convert.rMR {FishResp}

Convert Raw Respirometry Data (rMR)

Description

This function is the modification of the function DO.unit.convert from the R package rMR allowing to convert raw respirometry data from one DO unit to another obtained in multichannel respirometry systems.

Usage

convert.rMR(import.file, export.file,
            n.chamber = c(1,2,3,4,5,6,7,8),
            logger = c("AutoResp", "FishResp", "QboxAqua"),
            DO.units.in, DO.units.out, salinity = 0,
            bar.press = 101.325, bar.units.in = "kpa")

Arguments

import.file

the name of a file with raw respirometry data which should be imported to convert DO units

export.file

the name of a file with results of the DO unit conversion

n.chamber

integer: the number of chambers used in an experiment (including empty ones)

logger

string: the name of a logger software used for intermittent-flow respirometry. Note, that both 'OxyView' and 'Pyro Oxygen Logger' used in couple with the 'AquaResp' software should be converted to the 'FishResp' format before running this function (see the functions presens.aquaresp or pyroscience.aquaresp, respectively).

DO.units.in

string: dissolved oxygen unit in an imported file (more information can be found in the documentation of the function DO.unit.convert, R package rMR)

DO.units.out

string: dissolved oxygen unit in an exported file (more information can be found in the documentation of the function DO.unit.convert, R package rMR)

salinity

string: salinity is measured in ppm (more information can be found in the documentation of the function DO.unit.convert, R package rMR)

bar.press

string: ambient barometric pressure value (more information can be found in the documentation of the function DO.unit.convert, R package rMR)

bar.units.in

string: barometric pressure unit (more information can be found in the documentation of the function DO.unit.convert, R package rMR)

Value

The function exports a data frame with converted DO units.

Examples

## Not run: 
# Import raw data for active metabolic rate
AMR.path = system.file("extdata/stickleback/AMR_raw.txt.xz", package = "FishResp")

convert.rMR(import.file = AMR.path,
            export.file = "converted_AMR_raw.txt",
            n.chamber = 2, logger = "AutoResp", salinity = 0,
            DO.units.in = "mg/L", DO.units.out = "PP",
            bar.press = 101.325, bar.units.in = "kpa")

## End(Not run)