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stan code for estimating eta and rho hyperparameters of the squared exponential kernel within a Gaussian Process.
// Predict from Gaussian Process
// estimate sigma_sq and rho_sq
// All data parameters must be passed as a list to the Stan call
// Based on original file from
data {
int<lower=1> N1;
vector[N1] x1;
vector[N1] y1;
int<lower=1> N2;
vector[N2] x2;
real sigma_sq;
transformed data {
int<lower=1> N;
vector[N1+N2] x;
vector[N1+N2] mu;
N <- N1 + N2;
for (n in 1:N1) x[n] <- x1[n];
for (n in 1:N2) x[N1 + n] <- x2[n];
for (i in 1:N) mu[i] <- 0;
parameters {
vector[N2] y2;
real<lower=0> rho_sq;
real<lower=0> eta_sq;
transformed parameters {
model {
vector[N] y;
matrix[N, N] Sigma;
// off-diagonal elements
for (i in 1:(N-1)){
for (j in (i+1):N){
//// Squared Exponential (RBF) Kerenl
Sigma[i,j] <- eta_sq * exp(-rho_sq * pow(x[i] - x[j],2));
Sigma[j,i] <- Sigma[i,j];
// diagonal elements
for (k in 1:N){
Sigma[k,k] <- 1 + sigma_sq; // + jitter
rho_sq ~ cauchy(0,5);
eta_sq ~ cauchy(0,5);
for (n in 1:N1) y[n] <- y1[n];
for (n in 1:N2) y[N1 + n] <- y2[n];
y ~ multi_normal(mu,Sigma);
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