From dbab7da68e6aa3861982a51e892dde60d7ec0b1b Mon Sep 17 00:00:00 2001
From: Niels Dunnewind <niels@nielsdunnewind.nl>
Date: Fri, 18 Oct 2024 22:25:10 +0200
Subject: [PATCH] Implement baseline risk meta-regression for other models

---
 inst/stan/binomial_1par.stan       | 1 +
 inst/stan/binomial_2par.stan       | 5 +++++
 inst/stan/normal.stan              | 5 +++++
 inst/stan/ordered_multinomial.stan | 5 +++++
 inst/stan/poisson.stan             | 5 +++++
 5 files changed, 21 insertions(+)

diff --git a/inst/stan/binomial_1par.stan b/inst/stan/binomial_1par.stan
index a0ec7dbe..79e8ed20 100644
--- a/inst/stan/binomial_1par.stan
+++ b/inst/stan/binomial_1par.stan
@@ -34,6 +34,7 @@ transformed parameters {
       X_agd_arm * beta_tilde + offset_agd_arm :
       X_agd_arm * beta_tilde;
 
+    // Baseline risk meta-regression
     if (brmr_n_col > 0) {
       eta_agd_arm_noRE += (X_agd_arm[,1:totns] * mu - xbar_mu - 1) .* (X_agd_arm[,brmr_col] * beta_tilde[brmr_col]);
     }
diff --git a/inst/stan/binomial_2par.stan b/inst/stan/binomial_2par.stan
index 76cdb550..e541406c 100644
--- a/inst/stan/binomial_2par.stan
+++ b/inst/stan/binomial_2par.stan
@@ -37,6 +37,11 @@ transformed parameters {
       X_agd_arm * beta_tilde + offset_agd_arm :
       X_agd_arm * beta_tilde;
 
+    // Baseline risk meta-regression
+    if (brmr_n_col > 0) {
+      eta_agd_arm_noRE += (X_agd_arm[,1:totns] * mu - xbar_mu - 1) .* (X_agd_arm[,brmr_col] * beta_tilde[brmr_col]);
+    }
+
     if (nint_max > 1) { // -- If integration points are used --
       if (RE) {
 
diff --git a/inst/stan/normal.stan b/inst/stan/normal.stan
index 2b9bcd94..187dc3d8 100644
--- a/inst/stan/normal.stan
+++ b/inst/stan/normal.stan
@@ -39,6 +39,11 @@ transformed parameters {
       X_agd_arm * beta_tilde + offset_agd_arm :
       X_agd_arm * beta_tilde;
 
+    // Baseline risk meta-regression
+    if (brmr_n_col > 0) {
+      eta_agd_arm_noRE += (X_agd_arm[,1:totns] * mu - xbar_mu - 1) .* (X_agd_arm[,brmr_col] * beta_tilde[brmr_col]);
+    }
+
     if (nint_max > 1) { // -- If integration points are used --
       if (RE) {
 
diff --git a/inst/stan/ordered_multinomial.stan b/inst/stan/ordered_multinomial.stan
index 7bf77d2b..13e30793 100644
--- a/inst/stan/ordered_multinomial.stan
+++ b/inst/stan/ordered_multinomial.stan
@@ -87,6 +87,11 @@ transformed parameters {
           X_agd_arm * beta_tilde + offset_agd_arm :
           X_agd_arm * beta_tilde;
 
+    // Baseline risk meta-regression
+    if (brmr_n_col > 0) {
+      eta_agd_arm_noRE += (X_agd_arm[,1:totns] * mu - xbar_mu - 1) .* (X_agd_arm[,brmr_col] * beta_tilde[brmr_col]);
+    }
+
     if (nint_max > 1) { // -- If integration points are used --
 
       if (RE) {
diff --git a/inst/stan/poisson.stan b/inst/stan/poisson.stan
index 05dda8f9..02b39c7c 100644
--- a/inst/stan/poisson.stan
+++ b/inst/stan/poisson.stan
@@ -34,6 +34,11 @@ transformed parameters {
       X_agd_arm * beta_tilde + offset_agd_arm :
       X_agd_arm * beta_tilde;
 
+    // Baseline risk meta-regression
+    if (brmr_n_col > 0) {
+      eta_agd_arm_noRE += (X_agd_arm[,1:totns] * mu - xbar_mu - 1) .* (X_agd_arm[,brmr_col] * beta_tilde[brmr_col]);
+    }
+
     if (nint_max > 1) { // -- If integration points are used --
       if (RE) {