From 2ab48189d5b6c45232fadb91f601c966e32ff5e9 Mon Sep 17 00:00:00 2001
From: Kinh Nguyen <4459378+kklot@users.noreply.github.com>
Date: Fri, 17 Dec 2021 18:42:04 +0100
Subject: [PATCH 1/3] missing assignment logrw

(cherry picked from commit f5c01a0c448cf380ba6d3df791475b5b90fd78e0)
---
 R/likelihood.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/likelihood.R b/R/likelihood.R
index a55827c..1c9e05a 100644
--- a/R/likelihood.R
+++ b/R/likelihood.R
@@ -696,8 +696,8 @@ ldsamp <- function(theta, fp){
     else # logrw
       lpr <- dnorm(theta[1], 0.2, 1, log=TRUE)
 
-    if(fp$eppmod == "logrw")
-      bayes_lmvt(theta[2:fp$rt$n_rw], rw_prior_shape, rw_prior_rate)
+    if (fp$eppmod == "logrw")
+      lpr <- bayes_lmvt(theta[2:fp$rt$n_rw], rw_prior_shape, rw_prior_rate)
     else
       lpr <- bayes_lmvt(theta[2:nk], tau2_prior_shape, tau2_prior_rate)
 

From 984976d8ec2d5d8939176a8f942a211b1091b732 Mon Sep 17 00:00:00 2001
From: Kinh Nguyen <4459378+kklot@users.noreply.github.com>
Date: Fri, 17 Dec 2021 18:46:08 +0100
Subject: [PATCH 2/3] ldsamp fix overwriting log prior and rearrange

(cherry picked from commit a0b3c097324867e7e49b08cc31e3e3a26241540d)
---
 R/likelihood.R | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/R/likelihood.R b/R/likelihood.R
index 1c9e05a..286e7cc 100644
--- a/R/likelihood.R
+++ b/R/likelihood.R
@@ -691,16 +691,14 @@ ldsamp <- function(theta, fp){
 
     nk <- fp$numKnots
 
-    if(fp$eppmod == "rspline")  # u[1]
-      lpr <- dnorm(theta[1], 1.5, 1, log=TRUE)
-    else # logrw
-      lpr <- dnorm(theta[1], 0.2, 1, log=TRUE)
-
-    if (fp$eppmod == "logrw")
-      lpr <- bayes_lmvt(theta[2:fp$rt$n_rw], rw_prior_shape, rw_prior_rate)
-    else
-      lpr <- bayes_lmvt(theta[2:nk], tau2_prior_shape, tau2_prior_rate)
-
+    if (fp$eppmod == "rspline") { # u[1]
+      lpr <- dnorm(theta[1], 1.5, 1, log = TRUE)
+      lpr <- lpr + bayes_lmvt(theta[2:nk], tau2_prior_shape, tau2_prior_rate)
+    }
+    if (fp$eppmod == "logrw") {
+      lpr <- dnorm(theta[1], 0.2, 1, log = TRUE)
+      lpr <- lpr + bayes_lmvt(theta[2:fp$rt$n_rw], rw_prior_shape, rw_prior_rate)
+    }
 
     if(exists("r0logiotaratio", fp) && fp$r0logiotaratio)
       lpr <- lpr + dunif(theta[nk+1], r0logiotaratio.unif.prior[1], r0logiotaratio.unif.prior[2], log=TRUE)

From bf1e0bdee9207d20a1fba3da66c236d9dc4c0dc3 Mon Sep 17 00:00:00 2001
From: Kinh Nguyen <4459378+kklot@users.noreply.github.com>
Date: Fri, 17 Dec 2021 21:23:45 +0100
Subject: [PATCH 3/3] add theta[1] to lprior

---
 R/likelihood.R | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/likelihood.R b/R/likelihood.R
index 286e7cc..bf5333b 100644
--- a/R/likelihood.R
+++ b/R/likelihood.R
@@ -449,11 +449,13 @@ lprior <- function(theta, fp){
 
     nk <- fp$numKnots
 
-    if(fp$eppmod == "logrw")
-      lpr <- bayes_lmvt(theta[2:fp$numKnots], rw_prior_shape, rw_prior_rate)
-    else
-      lpr <- bayes_lmvt(theta[(1+fp$rtpenord):nk], tau2_prior_shape, tau2_prior_rate)
-
+    if (fp$eppmod == "logrw") {
+      lpr <- dnorm(theta[1], 0.2, 1, log = TRUE)
+      lpr <- lpr + bayes_lmvt(theta[2:fp$rt$n_rw], rw_prior_shape, rw_prior_rate)
+    } else {
+      lpr <- dnorm(theta[1], 1.5, 1, log = TRUE)
+      lpr <- lpr + bayes_lmvt(theta[(1 + fp$rtpenord):nk], tau2_prior_shape, tau2_prior_rate)
+    }
     if(exists("r0logiotaratio", fp) && fp$r0logiotaratio)
       lpr <- lpr + dunif(theta[nk+1], r0logiotaratio.unif.prior[1], r0logiotaratio.unif.prior[2], log=TRUE)
     else