array updates for newest Cmdstan; more piecewise tests

Author: Nicholas Clark

R/add_nmixture.R

@@ -15,13 +15,36 @@ add_nmixture = function(model_file,
     stop('Max abundances must be supplied as a variable named "cap" for N-mixture models',
          call. = FALSE)
   }
-  cap <- data_train$cap
+
+  if(inherits(data_train, 'data.frame')){
+    cap = data_train %>%
+      dplyr::arrange(series, time) %>%
+      dplyr::pull(cap)
+  } else {
+    cap = data.frame(series = data_train$series,
+                     cap = data_train$cap,
+                     time = data_train$time)%>%
+      dplyr::arrange(series, time) %>%
+      dplyr::pull(cap)
+  }
+
   if(!is.null(data_test)){
     if(!(exists('cap', where = data_test))) {
       stop('Max abundances must be supplied in test data as a variable named "cap" for N-mixture models',
            call. = FALSE)
     }
-    cap <- c(cap, data_test$cap)
+    if(inherits(data_test, 'data.frame')){
+      captest = data_test %>%
+        dplyr::arrange(series, time) %>%
+        dplyr::pull(cap)
+    } else {
+      captest = data.frame(series = data_test$series,
+                           cap = data_test$cap,
+                           time = data_test$time)%>%
+        dplyr::arrange(series, time) %>%
+        dplyr::pull(cap)
+    }
+    cap <- c(cap, captest)
   }
 
   validate_pos_integers(cap)
@@ -33,7 +56,7 @@ add_nmixture = function(model_file,
 
   model_data$cap <- as.vector(cap)
 
-  if(any(model_data$cap < model_data$y)){
+  if(any(model_data$cap[model_data$obs_ind] < model_data$flat_ys)){
     stop(paste0('Some "cap" terms are < the observed counts. This is not allowed'),
          call. = FALSE)
   }
@@ -243,7 +266,7 @@ add_nmixture = function(model_file,
                                                        'array[n, n_series] int latent_ypred;\n',
                                                        'array[total_obs] int latent_truncpred;\n',
                                                        'vector[n_nonmissing] flat_ps;\n',
-                                                       'int flat_caps[n_nonmissing];',
+                                                       'int flat_caps[n_nonmissing];\n',
                                                        'vector[total_obs] flat_trends;\n',
                                                        'vector[n_nonmissing] flat_trends_nonmis;\n',
                                                        'vector[total_obs] detprob;\n',

R/get_mvgam_priors.R

@@ -462,7 +462,7 @@ get_mvgam_priors = function(formula,
     }
 
     # Remove sigma prior if this is an N-mixture with no dynamics
-    if(add_nmix){
+    if(add_nmix & trend_model == 'None'){
       out <- out[-grep('vector<lower=0>[n_lv] sigma;',
                        out$param_name,
                        fixed = TRUE),]

R/gp.R

@@ -158,10 +158,15 @@ make_gp_additions = function(gp_details, data,
 
   # Add coefficient indices to attribute table and to Stan data
   for(covariate in seq_along(gp_att_table)){
-    # coef_indices <- grep(gp_att_table[[covariate]]$name,
-    #                      names(coef(mgcv_model)), fixed = TRUE)
-    coef_indices <- which(grepl(gp_att_table[[covariate]]$name,
-                                names(coef(mgcv_model)), fixed = TRUE) &
+    # coef_indices <- which(grepl(gp_att_table[[covariate]]$name,
+    #                             names(coef(mgcv_model)), fixed = TRUE) &
+    #                         !grepl(paste0(gp_att_table[[covariate]]$name,':'),
+    #                                names(coef(mgcv_model)), fixed = TRUE) == TRUE)
+
+    coef_indices <- which(grepl(paste0(gsub("([()])","\\\\\\1",
+                                            gp_att_table[[covariate]]$name),
+                                       '\\.+[0-9]'),
+                                names(coef(mgcv_model)), fixed = FALSE) &
                             !grepl(paste0(gp_att_table[[covariate]]$name,':'),
                                    names(coef(mgcv_model)), fixed = TRUE) == TRUE)
 

R/mvgam.R

@@ -1718,8 +1718,7 @@ mvgam = function(formula,
       # Auto-format the model file
       if(autoformat){
         if(requireNamespace('cmdstanr') & cmdstanr::cmdstan_version() >= "2.29.0") {
-          tmp_file <- cmdstanr::write_stan_file(vectorised$model_file)
-          vectorised$model_file <- .autoformat(tmp_file,
+          vectorised$model_file <- .autoformat(vectorised$model_file,
                                                overwrite_file = FALSE)
         }
         vectorised$model_file <- readLines(textConnection(vectorised$model_file),
@@ -1908,7 +1907,7 @@ mvgam = function(formula,
                                                cpp_options = list(stan_threads = TRUE))
           } else {
             cmd_mod <- cmdstanr::cmdstan_model(cmdstanr::write_stan_file(vectorised$model_file),
-                                               stanc_options = list('O1'))
+                                               stanc_options = list('O1'),)
           }
 
         } else {