Analyse methanol burn experiment

Usage

analyse_methanol_burn(
  filepath,
  methanolfilepath,
  room1 = TRUE,
  datetime_format = "%d-%m-%y %H:%M",
  code = "id",
  manual = NULL,
  save_csv = FALSE,
  path_to_save = NULL,
  combine = TRUE,
  method = "mean",
  start = NULL,
  end = NULL,
  notefilepath = NULL,
  keywords_dict = NULL,
  entry_exit_dict = NULL
)

Arguments

filepath

Path to the wric .txt file.

methanolfilepath

File path to a csv or Excel file with columns:

datetime: Timestamp of measurement, format %d-%m-%y %H:%M by default. Can override with datetime_format.
methanol: Methanol mass (g) at each timestamp.

room1

Logical; if TRUE uses room1 data from WRIC file, else room2. This is only relevant for files generates by software version 1. Default is TRUE.

datetime_format

Character; format string for parsing methanol datetime column. Default is "%d-%m-%y %H:%M" (25-03-25 13:58).

code

Method for generating subject IDs ("id", "id+comment", "study+id" (only for software v2), or "manual").

manual

Custom codes for subjects in Room 1 and Room 2 if code is "manual".

save_csv

Logical, whether to save extracted metadata and data to CSV files.

path_to_save

Directory path for saving CSV files, NULL uses the current directory.

combine

Logical, whether to combine S1 and S2 measurements.

method

Method for combining measurements ("mean", "median", "s1", "s2", "min", "max").

start

character or POSIXct or NULL, rows before this will be removed, if NULL takes first row e.g "2023-11-13 11:43:00"

end

character or POSIXct or NULL, rows after this will be removed, if NULL takes last row e.g "2023-11-13 11:43:00"

notefilepath

String, Directory path of the corresponding note file (.txt)

keywords_dict

List, A dictionary of keywords used to extract protocol events from a note file. Each entry should be a named list with:

keywords: A character vector of keywords or phrases to match in the note comment. Matching is case-insensitive.
value: Numeric protocol value to assign when the keyword is detected.
type: Optional character, either "instant" or omitted. "instant" events are applied at the specified timestamp and revert to the previous protocol immediately after. Non-instant events set the protocol until another event occurs.

Behavior rules:

Non-instant events: Set the protocol value from their timestamp until another event overwrites it or until a stop keyword sets it to 0.
Instant events: Apply only at the timestamp of the note line, then revert to the protocol that was active immediately before.
Stop keywords: Always set the protocol to 0, regardless of previous state, unless overridden by an instant event.

If NULL, a default set of keywords is used.

entry_exit_dict

Nested List, used to extract entry/exit times from note file

Value

A list with:

per_interval: Data frame with per-timestep methanol burn, predicted CO2/O2, measured VO2/VCO2, deviations, RER
overall: Summary for the whole session
plots: List of ggplot objects (values shown correspond to the end of each interval)

Examples

if (FALSE) { # file.exists(path.expand("~/methanol.xlsx"))
methanol <- source(path.expand("~/methanol.xlsx"))
data_txt <- system.file("extdata", "data.txt", package = "wrictools")
analyse_methanol_burn (data_txt, methanol, room1 = FALSE)
}