fix a few cmdcheck issues

R/backends.R

@@ -638,10 +638,10 @@ read_csv_as_stanfit <- function(files, variables = NULL,
 
   # Can make LV models slightly more efficient by not filling in zeros in a loop
   if(any(grepl('lv_coefs_raw[i, j] = 0;', stan_file, fixed = TRUE))){
-    starts <- mvgam:::grepws('lv_coefs_raw[i, j] = 0;', stan_file) - 2
-    ends <- mvgam:::grepws('lv_coefs_raw[i, j] = 0;', stan_file) + 2
+    starts <- grepws('lv_coefs_raw[i, j] = 0;', stan_file) - 2
+    ends <- grepws('lv_coefs_raw[i, j] = 0;', stan_file) + 2
     stan_file <- stan_file[-c(starts:ends)]
-    stan_file[mvgam:::grepws('matrix[n_series, n_lv] lv_coefs_raw;', stan_file)] <-
+    stan_file[grepws('matrix[n_series, n_lv] lv_coefs_raw;', stan_file)] <-
       'matrix[n_series, n_lv] lv_coefs_raw = rep_matrix(0, n_series, n_lv);'
   }
 

R/globals.R

@@ -17,4 +17,4 @@ utils::globalVariables(c("y", "year", "smooth_vals", "smooth_num",
                          "name", "needed", "nmix_trendmap", "orig_formula",
                          "trial", "use_var1", "use_var1cor", "xcols_drop",
                          "time_lag", "dis_time", "maxt", "orig_rows",
-                         "matches", "time.", "file_name"))
+                         "matches", "time.", "file_name", ".data"))

R/monotonic.R

@@ -503,7 +503,7 @@ eval_smoothDotmodDotsmooth = function(smooth,
 
   # set some values to NA if too far from the data
   if (gratia::smooth_dim(smooth) == 2L && (!is.null(dist) && dist > 0)) {
-    eval_sm <- too_far_to_na(smooth,
+    eval_sm <- gratia::too_far_to_na(smooth,
                              input = eval_sm,
                              reference = model[["model"]],
                              cols = c(".estimate", ".se"),
@@ -561,7 +561,7 @@ eval_smoothDotmoiDotsmooth = function(smooth,
 
   # set some values to NA if too far from the data
   if (gratia::smooth_dim(smooth) == 2L && (!is.null(dist) && dist > 0)) {
-    eval_sm <- too_far_to_na(smooth,
+    eval_sm <- gratia::too_far_to_na(smooth,
                              input = eval_sm,
                              reference = model[["model"]],
                              cols = c(".estimate", ".se"),
@@ -626,7 +626,7 @@ eval_smoothDotmoiDotsmooth = function(smooth,
     ## if this is a by variable, filter the by variable for the required
     ## level now
     if (gratia::is_factor_by_smooth(smooth)) {
-      data <- data %>% filter(.data[[by_var]] == gratia::by_level(smooth))
+      data <- data %>% dplyr::filter(.data[[by_var]] == gratia::by_level(smooth))
     }
   }
   data

R/stan_utils.R

@@ -36,14 +36,14 @@ print.mvgammodel = function(x, ...){
 #' @export
 #' @importFrom brms stancode
 #' @rdname code
-stancode.mvgam_prefit = function(object){
+stancode.mvgam_prefit = function(object, ...){
 
   code(object)
 }
 
 #' @export
 #' @rdname code
-stancode.mvgam = function(object){
+stancode.mvgam = function(object, ...){
 
   code(object)
 }