From ea3e8755a810d9404693d8bfa063c51f6cda2ed3 Mon Sep 17 00:00:00 2001
From: Seth Harju <130184192+sethharju@users.noreply.github.com>
Date: Tue, 12 Sep 2023 14:42:10 -0700
Subject: [PATCH] Add files via upload

---
 .../extra-variance/hat-dispersed-binomial            |  5 +++++
 .../extra-variance/hat-dispersed-binomial-finite-pop | 11 +++++++++++
 .../extra-variance/pred-dispersed-binomial           |  7 +++++++
 .../pred-dispersed-binomial-finite-pop               | 12 ++++++++++++
 4 files changed, 35 insertions(+)
 create mode 100644 model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial
 create mode 100644 model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial-finite-pop
 create mode 100644 model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial
 create mode 100644 model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial-finite-pop

diff --git a/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial
new file mode 100644
index 00000000..8885d9d2
--- /dev/null
+++ b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial
@@ -0,0 +1,5 @@
+            HAT_EPS_TILDE
+            hat.strat.p[t, k] <- LINK
+                B[j.draw[k], 1, k] + B[j.draw[k], 2, k] * x.hat[t] +
+                  site.eps[j.draw[k], k]
+                )
diff --git a/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial-finite-pop b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial-finite-pop
new file mode 100644
index 00000000..d804d624
--- /dev/null
+++ b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/hat-dispersed-binomial-finite-pop
@@ -0,0 +1,11 @@
+            HAT_EPS_TILDE
+            hat.strat.p[t, k] <- ifelse(j.draw[k] <= y.n.site[k],
+              LINK
+                  B[min(j.draw[k], y.n.site[k]), 1, k] +
+                  B[min(j.draw[k], y.n.site[k]), 2, k] * x.hat[t] +
+                  site.eps[min(j.draw[k], y.n.site[k]), k]
+                  ),
+              LINK
+                  HAT_STRAT_LIN_PRED +
+                  hat.eps.tilde[t, k]
+                  ))
diff --git a/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial
new file mode 100644
index 00000000..2d48c13a
--- /dev/null
+++ b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial
@@ -0,0 +1,7 @@
+            PRED_EPS_TILDE
+            pred.strat.p[t, k] <- LINK
+                B[j.draw[k], 1, k] +
+                  B[j.draw[k], 2, k] * x.pred[i.pred[t, k]] +
+                  X.pred[i.pred[t, k], ] %*% Beta +
+                  site.eps[j.draw[k], k]
+            )
diff --git a/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial-finite-pop b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial-finite-pop
new file mode 100644
index 00000000..0f9cf00b
--- /dev/null
+++ b/model-api/src/model-builder/code-blocks/derived-quantities/stratum-level-inference/extra-variance/pred-dispersed-binomial-finite-pop
@@ -0,0 +1,12 @@
+            PRED_EPS_TILDE
+            pred.strat.p[t, k] <- ifelse(j.draw[k] <= y.n.site[k],
+              LINK
+                  B[min(j.draw[k], y.n.site[k]), 1, k] +
+                  B[min(j.draw[k], y.n.site[k]), 2, k] * x.pred[i.pred[t, k]] +
+                  X.pred[i.pred[t, k], ] %*% Beta +
+                  site.eps[min(j.draw[k], y.n.site[k]), k]
+                  ),
+              LINK
+                  HAT_STRAT_LIN_PRED +
+                  pred.eps.tilde[t, k]
+                  ))