Read an 'Agilent ChemStation' method

Reads the pump, diode array detector, autosampler and column thermostat settings from the module register files (LPMP1.REG, LDAD1.REG, LALS1.REG or LWLS1.REG, and LTHM1.REG) of a 'ChemStation' .M method directory. Revisions that store a module's settings as 'RapidControl' XML (e.g. AgilentPumpDriver1.RapidControl.MethodXML.xml) instead are read as 'OpenLab CDS' methods are by read_agilent_amx.

Usage

read_chemstation_method(
  path,
  what = c("pump", "dad", "sampler", "column"),
  format_out = c("data.frame", "tibble", "data.table"),
  gradient_format = c("wide", "long")
)

Arguments

path: Path to a .M directory, or to a .D directory holding a copy of its method.
what: One or more instrument modules to read: any combination of "pump", "dad", "sampler" and "column". Defaults to all four.
format_out: Class of the solvents, gradient, signals and temp_controls tables: "data.frame", "tibble" or "data.table".
gradient_format: Whether to return the gradient in "wide" (default) or "long" format.

Value

A named list with one element per module read. A module the method has no settings for is left out with a warning, and it is an error if none of the requested modules are present. The sampler module is returned as autosampler. The elements are those of read_agilent_amx, with NA for a setting the method does not record:

pump: a list with scalar elements flow_mL_min, stop_time_min, post_time_min, pressure_low_bar and pressure_high_bar, plus:

solvents: a table of the channels in use, with columns channel, percentage (at the start of the run) and solvent (the name entered for it, or NA).
gradient: the timetable. Wide format: time_min and a pct_<channel> column per channel in use, plus flow_mL_min if the timetable sets the flow. Long format: time_min, channel and percent, where a flow channel holds the flow in mL/min. An empty timetable gives the starting composition at time 0.

dad: a list with scalar elements peakwidth_code, slitwidth_nm, uv_lamp_required, vis_lamp_required, spectra_from_nm, spectra_to_nm and spectra_step_nm, plus signals, a table of the stored signals with columns id, wavelength_nm, bandwidth_nm, reference_nm and reference_bandwidth_nm (NA without a reference). peakwidth_code is the stored code for the detector's peak width setting, which sets its data rate and response time; for example, 4 is "> 0.1 min". It is not decoded, since detector models offer different settings.

autosampler: a list with scalar elements thermostat_installed, draw_speed_uL_min, eject_speed_uL_min, wait_after_draw_min, injection_volume_uL and wash_time_s. Register files record only the speeds and the injection volume.

column: a list with scalar element post_time_min (NA when off), plus temp_controls, a two-row table (Left, Right) with columns side, temperature_C, not_ready_limit_C and equilibration_time_min. A temperature stored below absolute zero (e.g. -274) is NA; this may mean no temperature was set.

Details

Depending on how 'ChemStation' is configured, a .D directory may hold a copy of the method it was acquired with, in ACQ.M or, in older revisions, RUN.M. path can then be the .D directory itself. Its DA.M holds the data analysis method instead, whose pump settings may not be those the run was acquired with; reading it gives a warning.

The gradient follows the pump's timetable, with each parameter changing linearly between the times it is set. Channel A is the pump's primary channel and delivers whatever the other channels leave, so it is always included and its share is computed rather than read.

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
method <- read_chemstation_method("path/to/METHOD.M")
method$pump$gradient
} # }