Bulk Process TROLL Sonde Profiles

TROLL_profile_compiler() reads raw TROLL sonde data, identifies stationary periods, evaluates sensor stability for each parameter, optionally summarizes results, and provides optional plotting of raw and final summarized data.

Usage

TROLL_profile_compiler(
  path,
  depth_col = depth_m,
  datetime_col = DateTime,
  stn_depthrange = 0.1,
  stn_secs = 45,
  stn_rollwindow_secs = 10,
  stbl_settle_secs = 10,
  stbl_min_secs = 5,
  stbl_range_thresholds = NULL,
  summarize_data = TRUE,
  drop_cols = TRUE,
  plot = c(Final = FALSE, Stationary = FALSE),
  debug = FALSE
)

Arguments

path

Character. Path to the raw TROLL CSV file.

depth_col

Unquoted column name for water depth (numeric data).

datetime_col

Unquoted column name for date-time (POSIXct, POSIXt, or Date).

stn_depthrange

Numeric. Depth range threshold for is_stationary().

stn_secs

Numeric. Minimum time (seconds) required for a stationary block to be considered fully stationary (flagged by: is_stationary_status = 999).

stn_rollwindow_secs

Numeric. Window size (seconds) used to compute rolling range for stationary detection.

stbl_settle_secs

Numeric. Seconds to trim from the start of each stationary block.

stbl_min_secs

Numeric. Minimum seconds used to calculate a summary statistic if stability is not reached within a stationary period.

stbl_range_thresholds

Optional named numeric vector. Custom stability thresholds per parameter. See stability_ranges for defaults and naming.

summarize_data

Logical. If TRUE, returns both `$Flagged_Data` and `$Summary_Data` (medians) as a list.

drop_cols

Logical. If TRUE, removes intermediate processing columns.

plot

Logical or named logical vector. Controls optional plotting from is_stationary and TROLL_stable_summary. Default is c(Final = FALSE, Stationary = FALSE).

debug

Logical. If TRUE, prints the parameters being looped over during stability calculation to aid in debugging.

Value

The output depends on the summarize_data argument:

If summarize_data = FALSE

Returns a data.frame with original sensor data and appended _stable logical flags.

If summarize_data = TRUE

Returns a list containing:

• Flagged_Data: The full data frame with stability flags.

• Summary_Data: A summarized tibble of median sensor readings for each stable stationary period.

Details

This function executes the TROLL processing workflow in the following order:

1. Ingestion & Cleanup: Reads data via TROLL_read_data() and standardizes names via TROLL_rename_cols().

2. Stationary Detection: Uses is_stationary() to identify depths where the sonde was held steady. Arguments for this step are prefixed with stn_.

3. Stability Evaluation: Calls TROLL_sensor_stable() for each parameter to identify "equilibrated" data points. Arguments for this step are prefixed with stbl_. Core parameters in data are automatically detected from: troll_column_dictionary[troll_column_dictionary$stbl_calc==TRUE,].

4. Summarization: If requested, calculates median values for stable windows at each depth using TROLL_stable_summary().

5. Visualization: Optionally generates diagnostic plots comparing raw profiles to filtered stationary/stable points.

See also

TROLL_read_data, TROLL_rename_cols, is_stationary, TROLL_sensor_stable, TROLL_stable_summary

Examples

if (FALSE) { # \dontrun{
# Standard profile compilation
result <- TROLL_profile_compiler(
  path = "extdata/sonde_file.csv",
  depth_col = depth_m,
  datetime_col = DateTime,
  stn_depthrange = 0.1,
  stn_secs = 45,
  stbl_min_secs = 5,
  plot = c(Final = TRUE, Stationary = FALSE)
)

# Access results
head(result$Flagged_Data)
head(result$Summary_Data)
} # }