From 9b93bf3c512252b0050db39133858512a796b516 Mon Sep 17 00:00:00 2001
From: "C. Regouby" <christophe.regouby@free.fr>
Date: Fri, 14 Jun 2024 20:17:36 +0200
Subject: [PATCH] fix check() warning and notes

---
 DESCRIPTION   | 2 +-
 R/parsnip.R   | 7 ++-----
 R/plot.R      | 4 ++--
 man/tabnet.Rd | 9 ++++++---
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ed921305..685f68ea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -42,7 +42,6 @@ Imports:
     tune,
     utils,
     vctrs,
-    vip,
     withr,
     zeallot
 Suggests: 
@@ -55,6 +54,7 @@ Suggests:
     testthat (>= 3.0.0),
     tidymodels,
     tidyverse,
+    vip,
     visdat,
     workflows,
     yardstick
diff --git a/R/parsnip.R b/R/parsnip.R
index 98bfb728..f2052896 100644
--- a/R/parsnip.R
+++ b/R/parsnip.R
@@ -426,6 +426,7 @@ add_parsnip_tabnet <- function() {
 #' @param mode A single character string for the type of model. Possible values
 #'   for this model are "unknown", "regression", or "classification".
 #' @inheritParams tabnet_config
+#' @inheritParams tabnet_fit
 #'
 #' @inheritSection tabnet_fit Threading
 #' @seealso tabnet_fit
@@ -444,8 +445,7 @@ add_parsnip_tabnet <- function() {
 #'
 #' @export
 tabnet <- function(mode = "unknown",  cat_emb_dim = NULL, decision_width = NULL, attention_width = NULL,
-                   num_steps = NULL, mask_type = NULL, mlp_hidden_multiplier = NULL, mlp_activation = NULL,
-                   encoder_activation = NULL, num_independent = NULL, num_shared = NULL,
+                   num_steps = NULL, mask_type = NULL, num_independent = NULL, num_shared = NULL,
                    num_independent_decoder = NULL, num_shared_decoder = NULL, penalty = NULL,
                    feature_reusage = NULL, momentum = NULL, epochs = NULL, batch_size = NULL,
                    virtual_batch_size = NULL, learn_rate = NULL, optimizer = NULL, loss = NULL,
@@ -471,9 +471,6 @@ tabnet <- function(mode = "unknown",  cat_emb_dim = NULL, decision_width = NULL,
     attention_width = rlang::enquo(attention_width),
     num_steps = rlang::enquo(num_steps),
     mask_type = rlang::enquo(mask_type),
-    mlp_hidden_multiplier = rlang::enquo(mlp_hidden_multiplier),
-    mlp_activation = rlang::enquo(mlp_activation),
-    encoder_activation = rlang::enquo(encoder_activation),
     num_independent = rlang::enquo(num_independent),
     num_shared = rlang::enquo(num_shared),
     num_independent_decoder = rlang::enquo(num_independent_decoder),
diff --git a/R/plot.R b/R/plot.R
index d05fec45..c1b681cd 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -40,8 +40,8 @@ autoplot.tabnet_fit <- function(object, ...) {
 
   if ("checkpoint" %in% names(collect_metrics)) {
     checkpoints <- collect_metrics %>%
-      dplyr::filter(checkpoint == TRUE, dataset == "train") %>%
-      dplyr::select(-checkpoint) %>%
+      dplyr::filter(.data$checkpoint == TRUE, dataset == "train") %>%
+      dplyr::select(-.data$checkpoint) %>%
       dplyr::mutate(size = 2)
     p +
       ggplot2::geom_point(data = checkpoints, ggplot2::aes(x = epoch, y = loss, color = dataset, size = .data$size ))
diff --git a/man/tabnet.Rd b/man/tabnet.Rd
index 5b19c9c4..d4684b10 100644
--- a/man/tabnet.Rd
+++ b/man/tabnet.Rd
@@ -11,9 +11,6 @@ tabnet(
   attention_width = NULL,
   num_steps = NULL,
   mask_type = NULL,
-  mlp_hidden_multiplier = NULL,
-  mlp_activation = NULL,
-  encoder_activation = NULL,
   num_independent = NULL,
   num_shared = NULL,
   num_independent_decoder = NULL,
@@ -142,6 +139,12 @@ display a warning.}
 \item{early_stopping_patience}{Number of epochs without improving until stopping training. (default=5)}
 
 \item{skip_importance}{if feature importance calculation should be skipped (default: \code{FALSE})}
+
+\item{tabnet_model}{A previously fitted TabNet model object to continue the fitting on.
+if \code{NULL} (the default) a brand new model is initialized.}
+
+\item{from_epoch}{When a \code{tabnet_model} is provided, restore the network weights from a specific epoch.
+Default is last available checkpoint for restored model, or last epoch for in-memory model.}
 }
 \value{
 A TabNet \code{parsnip} instance. It can be used to fit tabnet models using