convert.respirometry: Convert Raw Respirometry Data (respirometry)

Description Usage Arguments Value Examples

View source: R/convert.respirometry.R

Description

This function is the modification of the function conv_o2 from the R package respirometry allowing to convert raw respirometry data from one DO unit to another obtained in multichannel respirometry systems.

Usage

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convert.respirometry(import.file, export.file,
                     n.chamber = c(1,2,3,4,5,6,7,8),
                     logger = c("AutoResp", "FishResp", "QboxAqua"),
                     from, to, sal = 0, atm_pres = 1013.25)

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).

from

string: dissolved oxygen unit in an imported file (more information can be found in the documentation of the function conv_o2, R package respirometry)

to

string: dissolved oxygen unit in an exported file (more information can be found in the documentation of the function conv_o2, R package respirometry)

sal

string: salinity is measured in ppm (more information can be found in the documentation of the function conv_o2, R package respirometry)

atm_pres

string: ambient atmospheric pressure value (more information can be found in the documentation of the function conv_o2, R package respirometry)

Value

The function exports a data frame with converted DO units.

Examples

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# Import raw data for standard metabolic rate
SMR.path = system.file("extdata/stickleback/SMR_raw.txt.xz", package = "FishResp")

convert.respirometry(import.file = SMR.path,
                     export.file = "converted_SMR_raw.txt",
                     n.chamber = 1, logger = "AutoResp",
                     from = "mg_per_l", to = "mmol_per_l",
                     sal = 0, atm_pres = 1013.25)

FishResp documentation built on Oct. 22, 2018, 9:03 a.m.