From 6de7a1658bd7e304b86db5984b63960b8eee3713 Mon Sep 17 00:00:00 2001
From: Nicholas Clark <nicholas.j.clark1214@gmail.com>
Date: Thu, 31 Aug 2023 16:52:49 +1000
Subject: [PATCH] small bug fix in extraction funs

---
 R/as.data.frame.mvgam.R | 8 ++++----
 R/index-mvgam.R         | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/as.data.frame.mvgam.R b/R/as.data.frame.mvgam.R
index 2b709bdc..263d7c9a 100644
--- a/R/as.data.frame.mvgam.R
+++ b/R/as.data.frame.mvgam.R
@@ -369,7 +369,7 @@ validate_variables = function(x, variable, regex = FALSE){
            call. = FALSE)
     }
     to_extract <- 'rho'
-    newnames <- x$sp_names
+    newnames <- paste0(x$sp_names, '_rho')
   }
 
   if(variable[1] == 'linpreds'){
@@ -412,7 +412,7 @@ validate_variables = function(x, variable, regex = FALSE){
 
     to_extract <- 'rho_trend'
     newnames <- paste0(unlist(purrr::map(x$trend_mgcv_model$smooth,
-                                         'label')), '_trend')
+                                         'label')), '_rho_trend')
   }
 
   if(variable[1] == 'trend_linpreds'){
@@ -453,8 +453,8 @@ validate_variables = function(x, variable, regex = FALSE){
             vars_to_extract[[i]] <- unname(unlist(purrr::map(all_vars, 'orig_name'))[
               grepl(variable[i], unlist(purrr::map(all_vars, 'orig_name')))])
 
-            names_to_use[[i]] <- unname(unlist(purrr::map(all_vars, 'orig_name'))[
-              grepl(variable[i], unlist(purrr::map(all_vars, 'alias')))])
+            names_to_use[[i]] <- unname(unlist(purrr::map(all_vars, 'alias'))[
+              grepl(variable[i], unlist(purrr::map(all_vars, 'orig_name')))])
           }
         }
       }
diff --git a/R/index-mvgam.R b/R/index-mvgam.R
index b10cf277..2132aa7a 100644
--- a/R/index-mvgam.R
+++ b/R/index-mvgam.R
@@ -136,14 +136,14 @@ variables.mvgam = function(x, ...){
   if(any(grepl(paste(c('sigma', 'alpha_gp',
                        'rho_gp',
                        'ar1', 'ar2',
-                       'ar3', '//bA//b',
+                       'ar3', 'A',
                        'Sigma'), collapse = '|'),
                parnames) &
          !grepl('sigma_obs', parnames, fixed = TRUE))){
     trend_pars <- grepl(paste(c('sigma', 'alpha_gp',
                                 'rho_gp',
                                 'ar1', 'ar2',
-                                'ar3', '//bA//b',
+                                'ar3', 'A',
                                 'Sigma'), collapse = '|'),
                         parnames) &
       !grepl('sigma_obs', parnames, fixed = TRUE)