allow trend intercept if trend_map supplied

nicholasjclark · Jul 1, 2024 · ef913d8 · ef913d8
1 parent 5f5845b
commit ef913d8
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git 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
@@ -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 {