0, sigma_0, true);
log_prior_phi = R::dbeta(phi, a_0, b_0, true); // phi~Beta(a_0,b_0)
log_prior_sigma_eta = R::dgamma(1/(sigma_eta*sigma_eta), n_0/2, 2/S_0, true)
- 2 * log(sigma_eta*sigma_eta); // sigma_eta^2~IG(n_0/2,S_0/2)
/*---対数尤度の計算---*/
double loglike = loglikelihood(s, mu, phi, sigma_eta, rho, m, v, a, b, Y_star, d, mu_0, sigma_0, T);
/*---ヤコビアンの計算---*/
double jacobian = phi_ + sigma_eta_ + rho_ + 2*log(2)
- 2*log(exp(phi_)+1) - 2*log(exp(rho_)+1);
/*---事後分布の計算---*/
double result = loglike + log_prior_phi + log_prior_sigma_eta + log_prior_mu + jacobian;
return(result);
}
arma::vec deriv1(arma::vec x, double mu, // x={phi_, sigma_eta_, rho_}
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0){
int i;
arma::vec e = arma::zeros(3);
double epsilon = 0.001;
arma::vec result = arma::zeros(3);
for(i = 0; i < 3; i++){
e[i] = 1;
result[i] = (
calc_posterior_maximize(x+epsilon*e, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0)
- calc_posterior_maximize(x-epsilon*e, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0))
/ (2*epsilon);
e[i] = 0;
}
return(result);
}
arma::mat deriv2(arma::vec x, double mu, // x={phi, sigma_eta, rho}
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0){
int i, j;
arma::vec e_i, e_j;
e_i = arma::zeros(3);
e_j = arma::zeros(3);
double epsilon = 0.000001;
arma::mat result = arma::zeros(3,3);
for(i = 0; i < 3; i++){
for(j = 0; j < 3; j++){
e_i[i] = 1;
e_j[j] = 1;
result(i,j) = (
calc_posterior_maximize(x+epsilon*e_i+epsilon*e_j, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0)
+ calc_posterior_maximize(x-epsilon*e_i-epsilon*e_j, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0)
- calc_posterior_maximize(x-epsilon*e_i+epsilon*e_j, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0)
- calc_posterior_maximize(x+epsilon*e_i-epsilon*e_j, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0)
) / (4*epsilon*epsilon);
e_i[i] = 0;
e_j[j] = 0;
}
}
return(result);
}
arma::vec Opt(arma::vec x, double mu, // x={phi_, sigma_eta_, rho}
arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, double T,
double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0){
Rcpp::Environment stats("package:stats");
Rcpp::Function optim = stats["optim"];
Rcpp::List control = Rcpp::List::create(Rcpp::Named("fnscale") = -1.0);
Rcpp::List out = optim(Rcpp::_["par"] = x,
// Make sure this function is not exported! <- ??
Rcpp::_["fn"] = Rcpp::InternalFunction(&calc_posterior_maximize),
Rcpp::_["mu"] = mu, Rcpp::_["s"] = s, Rcpp::_["m"] = m, Rcpp::_["v"] = v, Rcpp::_["a"] = a,
Rcpp::_["b"] = b, Rcpp::_["Y_star"] = Y_star, Rcpp::_["d"] = d, Rcpp::_["T"] = T,
Rcpp::_["mu_0"] = mu_0, Rcpp::_["sigma_0"] = sigma_0, Rcpp::_["a_0"] = a_0, Rcpp::_["b_0"] = b_0,
Rcpp::_["n_0"] = n_0, Rcpp::_["S_0"] = S_0,
Rcpp::_["method"] = "Nelder-Mead",
Rcpp::_["control"] = control,
Rcpp::_["hessian"] = false);
arma::vec result = out["par"];
return(result);
}
arma::vec aug_kalman_filter(arma::vec s,
arma::vec m, arma::vec v, arma::vec a, arma::vec b,
arma::vec Y_star, arma::vec d, int T,
double mu, double mu_0, double sigma_0, double a_0, double b_0, double n_0, double S_0,
bool call_r_opt_func){
double alpha, phi, phi_, sigma_eta, sigma_eta_, rho, rho_, threshold;
arma::vec x, deriv1_vec;
bool found_max;
/*---最大化問題---*/
threshold = 0.0001; // 閾値
phi = 0.8; // 初期値
phi_ = log((1+phi)/(1-phi)); // 定義域が実数全体になるように変数変換
sigma_eta = 0.15;
sigma_eta_= log(sigma_eta);
rho = -0.3;
rho_ = log((1+rho)/(1-rho));
x = {phi_, sigma_eta_, rho_};
if(call_r_opt_func==true){
x = Opt(x, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0);
}else{
found_max = false; // 終了要件
while(found_max == false){
alpha = 0.001; // 学習率
deriv1_vec = deriv1(x, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0);
if(arma::sum(arma::abs(deriv1_vec)) < threshold){
found_max = true;
break;
}else{
x = x + alpha * deriv1_vec;
}
}
}
/*---二階微分の計算---*/
arma::mat deriv2_mat = deriv2(x, mu, s, m, v, a, b, Y_star, d, T, mu_0, sigma_0, a_0, b_0, n_0, S_0);
/*---varthetaのサンプリング---*/
arma::mat inverse_deriv2_mat = arma::inv(deriv2_mat);
arma::vec vartheta = x + inverse_deriv2_mat * Rcpp::as<arma::vec>(Rcpp::rnorm(3,0,1));
phi_ = vartheta[0];
sigma_eta_ = vartheta[1];
rho_ = vartheta[2];
phi = (exp(phi_)-1) / (exp(phi_)+1);
sigma_eta = exp(sigma_eta_);
rho = (exp(rho_)-1) / (exp(rho_)+1);
/*---muのサンプリング---*/
double C_1, mu_1;
Rcpp::List kalman_list;
kalman_list = kalman_filter(s, mu, phi, sigma_eta, rho, m, v, a, b, Y_star, d, T);
arma::vec D = kalman_list[1];
arma::vec f = kalman_list[4];
arma::vec F = kalman_list[5];
C_1 = 1 / ( 1/sigma_0 + arma::sum(F%(1/D)%F) );
mu_1 = C_1 * ( mu_0/sigma_0 + arma::sum(F%(1/D)%f) );
mu = R::rnorm(mu_1, C_1);
arma::vec result = {mu, phi, sigma_eta, rho};
return(result);
}