respirometry (version 2.0.0)

import_witrox: Import data from a Loligo Systems Witrox O2 transmitter

Description

Imports the standard txt file output from Loligo Systems Witrox fiber optic O2 transmitters and converts the data into one or more data frames.

Usage

import_witrox(
  file,
  o2_unit = "percent_a.s.",
  date = "%m/%d/%Y %I:%M:%S %p",
  overwrite_sal = NULL,
  drop_channels = TRUE,
  split_channels = FALSE
)

Value

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

TIME

Date and time, POSIXlt format.

DURATION

Duration of measurement trial (minutes).

ATM_PRES

Atmospheric pressure (mbar).

CH_X_PHASE

Phase recorded. Phase is inversely related to O2.

CH_X_TEMP

Temperature recorded or defined at beginning of measurement trial.

CH_X_SAL

Salinity (psu).

CH_X_O2

Oxygen measurement in desired unit as determined by o2_unit.

...

Channel columns (CH_...) are repeated for each channel.

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

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).

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.

Author

Matthew A. Birk,

Details

The following Loligo Systems fiber optic O2 transmitters are supported:

• Witrox 4

If you would like support for the Witrox 1, email me a data file from this device.

See Also

import_pyroscience_workbench, import_firesting, import_presens, conv_o2

Examples

if (FALSE) {
file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
import_witrox(file, o2_unit = 'umol_per_l')

# Oops. I forgot to change the salinity value when I calibrated
# the instrument. Override the values in the file for 35 psu.
import_witrox(file, o2_unit = 'umol_per_kg', overwrite_sal = 35)

# I want each channel as a separate data frame.
data_list <- import_witrox(file, split_channels = TRUE)
data_list$CH_3 # here's the channel 3 data frame.
}