import_firesting {respirometry}

Import data from Pyro Oxygen Logger

Description

Imports the standard txt file output from Pyroscience's deprecated Pyro Oxygen Logger software and converts the data into one or more data frames. If using the newer Pyroscience Workbench software, use import_pyroscience_workbench instead.

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.

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.

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.

Note

Oxygen conversions are estimates based on the marelac package.

Author(s)

Matthew A. Birk, [e-mail]

See Also

import_pyroscience_workbench, import_presens, import_witrox, conv_o2

Examples

## Not run: 
file <- system.file('extdata', 'pyro_oxygen_logger_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.

## End(Not run)