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 output (for 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". Elements present depend on what; 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 data.frame of active solvent channels: channel, percentage, solvent.
gradient: A data.frame of timetable entries. Wide format (default): time_min plus one pct_<channel> column per active channel. Long format: time_min, channel, percent.

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 data.frame of active signals: id, wavelength_nm, bandwidth_nm.

comp — a list with scalar element post_time_min, plus:

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

sampler — 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.