import_firesting: Import data from a FireSting O2 transmitter

Description

Imports the standard txt file output from FireSting O2 transmitters and converts the data into one or more data frames.

Usage

import_firesting(
  file,
  o2_unit = "percent_a.s.",
  date = "%m/%d/%Y %X",
  overwrite_sal = NULL,
  keep_metadata = FALSE,
  drop_channels = TRUE,
  split_channels = FALSE
)

Arguments

file

a character string. The filepath for the file to be read.

o2_unit

a character string. The unit of O2 measurement to be output in the data frame. Options are described in conv_o2.

date

a character string. The date format to be passed to strptime.

overwrite_sal

Default NULL. To overwrite the salinity value(s) from calibration, enter a single numeric value for all channels or a numeric vector with values for each channel. Salinity of water sample (psu).

keep_metadata

logical. Should metadata from the file be returned as extra columns in the returned data frame? Default is FALSE.

drop_channels

logical. Should channels without any O2 data be dropped? Default is TRUE.

split_channels

logical. Should a list of data frames be returned with a separate data frame for each channel? Default is FALSE.

Value

A data frame (or list of data frames) is returned.

TIME: Date and time, POSIXlt format.
DURATION: Duration of measurement trial (minutes).
CH_X_O2: Oxygen measurement in desired unit as determined by o2_unit.
CH_X_TEMP: Temperature recorded or defined at beginning of measurement trial.
CH_X_SAL: Salinity (psu).
...: Channel columns (CH_...) are repeated for each channel.
COMMENT: Comments from FireSting file.

If keep_metadata = TRUE, then the following columns are appended to the returned data frame:

ATM_PRES: Atmospheric pressure (mbar).
HUMIDITY: Relative humidity (% RH).
PROBE_TEMP: Probe temperature.
INTERNAL_TEMP: Transmitter internal temperature.
ANALOG_IN: Voltage input from the extension port (mV).
CH_X_PHASE: Phase recorded. Phase is inversely related to O2.
CH_X_INTENSITY: Intensity is an indicator of the quality of the signal. A low intensity warning is produced by the transmitter below 10 mV.
CH_X_AMB_LIGHT: Ambient light on the sensor. Expressed in mV.

If split_channels = TRUE, then "CH_X_" is removed from the column names and multiple data frames are returned in a named list.

Details

The following FireSting fiber optic O2 transmitters are supported:

FireStingO2
FireStingO2 (1st generation)

If you would like support for the Piccolo2, FireStingO2-Mini, TeX4, or any OEM instruments, email me a data file from the device.

Examples

Run this code

# NOT RUN {
file <- system.file('extdata', 'firesting_file.txt', package = 'respirometry')
import_firesting(file, o2_unit = 'umol_per_l')

# I want each channel as a separate data frame.
data_list <- import_firesting(file, split_channels = TRUE)
data_list$CH_3 # here's the channel 3 data frame.
# }
# NOT RUN {
# }

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