From 0c2313b628298d14c2e961b531428314219f9d30 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Thu, 9 Apr 2026 11:52:11 +0000
Subject: [PATCH 01/23] feat: replace logger with lightweight console logging +
 ZIP export

Replace the logger package dependency with an internal logging system
that outputs to the R console and captures logs in memory. The session
log can be exported as session_log.txt in the ZIP download.

- Add inst/shiny/functions/logging.R with log_trace/debug/info/success/
  warn/error functions, glue interpolation, configurable threshold via
  aNCA_LOG_LEVEL env var, and in-memory buffer
- Remove setup_logger and log_debug_list from utils.R (now in logging.R)
- Remove require(logger) from app.R
- Move logger from Imports back to Suggests in DESCRIPTION
- Add session_log to ZIP export tree and file filtering

Closes #1210

Co-authored-by: Ona <no-reply@ona.com>
---
 DESCRIPTION                      |  2 +-
 inst/shiny/app.R                 |  1 -
 inst/shiny/functions/logging.R   | 76 ++++++++++++++++++++++++++++++++
 inst/shiny/functions/utils.R     | 42 ------------------
 inst/shiny/functions/zip-utils.R | 21 +++++++++
 inst/shiny/modules/tab_nca/zip.R |  5 ++-
 6 files changed, 101 insertions(+), 46 deletions(-)
 create mode 100644 inst/shiny/functions/logging.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 76abed03b..997eeab3f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -33,7 +33,6 @@ Imports:
     glue,
     htmltools,
     htmlwidgets,
-    logger,
     magrittr,
     PKNCA (>= 0.12.1),
     plotly (>= 4.11.0),
@@ -67,6 +66,7 @@ Suggests:
     jsonlite,
     knitr,
     lintr (>= 3.2.0),
+    logger,
     markdown,
     mockery,
     nestcolor,
diff --git a/inst/shiny/app.R b/inst/shiny/app.R
index 6d9bef118..2fa5de7fb 100644
--- a/inst/shiny/app.R
+++ b/inst/shiny/app.R
@@ -3,7 +3,6 @@ require(aNCA)
 require(bslib)
 require(dplyr)
 require(htmlwidgets)
-require(logger)
 require(formatters)
 require(magrittr)
 require(plotly)
diff --git a/inst/shiny/functions/logging.R b/inst/shiny/functions/logging.R
new file mode 100644
index 000000000..4a13a242c
--- /dev/null
+++ b/inst/shiny/functions/logging.R
@@ -0,0 +1,76 @@
+# Lightweight logging system for the aNCA Shiny app.
+#
+# Replaces the `logger` package with console-only output and in-memory
+# log capture for ZIP export. Supports glue-style interpolation and
+# paste-style multi-argument calls.
+#
+# Log levels: TRACE < DEBUG < INFO < SUCCESS < WARN < ERROR
+# Default threshold: INFO (configurable via aNCA_LOG_LEVEL env var).
+
+.log_env <- new.env(parent = emptyenv())
+.log_env$threshold <- "INFO"
+.log_env$buffer <- character(0)
+
+.LOG_LEVELS <- c(TRACE = 1L, DEBUG = 2L, INFO = 3L, SUCCESS = 4L, WARN = 5L, ERROR = 6L)
+
+#' Initialise the logging system.
+#'
+#' Reads the threshold from the `aNCA_LOG_LEVEL` environment variable
+#' (default `"INFO"`) and clears the in-memory log buffer.
+setup_logger <- function() {
+  level <- toupper(Sys.getenv("aNCA_LOG_LEVEL", "INFO"))
+  if (!level %in% names(.LOG_LEVELS)) level <- "INFO"
+  .log_env$threshold <- level
+  .log_env$buffer <- character(0)
+}
+
+#' Core logging function.
+#' @param level Character: one of the log level names.
+#' @param ... Message parts. If the first argument contains `{`, it is
+#'   evaluated as a glue string in the caller's environment. Otherwise
+#'   all arguments are pasted together.
+#' @noRd
+.log_msg <- function(level, ...) {
+  if (.LOG_LEVELS[[level]] < .LOG_LEVELS[[.log_env$threshold]]) return(invisible(NULL))
+
+  args <- list(...)
+  if (length(args) == 0L) {
+    msg <- ""
+  } else if (length(args) == 1L && grepl("\\{", args[[1]])) {
+    msg <- tryCatch(
+      glue::glue(args[[1]], .envir = parent.frame(2)),
+      error = function(e) paste0(args, collapse = "")
+    )
+  } else {
+    msg <- paste0(args, collapse = "")
+  }
+
+  timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
+  line <- paste0("[", timestamp, "] ", level, ": ", msg)
+
+  .log_env$buffer <- c(.log_env$buffer, line)
+  message(line)
+  invisible(NULL)
+}
+
+# Public log functions matching the logger API
+log_trace   <- function(...) .log_msg("TRACE", ...)
+log_debug   <- function(...) .log_msg("DEBUG", ...)
+log_info    <- function(...) .log_msg("INFO", ...)
+log_success <- function(...) .log_msg("SUCCESS", ...)
+log_warn    <- function(...) .log_msg("WARN", ...)
+log_error   <- function(...) .log_msg("ERROR", ...)
+
+#' Logs a list or data frame at DEBUG level.
+#'
+#' @param title Title for the log entry.
+#' @param l     List or data.frame to log.
+log_debug_list <- function(title, l) {
+  log_debug(aNCA:::.concatenate_list(title, l))
+}
+
+#' Return the in-memory log buffer as a character vector.
+#' @noRd
+get_log_buffer <- function() {
+  .log_env$buffer
+}
diff --git a/inst/shiny/functions/utils.R b/inst/shiny/functions/utils.R
index ae247ed42..ba264a160 100644
--- a/inst/shiny/functions/utils.R
+++ b/inst/shiny/functions/utils.R
@@ -1,45 +1,3 @@
-#' Sets up the logger package for the application.
-#'
-#' @details
-#' The application logs everything to a log file located in `/log` directory. If such folder
-#' does not exist, it will be created. Logfile for each session will be separate. The application
-#' will keep 5 log files at any given time - if this number is exceeded, the oldest log file
-#' will be deleted.
-#'
-#' In addition, information of the level specified by the user will be logged to console.
-#' As a default, this level is INFO - this is so that the user has good information on what is
-#' happening inside the app, but is not overwhelmed with tracing and debugging information. This
-#' level can be changed using `aNCA_LOG_LEVEL` environmental variable, set for example in
-#' `.Renviron` file.
-setup_logger <- function() {
-  log_layout(layout_glue_colors)
-  log_formatter(formatter_glue)
-  log_threshold(TRACE)
-  log_threshold(Sys.getenv("aNCA_LOG_LEVEL", "INFO"), index = 2)
-
-  log_dir <- "./log"
-  if (!dir.exists(log_dir)) dir.create(log_dir)
-  existing_logs <- list.files(log_dir, full.names = TRUE)
-  if (length(existing_logs) >= 5) file.remove(sort(existing_logs)[1]) # keep only five log files
-  logfile_name <- paste0(log_dir, "/aNCA_app_", format(Sys.time(), "%y%m%d-%H%M%S-"), ".log")
-
-  log_appender(appender_file(logfile_name))
-  log_appender(appender_console, index = 2)
-}
-
-#' Logs a list and data frame objects.
-#'
-#' @details
-#' Utilitary function for logging a list object (like mapping list or used settings) in
-#' a nice format. Parses a list into nice string and logs at DEBUG level. Can also process
-#' data frames, which will be converted into a list of rows.
-#'
-#' @param title Title for the logs.
-#' @param l     List object to be parsed into log. Can also be a data.frame.
-log_debug_list <- function(title, l) {
-  log_debug(aNCA:::.concatenate_list(title, l))
-}
-
 #' Needed to properly reset reactable.extras widgets
 #'
 #' @details
diff --git a/inst/shiny/functions/zip-utils.R b/inst/shiny/functions/zip-utils.R
index e6ce38f9a..f7b548e5f 100644
--- a/inst/shiny/functions/zip-utils.R
+++ b/inst/shiny/functions/zip-utils.R
@@ -426,6 +426,12 @@ prepare_export_files <- function(target_dir,
                  detail = "Saving session info...")
     .export_session_info(target_dir)
   }
+
+  if ("session_log" %in% input$res_tree) {
+    progress$set(message = "Creating exports...",
+                 detail = "Saving session log...")
+    .export_session_log(target_dir)
+  }
   progress$inc(0.8)
 
   .clean_export_dir(target_dir, input, custom_names)
@@ -638,6 +644,17 @@ prepare_export_files <- function(target_dir,
   writeLines(lines, file.path(target_dir, "session_info.txt"))
 }
 
+#' Export the in-memory session log to a text file.
+#' @param target_dir Target directory for the export.
+#' @keywords internal
+.export_session_log <- function(target_dir) {
+  log_buffer <- get_log_buffer()
+  if (length(log_buffer) == 0L) {
+    log_buffer <- "(No log entries captured during this session.)"
+  }
+  writeLines(log_buffer, file.path(target_dir, "session_log.txt"))
+}
+
 #' Clean Export Directory
 #' @param target_dir Target directory to clean
 #' @param input Shiny input object
@@ -675,6 +692,10 @@ prepare_export_files <- function(target_dir,
     files_req <- c(files_req, grep("session_info\\.txt$", all_files,
                                    value = TRUE))
   }
+  if ("session_log" %in% fnames) {
+    files_req <- c(files_req, grep("session_log\\.txt$", all_files,
+                                   value = TRUE))
+  }
   file.remove(all_files[!all_files %in% files_req])
 
   # Recursive directory cleanup — remove dirs that contain no files at any depth
diff --git a/inst/shiny/modules/tab_nca/zip.R b/inst/shiny/modules/tab_nca/zip.R
index e70b08f5d..142a9e668 100644
--- a/inst/shiny/modules/tab_nca/zip.R
+++ b/inst/shiny/modules/tab_nca/zip.R
@@ -658,7 +658,7 @@ zip_server <- function(id, res_nca, adnca_data, settings, grouping_vars) {
     }
     items$extras            <- TREE_LIST$extras
   } else {
-    items$extras <- TREE_LIST$extras[c("settings_file", "session_info")]
+    items$extras <- TREE_LIST$extras[c("settings_file", "session_info", "session_log")]
   }
 
   items
@@ -693,7 +693,8 @@ TREE_LIST <- list(
     results_slides = "",
     r_script = "",
     settings_file = "",
-    session_info = ""
+    session_info = "",
+    session_log = ""
   )
 )
 

From 41b9403391f286685d33d3468db330dd92ac7a80 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:03:20 +0000
Subject: [PATCH 02/23] feat: add log-points for NCA settings changes

Log analyte, specimen, profile, method, min half-life points,
and flag rule changes at INFO level.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/settings.R | 25 +++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 1a2d80642..9fdac1834 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -273,6 +273,8 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
+      log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))
+
       settings <- .consume_settings()
 
       all_pcspec <- unique(data()$PCSPEC) %>% na.omit()
@@ -307,6 +309,8 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
+      log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))
+
       settings <- .consume_settings()
 
       all_analyte <- unique(data()$PARAM) %>% na.omit()
@@ -328,6 +332,15 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       .update_profile(settings)
     })
 
+    # Log method and min half-life points changes
+    observeEvent(input$method, {
+      log_info("Extrapolation method changed: {input$method}")
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$min_hl_points, {
+      log_info("Min. half-life points changed: {input$min_hl_points}")
+    }, ignoreInit = TRUE)
+
     # Include keyboard limits for the settings GUI display
 
     # Keyboard limits for the setting thresholds
@@ -337,6 +350,18 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "LAMZSPN_threshold", min = 0, lab = "LAMZSPN")
     limit_input_value(input, session, "min_hl_points", max = 10, min = 2, lab = "Min. HL Points")
 
+    # Log flag rule changes
+    .flag_names <- c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN")
+    lapply(.flag_names, function(flag) {
+      observeEvent(input[[paste0(flag, "_rule")]], {
+        state <- if (input[[paste0(flag, "_rule")]]) "enabled" else "disabled"
+        log_info("Flag rule {flag} {state}")
+      }, ignoreInit = TRUE)
+      observeEvent(input[[paste0(flag, "_threshold")]], {
+        log_info("Flag rule {flag} threshold changed: {input[[paste0(flag, '_threshold')]]}")
+      }, ignoreInit = TRUE)
+    })
+
     # Reactive value to store the partial intervals data table
     # Define the parameters that can be used for partial area calculations
     PARTIAL_INT_PARAMS <- metadata_nca_parameters %>%

From 5922af8ffd0047a68f9d54740858de59de9b5056 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:03:32 +0000
Subject: [PATCH 03/23] feat: add debug log-point for selected parameter names

Log the full list of selected parameters at DEBUG level
alongside the existing INFO count message.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/parameter_selection.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 5d5e860fe..474a3a808 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -287,6 +287,9 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
           n_params <- if (is.null(params)) 0 else length(params)
 
           log_info("Parameter selection for '{study_type}': {n_params} parameters selected.")
+          if (n_params > 0) {
+            log_debug("Parameters for '{study_type}': ", paste(params, collapse = ", "))
+          }
         }, ignoreNULL = FALSE, ignoreInit = TRUE)
       })
     })

From 7ce0384c37e37b97a3d0db161590a5725293ab4f Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:04:00 +0000
Subject: [PATCH 04/23] feat: add log-points for slope selector user actions

Upgrade slope rule add/remove from TRACE to INFO level.
Add DEBUG summary of slope rules count on table changes.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/manual_slopes_table.R | 4 ++--
 inst/shiny/modules/tab_nca/setup/slope_selector.R      | 5 +++++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
index 5475c0466..88bd9db3f 100644
--- a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
+++ b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
@@ -93,7 +93,7 @@ manual_slopes_table_server <- function(
 
     # Add a new row to the table when the user clicks the add button
     observeEvent(input$add_rule, {
-      log_trace("{id}: adding manual slopes row")
+      log_info("Slope selector: adding manual slope rule")
       first_group <- slopes_pknca_groups()[1, ]
       time_col <- pknca_data()$conc$columns$time
       new_row <- cbind(
@@ -126,7 +126,7 @@ manual_slopes_table_server <- function(
 
     # Remove selected rows from the table when the user clicks the remove button
     observeEvent(input$remove_rule, {
-      log_trace("{id}: removing manual slopes row")
+      log_info("Slope selector: removing manual slope rule")
       selected <- getReactableState("manual_slopes", "selected")
       req(selected)
       edited_slopes <- manual_slopes()[-selected, ]
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 4a926a7c5..a903b76b6 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -250,6 +250,11 @@ slope_selector_server <- function( # nolint
     observeEvent(manual_slopes(), {
       req(manual_slopes())
 
+      n_rules <- nrow(manual_slopes())
+      n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
+      n_incl <- n_rules - n_excl
+      log_debug("Slope rules updated: {n_rules} total ({n_incl} inclusions, {n_excl} exclusions)")
+
       # Update reactable with rules
       reactable::updateReactable(
         outputId = "manual_slopes",

From ef5b7def557de68ae04304c08833b2704e19dff7 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:04:39 +0000
Subject: [PATCH 05/23] feat: add log-points for general exclusion changes

Log exclusion add (with row count, type, reason), removal,
and settings restore at INFO level.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 .../modules/tab_nca/setup/general_exclusions.R  | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/general_exclusions.R b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
index 157258962..6de6c2220 100644
--- a/inst/shiny/modules/tab_nca/setup/general_exclusions.R
+++ b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
@@ -131,6 +131,7 @@ general_exclusions_server <- function(
 
         xbtn_counter(max(new_ids))
         exclusion_list(rehydrated_list)
+        log_info("Exclusions restored from settings: ", length(overrides), " rules loaded")
       }
     })
 
@@ -156,6 +157,21 @@ general_exclusions_server <- function(
 
     # Add a new exclusion when the Add button is pressed
     observeEvent(input$add_exclusion_reason, {
+      rows_sel <- getReactableState("conc_table-table", "selected")
+      reason <- input$exclusion_reason
+      nca_checked <- isTRUE(input$cb_manual_nca)
+      tlg_checked <- isTRUE(input$cb_tlg)
+
+      if (length(rows_sel) > 0 && nzchar(reason) && (nca_checked || tlg_checked)) {
+        type_label <- if (nca_checked && tlg_checked) "NCA + TLG"
+          else if (nca_checked) "NCA"
+          else "TLG"
+        log_info(
+          "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+          ", reason='", reason, "'"
+        )
+      }
+
       .handle_add_exclusion(
         input, session, exclusion_list, xbtn_counter
       )
@@ -167,6 +183,7 @@ general_exclusions_server <- function(
       lapply(lst, function(item) {
         xbtn_id <- item$xbtn_id
         observeEvent(input[[xbtn_id]], {
+          log_info("Exclusion removed: reason='", item$reason, "'")
           current <- exclusion_list()
           exclusion_list(
             Filter(function(x) x$xbtn_id != xbtn_id, current)

From 4a4b92dd6e4f30a699e44f18fc07a7df1486bb76 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:05:02 +0000
Subject: [PATCH 06/23] feat: add log-points for profile selection and data
 imputation

Log NCA profile changes, BLQ strategy changes, and C0
imputation toggle at INFO level.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/data_imputation.R | 9 +++++++++
 inst/shiny/modules/tab_nca/setup/settings.R        | 1 +
 2 files changed, 10 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/data_imputation.R b/inst/shiny/modules/tab_nca/setup/data_imputation.R
index eb5c5f6f9..065952f1c 100644
--- a/inst/shiny/modules/tab_nca/setup/data_imputation.R
+++ b/inst/shiny/modules/tab_nca/setup/data_imputation.R
@@ -196,6 +196,15 @@ data_imputation_server <- function(id, settings_override) {
       }
     })
 
+    observeEvent(input$select_blq_strategy, {
+      log_info("BLQ imputation strategy changed: {input$select_blq_strategy}")
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$should_impute_c0, {
+      state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
+      log_info("Start concentration imputation {state}")
+    }, ignoreInit = TRUE)
+
     blq_imputation_rule <- reactive({
       req(input$select_blq_strategy)
       rule_list <- switch(input$select_blq_strategy,
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 9fdac1834..c4b5eb9ba 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -260,6 +260,7 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         available_choices = profile_choices,
         override_val = settings$profile
       )
+      log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
       updatePickerInput(
         session, "select_profile",
         choices = profile_choices, selected = target_profile

From 91ca90b5b2e2149bfbe0a216f03e2e7a0f6d852b Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 13:20:38 +0000
Subject: [PATCH 07/23] fix: use paste-style logging to avoid glue parent.frame
 issues

Replace all glue-style log calls ({var}) with paste-style
(multiple arguments) to avoid parent.frame(2) scoping issues
in closures and observeEvent callbacks. Guard profile log
against NA values.

Co-authored-by: Ona <no-reply@ona.com>
---
 .../modules/tab_nca/setup/data_imputation.R   |  4 ++--
 .../tab_nca/setup/parameter_selection.R       |  2 +-
 inst/shiny/modules/tab_nca/setup/settings.R   | 23 +++++++++++--------
 .../modules/tab_nca/setup/slope_selector.R    |  2 +-
 4 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/data_imputation.R b/inst/shiny/modules/tab_nca/setup/data_imputation.R
index 065952f1c..a793c08ba 100644
--- a/inst/shiny/modules/tab_nca/setup/data_imputation.R
+++ b/inst/shiny/modules/tab_nca/setup/data_imputation.R
@@ -197,12 +197,12 @@ data_imputation_server <- function(id, settings_override) {
     })
 
     observeEvent(input$select_blq_strategy, {
-      log_info("BLQ imputation strategy changed: {input$select_blq_strategy}")
+      log_info("BLQ imputation strategy changed: ", input$select_blq_strategy)
     }, ignoreInit = TRUE)
 
     observeEvent(input$should_impute_c0, {
       state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
-      log_info("Start concentration imputation {state}")
+      log_info("Start concentration imputation ", state)
     }, ignoreInit = TRUE)
 
     blq_imputation_rule <- reactive({
diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 474a3a808..5b9b8df80 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -288,7 +288,7 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
 
           log_info("Parameter selection for '{study_type}': {n_params} parameters selected.")
           if (n_params > 0) {
-            log_debug("Parameters for '{study_type}': ", paste(params, collapse = ", "))
+            log_debug("Parameters for '", study_type, "': ", paste(params, collapse = ", "))
           }
         }, ignoreNULL = FALSE, ignoreInit = TRUE)
       })
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index c4b5eb9ba..a6817ea6b 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -260,7 +260,9 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         available_choices = profile_choices,
         override_val = settings$profile
       )
-      log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
+      if (length(target_profile) > 0 && !anyNA(target_profile)) {
+        log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
+      }
       updatePickerInput(
         session, "select_profile",
         choices = profile_choices, selected = target_profile
@@ -335,11 +337,11 @@ settings_server <- function(id, data, adnca_data, settings_override) {
 
     # Log method and min half-life points changes
     observeEvent(input$method, {
-      log_info("Extrapolation method changed: {input$method}")
+      log_info("Extrapolation method changed: ", input$method)
     }, ignoreInit = TRUE)
 
     observeEvent(input$min_hl_points, {
-      log_info("Min. half-life points changed: {input$min_hl_points}")
+      log_info("Min. half-life points changed: ", input$min_hl_points)
     }, ignoreInit = TRUE)
 
     # Include keyboard limits for the settings GUI display
@@ -352,14 +354,15 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "min_hl_points", max = 10, min = 2, lab = "Min. HL Points")
 
     # Log flag rule changes
-    .flag_names <- c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN")
-    lapply(.flag_names, function(flag) {
-      observeEvent(input[[paste0(flag, "_rule")]], {
-        state <- if (input[[paste0(flag, "_rule")]]) "enabled" else "disabled"
-        log_info("Flag rule {flag} {state}")
+    lapply(c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN"), function(flag) {
+      rule_id <- paste0(flag, "_rule")
+      threshold_id <- paste0(flag, "_threshold")
+      observeEvent(input[[rule_id]], {
+        state <- if (input[[rule_id]]) "enabled" else "disabled"
+        log_info("Flag rule ", flag, " ", state)
       }, ignoreInit = TRUE)
-      observeEvent(input[[paste0(flag, "_threshold")]], {
-        log_info("Flag rule {flag} threshold changed: {input[[paste0(flag, '_threshold')]]}")
+      observeEvent(input[[threshold_id]], {
+        log_info("Flag rule ", flag, " threshold changed: ", input[[threshold_id]])
       }, ignoreInit = TRUE)
     })
 
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index a903b76b6..7be204110 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -253,7 +253,7 @@ slope_selector_server <- function( # nolint
       n_rules <- nrow(manual_slopes())
       n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
       n_incl <- n_rules - n_excl
-      log_debug("Slope rules updated: {n_rules} total ({n_incl} inclusions, {n_excl} exclusions)")
+      log_debug("Slope rules updated: ", n_rules, " total (", n_incl, " inclusions, ", n_excl, " exclusions)")
 
       # Update reactable with rules
       reactable::updateReactable(

From 47f533b8f87551b9f3480e766062ca3bf05e26fd Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:03:20 +0000
Subject: [PATCH 08/23] feat: add log-points for NCA settings changes

Log analyte, specimen, profile, method, min half-life points,
and flag rule changes at INFO level.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/settings.R | 25 +++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index b8818a9f4..e9f78c707 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -301,6 +301,8 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
+      log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))
+
       settings <- .consume_settings()
 
       all_pcspec <- unique(data()$PCSPEC) %>% na.omit()
@@ -335,6 +337,8 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
+      log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))
+
       settings <- .consume_settings()
 
       all_analyte <- unique(data()$PARAM) %>% na.omit()
@@ -356,6 +360,15 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       .update_profile(settings)
     })
 
+    # Log method and min half-life points changes
+    observeEvent(input$method, {
+      log_info("Extrapolation method changed: {input$method}")
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$min_hl_points, {
+      log_info("Min. half-life points changed: {input$min_hl_points}")
+    }, ignoreInit = TRUE)
+
     # Include keyboard limits for the settings GUI display
 
     # Keyboard limits for the setting thresholds
@@ -365,6 +378,18 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "LAMZSPN_threshold", min = 0, lab = "LAMZSPN")
     limit_input_value(input, session, "min_hl_points", max = 10, min = 2, lab = "Min. HL Points")
 
+    # Log flag rule changes
+    .flag_names <- c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN")
+    lapply(.flag_names, function(flag) {
+      observeEvent(input[[paste0(flag, "_rule")]], {
+        state <- if (input[[paste0(flag, "_rule")]]) "enabled" else "disabled"
+        log_info("Flag rule {flag} {state}")
+      }, ignoreInit = TRUE)
+      observeEvent(input[[paste0(flag, "_threshold")]], {
+        log_info("Flag rule {flag} threshold changed: {input[[paste0(flag, '_threshold')]]}")
+      }, ignoreInit = TRUE)
+    })
+
     # Reactive value to store the partial intervals data table
     # Define the parameters that can be used for partial area calculations
     PARTIAL_INT_PARAMS <- metadata_nca_parameters %>%

From 550e0bb0f5d4570e580fc6a482e8178fed1bbbe0 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:03:32 +0000
Subject: [PATCH 09/23] feat: add debug log-point for selected parameter names

Log the full list of selected parameters at DEBUG level
alongside the existing INFO count message.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/parameter_selection.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 5d5e860fe..474a3a808 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -287,6 +287,9 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
           n_params <- if (is.null(params)) 0 else length(params)
 
           log_info("Parameter selection for '{study_type}': {n_params} parameters selected.")
+          if (n_params > 0) {
+            log_debug("Parameters for '{study_type}': ", paste(params, collapse = ", "))
+          }
         }, ignoreNULL = FALSE, ignoreInit = TRUE)
       })
     })

From b3785048dd3e4a30872cae259722f2151e82a04c Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:04:00 +0000
Subject: [PATCH 10/23] feat: add log-points for slope selector user actions

Upgrade slope rule add/remove from TRACE to INFO level.
Add DEBUG summary of slope rules count on table changes.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/manual_slopes_table.R | 4 ++--
 inst/shiny/modules/tab_nca/setup/slope_selector.R      | 5 +++++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
index 5475c0466..88bd9db3f 100644
--- a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
+++ b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
@@ -93,7 +93,7 @@ manual_slopes_table_server <- function(
 
     # Add a new row to the table when the user clicks the add button
     observeEvent(input$add_rule, {
-      log_trace("{id}: adding manual slopes row")
+      log_info("Slope selector: adding manual slope rule")
       first_group <- slopes_pknca_groups()[1, ]
       time_col <- pknca_data()$conc$columns$time
       new_row <- cbind(
@@ -126,7 +126,7 @@ manual_slopes_table_server <- function(
 
     # Remove selected rows from the table when the user clicks the remove button
     observeEvent(input$remove_rule, {
-      log_trace("{id}: removing manual slopes row")
+      log_info("Slope selector: removing manual slope rule")
       selected <- getReactableState("manual_slopes", "selected")
       req(selected)
       edited_slopes <- manual_slopes()[-selected, ]
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 7f3cfe0f1..15575e5e1 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -272,6 +272,11 @@ slope_selector_server <- function( # nolint
     observeEvent(manual_slopes(), {
       req(manual_slopes())
 
+      n_rules <- nrow(manual_slopes())
+      n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
+      n_incl <- n_rules - n_excl
+      log_debug("Slope rules updated: {n_rules} total ({n_incl} inclusions, {n_excl} exclusions)")
+
       # Update reactable with rules
       reactable::updateReactable(
         outputId = "manual_slopes",

From 12273876fe4fbd98e496993b577805bbe2b3cf9c Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:04:39 +0000
Subject: [PATCH 11/23] feat: add log-points for general exclusion changes

Log exclusion add (with row count, type, reason), removal,
and settings restore at INFO level.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 .../modules/tab_nca/setup/general_exclusions.R  | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/general_exclusions.R b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
index 157258962..6de6c2220 100644
--- a/inst/shiny/modules/tab_nca/setup/general_exclusions.R
+++ b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
@@ -131,6 +131,7 @@ general_exclusions_server <- function(
 
         xbtn_counter(max(new_ids))
         exclusion_list(rehydrated_list)
+        log_info("Exclusions restored from settings: ", length(overrides), " rules loaded")
       }
     })
 
@@ -156,6 +157,21 @@ general_exclusions_server <- function(
 
     # Add a new exclusion when the Add button is pressed
     observeEvent(input$add_exclusion_reason, {
+      rows_sel <- getReactableState("conc_table-table", "selected")
+      reason <- input$exclusion_reason
+      nca_checked <- isTRUE(input$cb_manual_nca)
+      tlg_checked <- isTRUE(input$cb_tlg)
+
+      if (length(rows_sel) > 0 && nzchar(reason) && (nca_checked || tlg_checked)) {
+        type_label <- if (nca_checked && tlg_checked) "NCA + TLG"
+          else if (nca_checked) "NCA"
+          else "TLG"
+        log_info(
+          "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+          ", reason='", reason, "'"
+        )
+      }
+
       .handle_add_exclusion(
         input, session, exclusion_list, xbtn_counter
       )
@@ -167,6 +183,7 @@ general_exclusions_server <- function(
       lapply(lst, function(item) {
         xbtn_id <- item$xbtn_id
         observeEvent(input[[xbtn_id]], {
+          log_info("Exclusion removed: reason='", item$reason, "'")
           current <- exclusion_list()
           exclusion_list(
             Filter(function(x) x$xbtn_id != xbtn_id, current)

From dacc0c2c98e2c68d76a34b54f4ccf2733b01626f Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:05:02 +0000
Subject: [PATCH 12/23] feat: add log-points for profile selection and data
 imputation

Log NCA profile changes, BLQ strategy changes, and C0
imputation toggle at INFO level.

Closes #1219 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/data_imputation.R | 9 +++++++++
 inst/shiny/modules/tab_nca/setup/settings.R        | 1 +
 2 files changed, 10 insertions(+)

diff --git a/inst/shiny/modules/tab_nca/setup/data_imputation.R b/inst/shiny/modules/tab_nca/setup/data_imputation.R
index eb5c5f6f9..065952f1c 100644
--- a/inst/shiny/modules/tab_nca/setup/data_imputation.R
+++ b/inst/shiny/modules/tab_nca/setup/data_imputation.R
@@ -196,6 +196,15 @@ data_imputation_server <- function(id, settings_override) {
       }
     })
 
+    observeEvent(input$select_blq_strategy, {
+      log_info("BLQ imputation strategy changed: {input$select_blq_strategy}")
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$should_impute_c0, {
+      state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
+      log_info("Start concentration imputation {state}")
+    }, ignoreInit = TRUE)
+
     blq_imputation_rule <- reactive({
       req(input$select_blq_strategy)
       rule_list <- switch(input$select_blq_strategy,
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index e9f78c707..4b0bbf535 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -288,6 +288,7 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         available_choices = profile_choices,
         override_val = settings$profile
       )
+      log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
       updatePickerInput(
         session, "select_profile",
         choices = profile_choices, selected = target_profile

From 893084b29126588a55753acbda649cfb4c317894 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 13:20:38 +0000
Subject: [PATCH 13/23] fix: use paste-style logging to avoid glue parent.frame
 issues

Replace all glue-style log calls ({var}) with paste-style
(multiple arguments) to avoid parent.frame(2) scoping issues
in closures and observeEvent callbacks. Guard profile log
against NA values.

Co-authored-by: Ona <no-reply@ona.com>
---
 .../modules/tab_nca/setup/data_imputation.R   |  4 ++--
 .../tab_nca/setup/parameter_selection.R       |  2 +-
 inst/shiny/modules/tab_nca/setup/settings.R   | 23 +++++++++++--------
 .../modules/tab_nca/setup/slope_selector.R    |  2 +-
 4 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/data_imputation.R b/inst/shiny/modules/tab_nca/setup/data_imputation.R
index 065952f1c..a793c08ba 100644
--- a/inst/shiny/modules/tab_nca/setup/data_imputation.R
+++ b/inst/shiny/modules/tab_nca/setup/data_imputation.R
@@ -197,12 +197,12 @@ data_imputation_server <- function(id, settings_override) {
     })
 
     observeEvent(input$select_blq_strategy, {
-      log_info("BLQ imputation strategy changed: {input$select_blq_strategy}")
+      log_info("BLQ imputation strategy changed: ", input$select_blq_strategy)
     }, ignoreInit = TRUE)
 
     observeEvent(input$should_impute_c0, {
       state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
-      log_info("Start concentration imputation {state}")
+      log_info("Start concentration imputation ", state)
     }, ignoreInit = TRUE)
 
     blq_imputation_rule <- reactive({
diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 474a3a808..5b9b8df80 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -288,7 +288,7 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
 
           log_info("Parameter selection for '{study_type}': {n_params} parameters selected.")
           if (n_params > 0) {
-            log_debug("Parameters for '{study_type}': ", paste(params, collapse = ", "))
+            log_debug("Parameters for '", study_type, "': ", paste(params, collapse = ", "))
           }
         }, ignoreNULL = FALSE, ignoreInit = TRUE)
       })
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 4b0bbf535..0b4d39fc1 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -288,7 +288,9 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         available_choices = profile_choices,
         override_val = settings$profile
       )
-      log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
+      if (length(target_profile) > 0 && !anyNA(target_profile)) {
+        log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
+      }
       updatePickerInput(
         session, "select_profile",
         choices = profile_choices, selected = target_profile
@@ -363,11 +365,11 @@ settings_server <- function(id, data, adnca_data, settings_override) {
 
     # Log method and min half-life points changes
     observeEvent(input$method, {
-      log_info("Extrapolation method changed: {input$method}")
+      log_info("Extrapolation method changed: ", input$method)
     }, ignoreInit = TRUE)
 
     observeEvent(input$min_hl_points, {
-      log_info("Min. half-life points changed: {input$min_hl_points}")
+      log_info("Min. half-life points changed: ", input$min_hl_points)
     }, ignoreInit = TRUE)
 
     # Include keyboard limits for the settings GUI display
@@ -380,14 +382,15 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "min_hl_points", max = 10, min = 2, lab = "Min. HL Points")
 
     # Log flag rule changes
-    .flag_names <- c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN")
-    lapply(.flag_names, function(flag) {
-      observeEvent(input[[paste0(flag, "_rule")]], {
-        state <- if (input[[paste0(flag, "_rule")]]) "enabled" else "disabled"
-        log_info("Flag rule {flag} {state}")
+    lapply(c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN"), function(flag) {
+      rule_id <- paste0(flag, "_rule")
+      threshold_id <- paste0(flag, "_threshold")
+      observeEvent(input[[rule_id]], {
+        state <- if (input[[rule_id]]) "enabled" else "disabled"
+        log_info("Flag rule ", flag, " ", state)
       }, ignoreInit = TRUE)
-      observeEvent(input[[paste0(flag, "_threshold")]], {
-        log_info("Flag rule {flag} threshold changed: {input[[paste0(flag, '_threshold')]]}")
+      observeEvent(input[[threshold_id]], {
+        log_info("Flag rule ", flag, " threshold changed: ", input[[threshold_id]])
       }, ignoreInit = TRUE)
     })
 
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 15575e5e1..dd4f6ce8e 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -275,7 +275,7 @@ slope_selector_server <- function( # nolint
       n_rules <- nrow(manual_slopes())
       n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
       n_incl <- n_rules - n_excl
-      log_debug("Slope rules updated: {n_rules} total ({n_incl} inclusions, {n_excl} exclusions)")
+      log_debug("Slope rules updated: ", n_rules, " total (", n_incl, " inclusions, ", n_excl, " exclusions)")
 
       # Update reactable with rules
       reactable::updateReactable(

From 0eb099fc4b4d8c4b37b0f512aaa6e5a1f65e32b6 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:05:46 +0000
Subject: [PATCH 14/23] feat: add header block to exported session_log.txt

Include explanation of what the log captures, current threshold,
visible levels, and a link to the full reference page.

Closes #1220 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/functions/zip-utils.R | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/inst/shiny/functions/zip-utils.R b/inst/shiny/functions/zip-utils.R
index 54feab18b..8054ec202 100644
--- a/inst/shiny/functions/zip-utils.R
+++ b/inst/shiny/functions/zip-utils.R
@@ -651,10 +651,38 @@ prepare_export_files <- function(target_dir,
 #' @keywords internal
 .export_session_log <- function(target_dir) {
   log_buffer <- get_log_buffer()
+
+  threshold <- .log_env$threshold
+  header <- c(
+    "# aNCA Session Log",
+    "#",
+    "# This file contains application events captured during your session.",
+    "# It records data upload, mapping, NCA settings, parameter selection,",
+    "# slope adjustments, exclusions, calculation results, and exports.",
+    "#",
+    "# Warnings and errors from these operations are included when caught",
+    "# by the application. Unexpected R errors or warnings from third-party",
+    "# packages that are not explicitly handled will NOT appear here.",
+    "#",
+    paste0("# Log level: ", threshold,
+           " (configurable via aNCA_LOG_LEVEL env var)"),
+    paste0("# Levels shown at current threshold: ",
+           paste(names(.LOG_LEVELS)[.LOG_LEVELS >= .LOG_LEVELS[[threshold]]],
+                 collapse = ", ")),
+    "#",
+    "# For a full reference of logged events, see:",
+    "# https://pharmaverse.github.io/aNCA/articles/session_log.html",
+    "#",
+    paste0("# Generated: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z")),
+    "# -------------------------------------------------------------------",
+    ""
+  )
+
   if (length(log_buffer) == 0L) {
     log_buffer <- "(No log entries captured during this session.)"
   }
-  writeLines(log_buffer, file.path(target_dir, "session_log.txt"))
+
+  writeLines(c(header, log_buffer), file.path(target_dir, "session_log.txt"))
 }
 
 #' Clean Export Directory

From a12157389655dee927399f42fcb4d04e21e5dd6e Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:06:23 +0000
Subject: [PATCH 15/23] docs: add session log reference vignette

Developer website page documenting all logged events by workflow
stage, log levels, and configuration via aNCA_LOG_LEVEL.

Closes #1220 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 vignettes/session_log.Rmd | 201 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 201 insertions(+)
 create mode 100644 vignettes/session_log.Rmd

diff --git a/vignettes/session_log.Rmd b/vignettes/session_log.Rmd
new file mode 100644
index 000000000..183575b3f
--- /dev/null
+++ b/vignettes/session_log.Rmd
@@ -0,0 +1,201 @@
+---
+title: "Session Log Reference"
+description: >
+  Reference for the session log exported with aNCA results.
+  Describes what events are captured, log levels, and configuration.
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Session Log Reference}
+  %\VignetteEngine{knitr::knitr}
+  %\VignetteEncoding{UTF-8}
+---
+
+When you export results as a ZIP file, aNCA includes a `session_log.txt` that
+records application events from your session. This page explains what the log
+contains, how to read it, and how to configure its verbosity.
+
+## What the log captures
+
+The session log records events emitted by explicit logging calls placed
+throughout the aNCA Shiny application. Each line follows this format:
+
+```
+[2025-04-30 09:40:16] INFO: Calculating NCA results...
+```
+
+The log captures **application-level events** — not raw R console output.
+Only messages that pass through aNCA's internal `log_*()` functions appear
+in the file.
+
+### What is NOT captured
+
+- Unexpected R warnings or errors that are not wrapped in a `tryCatch` block
+  with a corresponding `log_warn()` or `log_error()` call.
+- Messages from third-party packages (e.g., `PKNCA`, `dplyr`) unless the
+  application explicitly catches and logs them.
+- Raw `cat()` or `print()` output from any source.
+
+## Log levels
+
+aNCA uses six log levels, ordered from most to least verbose:
+
+| Level | Purpose |
+|---|---|
+| **TRACE** | Fine-grained internal operations (module attachment, reactive updates) |
+| **DEBUG** | Detailed diagnostic data (parameter lists, slope rule dumps) |
+| **INFO** | Key user-facing operations (data upload, NCA calculation, setting changes) |
+| **SUCCESS** | Completion confirmations (data loaded, results calculated) |
+| **WARN** | Non-fatal issues (calculation warnings, incompatible settings) |
+| **ERROR** | Failures (calculation errors, file load failures) |
+
+The default threshold is **INFO**, meaning only INFO, SUCCESS, WARN, and ERROR
+messages appear. Set `aNCA_LOG_LEVEL=TRACE` or `aNCA_LOG_LEVEL=DEBUG` in your
+`.Renviron` file to see more detail.
+
+## Logged events by workflow stage
+
+The following table lists all events currently captured in the session log,
+organized by the stage of the workflow where they occur.
+
+### Startup
+
+| Event | Level |
+|---|---|
+| Application startup | INFO |
+| Application restarting | INFO |
+
+### Data Upload
+
+| Event | Level |
+|---|---|
+| Data upload initialized (with file path) | INFO |
+| All user data loaded | SUCCESS |
+| File loading errors | ERROR |
+| User data binding errors | ERROR |
+
+### Settings Restore
+
+| Event | Level |
+|---|---|
+| Settings restored from version | SUCCESS |
+| Settings loaded from file | SUCCESS |
+| Settings load failure | ERROR |
+| Incompatible settings (analyte, profile, specimen) | WARN |
+
+### Data Mapping
+
+| Event | Level |
+|---|---|
+| Processing data mapping | INFO |
+| Data mapping warnings | WARN |
+| Data mapping errors | ERROR |
+
+### Data Filtering
+
+| Event | Level |
+|---|---|
+| Data filtering warnings | WARN |
+
+### NCA Settings
+
+| Event | Level |
+|---|---|
+| Analyte selection changed | INFO |
+| Specimen selection changed | INFO |
+| NCA profile selection changed | INFO |
+| Extrapolation method changed | INFO |
+| Min. half-life points changed | INFO |
+| Flag rule enabled/disabled | INFO |
+| Flag rule threshold changed | INFO |
+| BLQ imputation strategy changed | INFO |
+| Start concentration imputation toggled | INFO |
+
+### Parameter Selection
+
+| Event | Level |
+|---|---|
+| Parameter count per study type | INFO |
+| Full parameter list per study type | DEBUG |
+
+### Slope Selector
+
+| Event | Level |
+|---|---|
+| Module server attachment | TRACE |
+| Plotly click detected | TRACE |
+| Manual slope rule added | INFO |
+| Manual slope rule removed | INFO |
+| Slope rules summary (inclusions/exclusions count) | DEBUG |
+| Manual slopes override applied | DEBUG |
+| Manual slopes override incompatible | WARN |
+| Slope edit table rendering | TRACE |
+
+### General Exclusions
+
+| Event | Level |
+|---|---|
+| Exclusion added (row count, type, reason) | INFO |
+| Exclusion removed | INFO |
+| Exclusions restored from settings | INFO |
+
+### NCA Calculation
+
+| Event | Level |
+|---|---|
+| Creating / updating PKNCA data object | TRACE |
+| PKNCA data object created | SUCCESS |
+| PKNCA data object creation error | ERROR |
+| Updating parameter selection data | TRACE |
+| Calculating NCA results | INFO |
+| NCA calculation warnings | WARN |
+| NCA results calculated | SUCCESS |
+| NCA calculation error | ERROR |
+| Invalid parameters | ERROR |
+
+### Exploration Plots
+
+| Event | Level |
+|---|---|
+| Rendering individual plots | INFO |
+| Computing mean plot | INFO |
+| Rendering boxplot | INFO |
+| Exploration plot saved (with overwrite flag) | INFO |
+| Exploration plot removed | INFO |
+
+### TLG Generation
+
+| Event | Level |
+|---|---|
+| TLG module server attachment | TRACE |
+| Submitted TLG list | DEBUG |
+| TLG list rendering error | ERROR |
+
+### Export
+
+| Event | Level |
+|---|---|
+| Downloading summary statistics as CSV | INFO |
+
+### Units & Other
+
+| Event | Level |
+|---|---|
+| Applying custom units specification | TRACE |
+
+## Configuring the log level
+
+Set the `aNCA_LOG_LEVEL` environment variable before starting the app.
+Valid values: `TRACE`, `DEBUG`, `INFO` (default), `SUCCESS`, `WARN`, `ERROR`.
+
+In your `.Renviron` file:
+
+```
+aNCA_LOG_LEVEL=DEBUG
+```
+
+Or set it in R before launching:
+
+```r
+Sys.setenv(aNCA_LOG_LEVEL = "TRACE")
+aNCA::run_app()
+```

From 6400c057c63f8cb97cfc21aa7ff1ebcac756ecd7 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:06:40 +0000
Subject: [PATCH 16/23] docs: add session log page to pkgdown navbar

Add 'Session Log Reference' entry under Developer Resources
in the website navigation.

Closes #1220 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 pkgdown/_pkgdown.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 815656825..392b6ecfe 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -29,6 +29,8 @@ navbar:
           href: articles/adding_tlg.html
         - text: Design & Architecture
           href: articles/design.html
+        - text: Session Log Reference
+          href: articles/session_log.html
         - text: Functions manual
           href: reference/index.html
     project:

From f62eaf291725923bd94ae852b1d87ea4232f5b75 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Tue, 14 Apr 2026 10:06:55 +0000
Subject: [PATCH 17/23] docs: add scope and reference link to logging.R header

Clarify what the log captures vs. what it does not, and link
to the full session log reference page.

Closes #1220 (partial)

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/functions/logging.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/inst/shiny/functions/logging.R b/inst/shiny/functions/logging.R
index 4a13a242c..ce29dedbc 100644
--- a/inst/shiny/functions/logging.R
+++ b/inst/shiny/functions/logging.R
@@ -6,6 +6,14 @@
 #
 # Log levels: TRACE < DEBUG < INFO < SUCCESS < WARN < ERROR
 # Default threshold: INFO (configurable via aNCA_LOG_LEVEL env var).
+#
+# The log captures application-level events only — not raw R console
+# output. Warnings and errors from third-party packages appear only
+# when explicitly caught by tryCatch blocks with log_warn/log_error.
+#
+# The in-memory buffer is exported as session_log.txt in the ZIP
+# download. For a full reference of logged events, see:
+# https://pharmaverse.github.io/aNCA/articles/session_log.html
 
 .log_env <- new.env(parent = emptyenv())
 .log_env$threshold <- "INFO"

From b26843bb3132024bba7559971d4d78bda3906daf Mon Sep 17 00:00:00 2001
From: Gero1999 <gerardojoro@gmail.com>
Date: Mon, 20 Apr 2026 13:43:42 +0200
Subject: [PATCH 18/23] refactor lintr

---
 inst/shiny/modules/tab_tlg.R | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/inst/shiny/modules/tab_tlg.R b/inst/shiny/modules/tab_tlg.R
index 83bcbaf0e..278219205 100644
--- a/inst/shiny/modules/tab_tlg.R
+++ b/inst/shiny/modules/tab_tlg.R
@@ -250,7 +250,11 @@ tab_tlg_server <- function(id, data) {
       panels <- lapply(tlg_order_graphs, function(g_id) {
         graph_ui <- {
           g_def <- .TLG_DEFINITIONS[[g_id]]
-          module_id <- paste0(g_id, paste0(sample(c(letters, 0:9), 5, replace = TRUE), collapse = ""))
+          module_id <- paste0(
+            g_id,
+            paste0(sample(c(letters, 0:9), 5, replace = TRUE),
+                   collapse = "")
+          )
 
           if (exists(g_def$fun)) {
             tlg_module_server(module_id, data, "graph", get(g_def$fun), g_def$options)
@@ -288,7 +292,11 @@ tab_tlg_server <- function(id, data) {
         panels <- lapply(tlg_order_listings, function(g_id) {
           list_ui <- {
             g_def <- .TLG_DEFINITIONS[[g_id]]
-            module_id <- paste0(g_id, paste0(sample(c(letters, 0:9), 5, replace = TRUE), collapse = ""))
+            module_id <- paste0(
+              g_id,
+              paste0(sample(c(letters, 0:9), 5, replace = TRUE),
+                     collapse = "")
+            )
 
             if (exists(g_def$fun)) {
               tlg_module_server(module_id, data, "listing", get(g_def$fun), g_def$options)

From 2a347e1898c18bf4ef0e93f7aac156f616150c62 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Mon, 20 Apr 2026 11:46:38 +0000
Subject: [PATCH 19/23] refactor: unify slope selector logging into single
 table-change message

Replace separate add/remove INFO messages with a single INFO
summary that fires on any slope table change (button clicks,
plotly point selections, cell edits). Demote add/remove to TRACE.

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/manual_slopes_table.R | 4 ++--
 inst/shiny/modules/tab_nca/setup/slope_selector.R      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
index 88bd9db3f..c70de323f 100644
--- a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
+++ b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
@@ -93,7 +93,7 @@ manual_slopes_table_server <- function(
 
     # Add a new row to the table when the user clicks the add button
     observeEvent(input$add_rule, {
-      log_info("Slope selector: adding manual slope rule")
+      log_trace("Slope selector: adding manual slope rule")
       first_group <- slopes_pknca_groups()[1, ]
       time_col <- pknca_data()$conc$columns$time
       new_row <- cbind(
@@ -126,7 +126,7 @@ manual_slopes_table_server <- function(
 
     # Remove selected rows from the table when the user clicks the remove button
     observeEvent(input$remove_rule, {
-      log_info("Slope selector: removing manual slope rule")
+      log_trace("Slope selector: removing manual slope rule")
       selected <- getReactableState("manual_slopes", "selected")
       req(selected)
       edited_slopes <- manual_slopes()[-selected, ]
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index dd4f6ce8e..dbef48589 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -275,7 +275,7 @@ slope_selector_server <- function( # nolint
       n_rules <- nrow(manual_slopes())
       n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
       n_incl <- n_rules - n_excl
-      log_debug("Slope rules updated: ", n_rules, " total (", n_incl, " inclusions, ", n_excl, " exclusions)")
+      log_info("Slope rules updated: ", n_rules, " total (", n_incl, " inclusions, ", n_excl, " exclusions)")
 
       # Update reactable with rules
       reactable::updateReactable(

From 1cb62440b42d7c919414488120044645c99007b9 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Thu, 23 Apr 2026 07:32:04 +0000
Subject: [PATCH 20/23] fix: address review feedback on log-points

- Suppress analyte/specimen/profile logs during initial data load
  using a filters_initialized guard
- Move profile log to dedicated observeEvent(input$select_profile)
  with ignoreInit = TRUE
- Move exclusion-add logging inside .handle_add_exclusion to avoid
  duplicating input reads
- Use 'selections' instead of 'inclusions' in slope log to match
  the UI terminology (TYPE == 'Selection')

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/functions/utils-exclusions.R       |  6 ++++
 .../tab_nca/setup/general_exclusions.R        | 15 ----------
 inst/shiny/modules/tab_nca/setup/settings.R   | 28 ++++++++++++++-----
 .../modules/tab_nca/setup/slope_selector.R    |  2 +-
 4 files changed, 28 insertions(+), 23 deletions(-)

diff --git a/inst/shiny/functions/utils-exclusions.R b/inst/shiny/functions/utils-exclusions.R
index 95c543eca..c2cdf22e4 100644
--- a/inst/shiny/functions/utils-exclusions.R
+++ b/inst/shiny/functions/utils-exclusions.R
@@ -90,6 +90,12 @@ EXCL_COLOR_BOTH <- "#FFD9B3"  # orange — NCA + TLG
     exclusion_list(append(current, list_new_reason))
     updateTextInput(session, "exclusion_reason", value = "")
     updateReactable(table_id, selected = NA)
+
+    type_label <- .exclusion_type_label(nca_checked, tlg_checked)
+    log_info(
+      "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+      ", reason='", reason, "'"
+    )
   }
 }
 
diff --git a/inst/shiny/modules/tab_nca/setup/general_exclusions.R b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
index 6de6c2220..4fe331d3e 100644
--- a/inst/shiny/modules/tab_nca/setup/general_exclusions.R
+++ b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
@@ -157,21 +157,6 @@ general_exclusions_server <- function(
 
     # Add a new exclusion when the Add button is pressed
     observeEvent(input$add_exclusion_reason, {
-      rows_sel <- getReactableState("conc_table-table", "selected")
-      reason <- input$exclusion_reason
-      nca_checked <- isTRUE(input$cb_manual_nca)
-      tlg_checked <- isTRUE(input$cb_tlg)
-
-      if (length(rows_sel) > 0 && nzchar(reason) && (nca_checked || tlg_checked)) {
-        type_label <- if (nca_checked && tlg_checked) "NCA + TLG"
-          else if (nca_checked) "NCA"
-          else "TLG"
-        log_info(
-          "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
-          ", reason='", reason, "'"
-        )
-      }
-
       .handle_add_exclusion(
         input, session, exclusion_list, xbtn_counter
       )
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 0b4d39fc1..912da6404 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -258,6 +258,10 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     # A guard flag prevents infinite observer loops.
     updating_filters <- reactiveVal(FALSE)
 
+    # Guard to suppress log noise during initial data load / settings restore.
+    # Set to TRUE after the first analyte cascade completes.
+    filters_initialized <- reactiveVal(FALSE)
+
     # settings_override is consumed once during the first cascade after
     # settings upload. After that, pending_settings is set to NULL so
     # subsequent user-driven changes are not overridden by stale values.
@@ -288,9 +292,6 @@ settings_server <- function(id, data, adnca_data, settings_override) {
         available_choices = profile_choices,
         override_val = settings$profile
       )
-      if (length(target_profile) > 0 && !anyNA(target_profile)) {
-        log_info("NCA profile selection changed: ", paste(target_profile, collapse = ", "))
-      }
       updatePickerInput(
         session, "select_profile",
         choices = profile_choices, selected = target_profile
@@ -302,9 +303,14 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       req(data(), input$select_analyte)
       if (updating_filters()) return()
       updating_filters(TRUE)
-      on.exit(updating_filters(FALSE))
+      on.exit({
+        updating_filters(FALSE)
+        if (!filters_initialized()) filters_initialized(TRUE)
+      })
 
-      log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))
+      if (filters_initialized()) {
+        log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))
+      }
 
       settings <- .consume_settings()
 
@@ -340,7 +346,9 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
-      log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))
+      if (filters_initialized()) {
+        log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))
+      }
 
       settings <- .consume_settings()
 
@@ -363,7 +371,13 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       .update_profile(settings)
     })
 
-    # Log method and min half-life points changes
+    # Log profile, method, and min half-life points changes
+    observeEvent(input$select_profile, {
+      if (filters_initialized()) {
+        log_info("NCA profile changed: ", paste(input$select_profile, collapse = ", "))
+      }
+    }, ignoreInit = TRUE)
+
     observeEvent(input$method, {
       log_info("Extrapolation method changed: ", input$method)
     }, ignoreInit = TRUE)
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index dbef48589..88deb6b46 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -275,7 +275,7 @@ slope_selector_server <- function( # nolint
       n_rules <- nrow(manual_slopes())
       n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
       n_incl <- n_rules - n_excl
-      log_info("Slope rules updated: ", n_rules, " total (", n_incl, " inclusions, ", n_excl, " exclusions)")
+      log_info("Slope rules updated: ", n_rules, " total (", n_incl, " selections, ", n_excl, " exclusions)")
 
       # Update reactable with rules
       reactable::updateReactable(

From 07a2d6e952ebb0448a28283f40a2a72d4955886d Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Fri, 24 Apr 2026 12:30:12 +0000
Subject: [PATCH 21/23] fix: consistent paste-style logging and init guards

- Convert remaining glue-style log calls to paste-style
  (parameter_selection.R log_info, manual_slopes_table.R log_trace)
- Add filters_initialized guard to method and min_hl_points
  observers to suppress logs during settings restore

Co-authored-by: Ona <no-reply@ona.com>
---
 inst/shiny/modules/tab_nca/setup/manual_slopes_table.R | 2 +-
 inst/shiny/modules/tab_nca/setup/parameter_selection.R | 2 +-
 inst/shiny/modules/tab_nca/setup/settings.R            | 8 ++++++--
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
index c70de323f..b7f0c8f1a 100644
--- a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
+++ b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
@@ -138,7 +138,7 @@ manual_slopes_table_server <- function(
     # Render the manual slopes table (reactable)
     output$manual_slopes <- renderReactable({
       req(manual_slopes())
-      log_trace("{id}: rendering slope edit data table")
+      log_trace(id, ": rendering slope edit data table")
       isolate({
         data <- manual_slopes()
       })
diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 5b9b8df80..994b91908 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -286,7 +286,7 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
           params <- selection_debounce()
           n_params <- if (is.null(params)) 0 else length(params)
 
-          log_info("Parameter selection for '{study_type}': {n_params} parameters selected.")
+          log_info("Parameter selection for '", study_type, "': ", n_params, " parameters selected.")
           if (n_params > 0) {
             log_debug("Parameters for '", study_type, "': ", paste(params, collapse = ", "))
           }
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index 912da6404..a6fe79ba4 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -379,11 +379,15 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     }, ignoreInit = TRUE)
 
     observeEvent(input$method, {
-      log_info("Extrapolation method changed: ", input$method)
+      if (filters_initialized()) {
+        log_info("Extrapolation method changed: ", input$method)
+      }
     }, ignoreInit = TRUE)
 
     observeEvent(input$min_hl_points, {
-      log_info("Min. half-life points changed: ", input$min_hl_points)
+      if (filters_initialized()) {
+        log_info("Min. half-life points changed: ", input$min_hl_points)
+      }
     }, ignoreInit = TRUE)
 
     # Include keyboard limits for the settings GUI display

From 0d78d9506f64a8815b5d9e430757b04dd9d8ce69 Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Mon, 27 Apr 2026 09:12:53 +0000
Subject: [PATCH 22/23] fix: suppress slope log on programmatic updates

Add user_changed_slopes flag to only log slope rule changes
triggered by user actions (plotly clicks, add/remove buttons),
not by settings restore or initial render.

Co-authored-by: Ona <no-reply@ona.com>
---
 .../modules/tab_nca/setup/slope_selector.R    | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 88deb6b46..5c9f2a05c 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -246,6 +246,9 @@ slope_selector_server <- function( # nolint
     manual_slopes <- slopes_table$manual_slopes
     refresh_reactable <- slopes_table$refresh_reactable
 
+    # Track user-initiated slope changes (buttons, plotly clicks)
+    user_changed_slopes <- reactiveVal(FALSE)
+
     # Define the click events for the point exclusion and selection in the slope plots
     last_click_data <- reactiveVal(NULL)
     observeEvent(event_data("plotly_click", priority = "event"), {
@@ -259,6 +262,7 @@ slope_selector_server <- function( # nolint
       )
       # Update reactive values: last click & manual slopes table
       last_click_data(click_result$last_click_data)
+      user_changed_slopes(TRUE)
       manual_slopes(click_result$manual_slopes)
 
       # render rectable anew #
@@ -266,16 +270,24 @@ slope_selector_server <- function( # nolint
       refresh_reactable(refresh_reactable() + 1)
     })
 
+    # Also flag user-initiated changes from add/remove buttons
+    observeEvent(slopes_table$refresh_reactable(), {
+      user_changed_slopes(TRUE)
+    }, ignoreInit = TRUE)
+
     #' Separate event handling updating displayed reactable upon every change (adding and removing
     #' rows, plots selection, edits). This needs to be separate call, since simply re-rendering
     #' the table would mean losing focus on text inputs when entering values.
     observeEvent(manual_slopes(), {
       req(manual_slopes())
 
-      n_rules <- nrow(manual_slopes())
-      n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
-      n_incl <- n_rules - n_excl
-      log_info("Slope rules updated: ", n_rules, " total (", n_incl, " selections, ", n_excl, " exclusions)")
+      if (user_changed_slopes()) {
+        n_rules <- nrow(manual_slopes())
+        n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
+        n_incl <- n_rules - n_excl
+        log_info("Slope rules updated: ", n_rules, " total (", n_incl, " selections, ", n_excl, " exclusions)")
+        user_changed_slopes(FALSE)
+      }
 
       # Update reactable with rules
       reactable::updateReactable(

From c0fe8c31bdbddbe4698c3dcca57040ef3323742c Mon Sep 17 00:00:00 2001
From: Gero1999 <Gero1999@users.noreply.github.com>
Date: Thu, 30 Apr 2026 14:38:14 +0000
Subject: [PATCH 23/23] fix: remove stale logger import and dead sub-module
 code

- Remove @importFrom logger log_info from imports-shiny.R and
  NAMESPACE (logger is no longer used, log_info is now in logging.R)
- Remove logger from DESCRIPTION Suggests (no remaining references)
- Remove dead observeEvent(study_types_list()) block from
  parameter_selection.R that referenced the old sub-module approach
  (param_selector_panel_server) which no longer exists in main
- Replace with debounced observer on selections_state() compatible
  with main's matrix-based parameter selection UI
- Update session_log.Rmd to remove DEBUG parameter list entry

Co-authored-by: Ona <no-reply@ona.com>
---
 DESCRIPTION                                   |  1 -
 NAMESPACE                                     |  2 +-
 R/imports-shiny.R                             |  1 -
 .../tab_nca/setup/parameter_selection.R       | 84 +++----------------
 vignettes/session_log.Rmd                     |  1 -
 5 files changed, 12 insertions(+), 77 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3ea2758d7..345d198e7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -66,7 +66,6 @@ Suggests:
     jsonlite,
     knitr,
     lintr (>= 3.2.0),
-    logger,
     markdown,
     mockery,
     nestcolor,
diff --git a/NAMESPACE b/NAMESPACE
index 55e4b9e59..03dacd0f5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -143,7 +143,7 @@ importFrom(glue,glue)
 importFrom(grid,convertUnit)
 importFrom(htmltools,tags)
 importFrom(htmlwidgets,onRender)
-importFrom(logger,log_info)
+
 importFrom(magrittr,`%>%`)
 importFrom(plotly,add_lines)
 importFrom(plotly,add_trace)
diff --git a/R/imports-shiny.R b/R/imports-shiny.R
index 119a2bfa7..2f6e36b92 100644
--- a/R/imports-shiny.R
+++ b/R/imports-shiny.R
@@ -7,7 +7,6 @@
 #' @importFrom bslib page_sidebar
 #' @importFrom htmltools tags
 #' @importFrom htmlwidgets onRender
-#' @importFrom logger log_info
 #' @importFrom reactable reactable
 #' @importFrom reactable.extras reactable_extras_dependency
 #' @importFrom shiny runApp
diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index 51b7e21b0..eb7cb590e 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -317,79 +317,17 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       )
     })
 
-    observeEvent(study_types_list(), {
-      req(selections_state())
-
-      current_types <- study_types_list()
-
-      # Define grouped structure of parameters for the sub-module
-      all_params_grouped <- all_params %>%
-        # Split the data frame into a list of data frames, one per TYPE
-        split(.$TYPE)
-
-      # Loop and create servers
-      map(current_types, function(study_type) {
-        # Define module ID
-        module_id <- gsub("[^A-Za-z0-9]", "_", study_type)
-
-        if (exists(module_id, envir = initialised_modules)) {
-          # If it exists, exit this iteration
-          return()
-        }
-
-        # If not, mark it as initialized
-        assign(module_id, TRUE, envir = initialised_modules)
-
-        current_type_selections <- reactive({
-          state <- selections_state()
-          req(state)
-          # Return vector of PKNCA codes where this study type is TRUE
-          state$PKNCA[state[[study_type]] == TRUE]
-        })
-
-        # Call the parameter selector panel server
-        selection_single_type_grouped <- param_selector_panel_server(
-          module_id,
-          all_params_grouped = all_params_grouped,
-          current_selection = current_type_selections
-        )
-
-        # Watch the module's return value
-        observeEvent(selection_single_type_grouped(), {
-          # Get the full master state
-          selections_df <- selections_state()
-
-          # Get the selected names from the module
-          selected_params <- selection_single_type_grouped()
-
-          # If the input is NULL (empty selection), treat it as an empty character vector
-          if (is.null(selected_params)) {
-            selected_params <- character(0)
-          }
-
-          # We compare the current state to the new state to avoid infinite loops
-          current_col <- selections_df[[study_type]]
-          new_col <- selections_df$PKNCA %in% selected_params
-
-          if (!identical(current_col, new_col)) {
-            selections_df[[study_type]] <- new_col
-            selections_state(selections_df)
-          }
-        }, ignoreNULL = FALSE, ignoreInit = TRUE)
-
-        selection_debounce <- debounce(selection_single_type_grouped, 2000)
-
-        observeEvent(selection_debounce(), {
-          params <- selection_debounce()
-          n_params <- if (is.null(params)) 0 else length(params)
-
-          log_info("Parameter selection for '", study_type, "': ", n_params, " parameters selected.")
-          if (n_params > 0) {
-            log_debug("Parameters for '", study_type, "': ", paste(params, collapse = ", "))
-          }
-        }, ignoreNULL = FALSE, ignoreInit = TRUE)
-      })
-    })
+    # Log parameter selection changes (debounced to avoid noise from rapid clicks)
+    selections_debounced <- debounce(selections_state, 2000)
+    observeEvent(selections_debounced(), {
+      state <- selections_debounced()
+      req(state)
+      study_types <- study_types_list()
+      for (st in study_types) {
+        n_params <- sum(state[[st]], na.rm = TRUE)
+        log_info("Parameter selection for '", st, "': ", n_params, " parameters selected.")
+      }
+    }, ignoreInit = TRUE)
 
     observeEvent(input$clear_all, {
       state <- selections_state()
diff --git a/vignettes/session_log.Rmd b/vignettes/session_log.Rmd
index 183575b3f..7e0d08546 100644
--- a/vignettes/session_log.Rmd
+++ b/vignettes/session_log.Rmd
@@ -115,7 +115,6 @@ organized by the stage of the workflow where they occur.
 | Event | Level |
 |---|---|
 | Parameter count per study type | INFO |
-| Full parameter list per study type | DEBUG |
 
 ### Slope Selector