Read Agilent AMX method file — read_agilent

Parses an Agilent .amx method archive, extracting instrument parameters from one or more of its driver sub-files.

Usage

read_agilent_amx(
  path,
  what = c("dad", "pump", "comp", "sampler"),
  path_out = NULL,
  format_out = c("data.frame", "tibble", "data.table"),
  gradient_format = c("wide", "long")
)

Arguments

path: Path to the .amx file.
what: One or more instrument modules to parse. Any combination of "dad", "pump", "comp", and "sampler". Defaults to all four.
path_out: Directory into which the archive is extracted. If NULL (default), a temporary directory is used and cleaned up on exit.
format_out: Class of the gradient, solvents, signals and temp_controls tables. Either "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 parsed module, plus "metadata". A module the archive has no driver file for is left out with a warning, and it is an error if none of the requested modules has one. The comp module is returned as column and sampler as autosampler. See below for the structure of each.

metadata — a list with scalar elements:

method_name: Original method name.
version: Method version string.
status: Approval state.
created: Creation timestamp (POSIXct, UTC).
created_by: Username of creator.
modified: Last-modified timestamp (POSIXct, UTC).
modified_by: Username of last modifier.

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

solvents: A table of active solvent channels: channel, percentage, solvent.
gradient: A table of timetable entries. Wide format (default): time_min plus one pct_<channel> column per active channel, and a flow_mL_min column if the timetable changes the flow. Long format: time_min, channel, percent, where a flow channel holds the flow in mL/min.

dad — a list with scalar elements peakwidth_nm, slitwidth_nm, uv_lamp_required, vis_lamp_required, spectra_from_nm, spectra_to_nm, spectra_step_nm, plus:

signals: A table of active signals: id, wavelength_nm, bandwidth_nm.

column — a list with scalar element post_time_min, plus:

temp_controls: Two-row table (Left/Right): side, temperature_C, not_ready_limit_C, equilibration_time_min.

autosampler — a list with scalar elements: thermostat_installed, draw_speed_uL_min, eject_speed_uL_min, wait_after_draw_min, injection_volume_uL, wash_time_s.

Examples

if (FALSE) { # \dontrun{
read_agilent_amx(path)
} # }