rtemis-org · egenn · Jan 8, 2026 · Oct 18, 2025 · Nov 2, 2025 · Nov 10, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rtemis
-Version: 0.99.1000
+Version: 0.99.1005
 Title: Advanced Machine Learning and Visualization
-Date: 2025-10-18
+Date: 2025-11-25
 Authors@R: person(given = "E.D.", family = "Gennatas", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0001-9280-3609"))
 Description: Advanced Machine Learning and Visualization for all.
 License: GPL (>= 3)

diff --git a/NAMESPACE b/NAMESPACE
@@ -138,6 +138,7 @@ export(plot_true_pred.Regression)
 export(plot_true_pred.RegressionRes)
 export(plot_varimp)
 export(preprocess)
+export(preprocessed)
 export(present)
 export(present.list)
 export(previewcolor)
@@ -149,6 +150,7 @@ export(recycle)
 export(regression_metrics)
 export(repr)
 export(repr_S7name)
+export(repr_ls)
 export(resample)
 export(rnormmat)
 export(rt_reactable)
@@ -187,7 +189,6 @@ export(setup_TabNet)
 export(setup_UMAP)
 export(setup_tSNE)
 export(sge_submit)
-export(show_ls)
 export(size)
 export(sparsernorm)
 export(summarize)

diff --git a/R/00_S7_init.R b/R/00_S7_init.R
@@ -5,6 +5,8 @@
 # References
 # S7 generics: https://rconsortium.github.io/S7/articles/generics-methods.html
 
+# --- Generics -------------------------------------------------------------------------------------
+
 #' String representation
 #'
 #' @details
@@ -366,3 +368,14 @@ get_output_type <- function(
 
   match.arg(output_type)
 } # /rtemis::get_output_type
+
+
+#' Get preprocessed data from Preprocessor
+#'
+#' @param x Preprocessor: A Preprocessor object.
+#' @param ... Not used.
+#'
+#' @return data.frame: The preprocessed data.
+#'
+#' @export
+preprocessed <- new_generic("preprocessed", "x")
diff --git a/R/01_S7_Hyperparameters.R b/R/01_S7_Hyperparameters.R
@@ -23,7 +23,7 @@ TUNED_STATUS_TUNED <- 1L
 
 # `resampled` values ----
 # 0: Running on single training set.
-# 1: Running on cross-validated training sets.
+# 1: Running on resampled training sets.
 
 #' @title Hyperparameters
 #'
@@ -32,10 +32,11 @@ TUNED_STATUS_TUNED <- 1L
 #'
 #' @field algorithm Character: Algorithm name.
 #' @field hyperparameters Named list of algorithm hyperparameter values.
-#' @field tuned Integer: Tuning status.
-#' @field resampled Integer: Cross-validation status.
 #' @field tunable_hyperparameters Character: Names of tunable hyperparameters.
 #' @field fixed_hyperparameters Character: Names of fixed hyperparameters.
+#' @field tuned Integer: Tuning status.
+#' @field resampled Integer: Outer resampling status.
+#' @field n_workers Integer: Number of workers to use for tuning.
 #'
 #' @author EDG
 #' @noRd
@@ -140,7 +141,7 @@ method(repr, Hyperparameters) <- function(
   )
   out <- paste0(
     out,
-    show_ls(
+    repr_ls(
       props(x)[-1],
       pad = pad,
       maxlength = maxlength,

diff --git a/R/02_S7_Metrics.R b/R/02_S7_Metrics.R
@@ -87,7 +87,7 @@ method(repr, RegressionMetrics) <- function(
   }
   out <- paste0(
     out,
-    show_ls(
+    repr_ls(
       x@metrics,
       print_class = FALSE,
       print_df = TRUE,
@@ -296,7 +296,7 @@ method(repr, MetricsRes) <- function(
   names(metricsl) <- names(x@mean_metrics)
   out <- paste0(
     out,
-    show_ls(
+    repr_ls(
       metricsl,
       print_class = FALSE,
       print_df = TRUE,

diff --git a/R/03_S7_Preprocessor.R b/R/03_S7_Preprocessor.R
@@ -90,7 +90,7 @@ method(repr, PreprocessorConfig) <- function(
   output_type <- get_output_type(output_type)
   paste0(
     repr_S7name("PreprocessorConfig", pad = pad, output_type = output_type),
-    show_ls(props(x), pad = pad, limit = limit, output_type = output_type)
+    repr_ls(props(x), pad = pad, limit = limit, output_type = output_type)
   )
 } # /rtemis::show.PreprocessorConfig
 
@@ -350,7 +350,7 @@ method(repr, Preprocessor) <- function(
   output_type <- get_output_type(output_type)
   out <- paste0(
     repr_S7name("Preprocessor", pad = pad, output_type = output_type),
-    show_ls(props(x), pad = pad, print_df = print_df)
+    repr_ls(props(x), pad = pad, print_df = print_df)
   )
 } # /rtemis::show.Preprocessor
 
@@ -385,3 +385,8 @@ method(`[`, Preprocessor) <- function(x, name) {
 method(`[[`, Preprocessor) <- function(x, name) {
   props(x)[[name]]
 }
+
+# preprocessed.Preprocessor ----
+method(preprocessed, Preprocessor) <- function(x) {
+  x@preprocessed
+}
diff --git a/R/05_S7_Tuner.R b/R/05_S7_Tuner.R
@@ -340,7 +340,7 @@ method(repr, GridSearch) <- function(
   )
   out <- paste(
     out,
-    show_ls(x@best_hyperparameters, output_type = output_type),
+    repr_ls(x@best_hyperparameters, output_type = output_type),
     sep = ""
   )
   out

diff --git a/R/06_S7_Supervised.R b/R/06_S7_Supervised.R
@@ -2,7 +2,7 @@
 # ::rtemis::
 # 2025 EDG rtemis.org
 
-# Refs & Res
+# References
 # https://github.com/RConsortium/S7/
 # https://rconsortium.github.io/S7
 # https://rconsortium.github.io/S7/articles/classes-objects.html?q=computed#computed-properties
@@ -412,6 +412,7 @@ get_explain_fn <- function(algorithm) {
   paste0("explain_", algorithm)
 }
 
+
 # Explain Supervised ----
 #' Explain Supervised
 #'

diff --git a/R/08_S7_ClusteringConfig.R b/R/08_S7_ClusteringConfig.R
@@ -53,7 +53,7 @@ method(repr, ClusteringConfig) <- function(
   )
   paste0(
     out,
-    show_ls(props(x)[["config"]], pad = pad, output_type = output_type)
+    repr_ls(props(x)[["config"]], pad = pad, output_type = output_type)
   )
 } # /show
 

diff --git a/R/09_S7_Clustering.R b/R/09_S7_Clustering.R
@@ -57,7 +57,7 @@ method(repr, Clustering) <- function(
   output_type <- get_output_type(output_type)
   paste0(
     repr_S7name(paste(x$algorithm, "Clustering")),
-    show_ls(props(x)[-1], pad = pad, output_type = output_type)
+    repr_ls(props(x)[-1], pad = pad, output_type = output_type)
   )
 } # /rtemis::show.Clustering
 

diff --git a/R/10_S7_DecompositionConfig.R b/R/10_S7_DecompositionConfig.R
@@ -65,7 +65,7 @@ method(repr, DecompositionConfig) <- function(
       pad = pad,
       output_type = output_type
     ),
-    show_ls(x["config"], pad = pad, limit = -1L, output_type = output_type)
+    repr_ls(x["config"], pad = pad, limit = -1L, output_type = output_type)
   )
 } # /rtemis::show.DecompositionConfig
 

diff --git a/R/11_S7_Decomposition.R b/R/11_S7_Decomposition.R
@@ -63,7 +63,7 @@ method(repr, Decomposition) <- function(
       pad = pad,
       output_type = output_type
     ),
-    show_ls(props(x)[-1], pad = pad, output_type = output_type)
+    repr_ls(props(x)[-1], pad = pad, output_type = output_type)
   )
 } # /rtemis::show.Decomposition
 

diff --git a/R/14_S7_utils.R b/R/14_S7_utils.R
@@ -401,7 +401,7 @@ print.CheckData <- function(
     } else {
       out <- paste(
         out,
-        bold(green("  * Everything looks good")),
+        highlight("  * Everything looks good"),
         sep = "\n"
       )
     }

diff --git a/R/fmt.R b/R/fmt.R
@@ -50,11 +50,12 @@ fmt <- function(
   thin = FALSE,
   muted = FALSE,
   bg = NULL,
+  pad = 0L,
   output_type = c("ansi", "html", "plain")
 ) {
   output_type <- match.arg(output_type)
 
-  switch(
+  out <- switch(
     output_type,
     "ansi" = {
       codes <- character()
@@ -157,7 +158,11 @@ fmt <- function(
       }
     },
     "plain" = x
-  )
+  ) # /switch
+  if (pad > 0L) {
+    out <- paste0(strrep(" ", pad), out)
+  }
+  out
 } # /rtemis::fmt
 
 
@@ -166,6 +171,7 @@ fmt <- function(
 #' A `fmt()` convenience wrapper for highlighting text.
 #'
 #' @param x Character: Text to highlight.
+#' @param pad Integer: Number of spaces to pad before text.
 #' @param output_type Character: Output type ("ansi", "html", "plain").
 #'
 #' @return Character: Formatted text with highlight.
@@ -175,9 +181,10 @@ fmt <- function(
 #' @keywords internal
 highlight <- function(
   x,
+  pad = 0L,
   output_type = c("ansi", "html", "plain")
 ) {
-  fmt(x, col = highlight_col, bold = TRUE, output_type = output_type)
+  fmt(x, col = highlight_col, bold = TRUE, pad = pad, output_type = output_type)
 } # /rtemis::highlight
 
 highlight2 <- function(
@@ -282,7 +289,7 @@ muted <- function(x, output_type = c("ansi", "html", "plain")) {
 #' @keywords internal
 #' @noRd
 gray <- function(x, output_type = c("ansi", "html", "plain")) {
-  fmt(x, col = "gray", output_type = output_type)
+  fmt(x, col = "#808080", output_type = output_type)
 } # /rtemis::gray
 
 

diff --git a/R/msg.R b/R/msg.R
@@ -19,7 +19,7 @@ datetime <- function(datetime_format = "%Y-%m-%d %H:%M:%S") {
 #' @noRd
 # Used by msg(), msg0(), msgstart()
 msgdatetime <- function(datetime_format = "%Y-%m-%d %H:%M:%S") {
-  message(gray(paste0(datetime(), gray(" "))), appendLF = FALSE)
+  message(gray(paste0(datetime(), " ")), appendLF = FALSE)
 }
 
 

diff --git a/R/read.R b/R/read.R
@@ -102,7 +102,7 @@ read <- function(
     check_dependencies("arrow")
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        highlight("\u25B6"),
         " Reading ",
         highlight(basename(path)),
         " using arrow::read_parquet()..."
@@ -113,7 +113,7 @@ read <- function(
   } else if (ext == "rds") {
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        bold(highlight("\u25B6")),
         " Reading ",
         highlight(basename(path)),
         "..."
@@ -124,7 +124,7 @@ read <- function(
     check_dependencies("openxlsx")
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        bold(highlight("\u25B6")),
         " Reading ",
         highlight(basename(path)),
         " using readxl::read_excel()..."
@@ -141,7 +141,7 @@ read <- function(
     check_dependencies("haven")
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        bold(highlight("\u25B6")),
         " Reading ",
         highlight(basename(path)),
         " using haven::read_dta()..."
@@ -153,7 +153,7 @@ read <- function(
     check_dependencies("seqinr")
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        bold(highlight("\u25B6")),
         " Reading ",
         highlight(basename(path)),
         " using seqinr::read.fasta()..."
@@ -169,7 +169,7 @@ read <- function(
     check_dependencies("farff")
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        bold(highlight("\u25B6")),
         " Reading ",
         highlight(basename(path)),
         " using farff::readARFF()..."
@@ -180,7 +180,7 @@ read <- function(
   } else {
     if (verbosity > 0L) {
       msg0(
-        bold(green("\u25B6")),
+        bold(highlight("\u25B6")),
         " Reading ",
         highlight(basename(path)),
         " using ",
@@ -332,7 +332,7 @@ msgread <- function(x, caller = "", use_basename = TRUE) {
     x <- basename(x)
   }
   msg0(
-    bold(green("\u25B6")),
+    bold(highlight("\u25B6")),
     " Reading ",
     highlight(x),
     "...",

diff --git a/R/rtemis_color_system.R b/R/rtemis_color_system.R
@@ -44,8 +44,8 @@ rt_teal <- rtemis_teal
 rt_purple <- rtemis_purple
 rt_magenta <- rtemis_magenta
 
-col_object <- rt_teal
 highlight_col <- rt_teal
+col_object <- rt_teal
 col_info <- highlight2_col <- lmd_burgundy
 col_outer <- rt_red
 col_tuner <- rt_orange # genlib orange
diff --git a/R/train_GLMNET.R b/R/train_GLMNET.R
@@ -201,17 +201,21 @@ explain_GLMNET <- function(model, x, dat_training, method = NULL) {
   if (!method %in% c("shapr")) {
     cli::cli_abort("Explain method for GLMNET must be 'shapr'")
   }
-  newdata <- as.matrix(
-    model.matrix(~., dat_training)[, -1, drop = FALSE]
-  )
+  x_mat <- model.matrix(~., x)[, -1, drop = FALSE]
+  dat_training_mat <- model.matrix(~., dat_training)[, -1, drop = FALSE]
   if (method == "shapr") {
+    phi0 <- if (model@type == "Classification") {
+      mean(model@predicted_prob_training)
+    } else {
+      mean(model@predicted_training)
+    }
     shapr::explain(
       model = model@model,
-      x_explain = x,
-      x_train = dat_training,
+      x_explain = x_mat,
+      x_train = dat_training_mat,
       predict_model = predict_GLMNET,
       approach = "ctree",
-      phi0 = mean(model@predicted_training)
+      phi0 = phi0
     )
   }
 } # /rtemis::explain_GLMNET
diff --git a/R/utils_art.R b/R/utils_art.R
@@ -308,7 +308,7 @@ show_col <- function(
   if (limit != -1L && length(x) > limit) {
     limit_text <- paste0(
       italic(
-        thin(
+        gray(
           paste0(
             "Showing first ",
             limit,
@@ -330,7 +330,7 @@ show_col <- function(
     if (limit != -1L && counter > limit) {
       more_text <- paste0(
         italic(
-          thin(
+          gray(
             paste0(
               "...",
               length(x) - limit,
-Original file line number
+Diff line change
@@ Expand Up / @@ -53,7 +53,7 @@ method(repr, ClusteringConfig) <- function( @@
       )
       paste0(
         out,
-        show_ls(props(x)[["config"]], pad = pad, output_type = output_type)
+        repr_ls(props(x)[["config"]], pad = pad, output_type = output_type)
       )
     } # /show
@@ Expand Down @@