respirometry (version 2.0.0)

import_presens: Import data from a PreSens O2 transmitter

Description

Imports the standard text file output from most single channel PreSens fiber optic O2 transmitters and converts the data into a data frame.

Usage

import_presens(
  file,
  o2_unit = "percent_a.s.",
  date = "%d/%m/%y",
  sal = 35,
  all_cols = FALSE,
  split_channels = FALSE
)

Value

A data frame is returned.

TIME

Date and time, POSIXct format.

DURATION

Duration of measurement trial (minutes).

O2

Oxygen measurement in desired unit as determined by o2_unit.

PHASE

Phase recorded. Phase is inversely related to O2. Not included in SDR SensorDish Reader files.

AMPLITUDE

Amplitude recorded. Amplitude is an indicator of the quality of the signal. A low amplitude warning is produced by the transmitter below 2500. Not included in SDR SensorDish Reader files.

TEMP

Temperature recorded or defined at beginning of measurement trial.

ATM_PRES

Atmospheric pressure (mbar).

SAL

Salinity (psu).

ERROR_CODE

Error code from transmitter. See PreSens user manual for translation of error code. Not included in SDR SensorDish Reader files.

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.

sal

salinity of water sample (psu). Default is 35 psu. Ignored for Fibox 4 files since salinity is provided by the file.

all_cols

logical. For Fibox 4 files only. Should all columns (including calibration data and serial numbers) be output?

split_channels

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

Author

Matthew A. Birk,

Details

The following PreSens fiber optic O2 transmitters are supported:

• Fibox 4

• Fibox 3

• Fibox 3 trace

• Fibox 3 LCD trace

• Microx TX3

• Microx TX3 trace

• SDR SensorDish Reader

If you would like support for another PreSens O2 meter, email the package maintainer a data file from the device you would like supported. It is very important to note that the PreSens fiber optics O2 transmitters that are supported with this function (except the Fibox 4) DO NOT account for salinity (i.e. they assume salinity = 0 ppt). If the water sample measured was not fresh water, the oxygen concentrations (e.g. mg per liter or umol per liter) are incorrect in the PreSens txt file. This function corrects these O2 concentrations based on the salinity value defined by the sal argument. Absolute partial pressures (i.e. hPa and torr) will also be slightly different due to the slight influence of salinity on water's vapor pressure. This difference is typically ~0.05% of the recorded value.

See Also

import_pyroscience_workbench, import_firesting, import_witrox, conv_o2

Examples

if (FALSE) {

# Import a Fibox 3 file.
file <- system.file('extdata', 'fibox_3_file.txt', package = 'respirometry')
import_presens(file, o2_unit = 'umol_per_l', sal = 25)

# Import a Fibox 4 file.
file <- system.file('extdata', 'fibox_4_file.csv', package = 'respirometry')
import_presens(file = file, date = '%d-%b-%Y')

# Import an SDR SensorDish Reader file.
file <- system.file('extdata', 'sdr_file.txt', package = 'respirometry')
import_presens(file = file, date = '%d.%m.%y%X')

}