From ef913d868619a836004e89756d9e510a4b022b5b Mon Sep 17 00:00:00 2001
From: Nicholas Clark <nicholas.j.clark1214@gmail.com>
Date: Tue, 2 Jul 2024 09:07:01 +1000
Subject: [PATCH] allow trend intercept if trend_map supplied

---
 R/mvgam.R      | 4 +++-
 R/stan_utils.R | 6 +++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/mvgam.R b/R/mvgam.R
index be899f9f..7cf62b29 100644
--- a/R/mvgam.R
+++ b/R/mvgam.R
@@ -1427,7 +1427,9 @@ mvgam = function(formula,
     # Add modifications for trend mapping and trend predictors, if
     # supplied
     trend_sp_names <- NA
+    if(add_nmix) drop_trend_int <- FALSE else drop_trend_int <- TRUE
     if(!missing(trend_map)){
+      drop_trend_int <- FALSE
       trend_map_setup <- trend_map_mods(model_file = vectorised$model_file,
                                         model_data = vectorised$model_data,
                                         trend_map = trend_map,
@@ -1460,7 +1462,7 @@ mvgam = function(formula,
           },
           model_file = vectorised$model_file,
           model_data = vectorised$model_data,
-          nmix = add_nmix,
+          drop_trend_int = drop_trend_int,
           drift = drift)
 
         vectorised$model_file <- trend_pred_setup$model_file
diff --git a/R/stan_utils.R b/R/stan_utils.R
index efb9d030..b57c2ea0 100644
--- a/R/stan_utils.R
+++ b/R/stan_utils.R
@@ -2441,7 +2441,7 @@ add_trend_predictors = function(trend_formula,
                                 data_test,
                                 model_file,
                                 model_data,
-                                nmix = FALSE,
+                                drop_trend_int = TRUE,
                                 drift = FALSE){
 
   #### Creating the trend mvgam model file and data structures ####
@@ -2457,8 +2457,8 @@ add_trend_predictors = function(trend_formula,
   }
 
   # Drop any intercept from the formula if this is not an N-mixture model
-  # as the intercept will almost surely be unidentifiable
-  if(!nmix){
+  # or a trend_map was supplied, as the intercept will almost surely be unidentifiable
+  if(drop_trend_int){
     if(attr(terms(trend_formula), 'intercept') == 1){
       trend_formula <- update(trend_formula, trend_y  ~ . -1)
     } else {