pyroscience.aquaresp: Convert Respirometry Data from PyroScience and AquaResp...

Description Usage Arguments Value Examples

View source: R/pyroscience.aquaresp.R

Description

The function is used to convert raw data from 'Pyro Oxygen Logger' (PyroScience) and a summary file from 'AquaResp' (free software) to 'FishResp' format. This function should be applied before usage of the functions import.test and import.meas. The output is a file containing raw respirometry data in the 'FishResp' format (see Details in import.test to read more information about the 'FishResp' format)

Usage

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pyroscience.aquaresp(pyroscience.file,
                     aquaresp.file,
                     fishresp.file,
                     n.chamber = c(1,2,3,4),
                     date.format = c("DMY", "MDY", "YMD"),
                     wait.phase = NA, measure.phase = NA)

Arguments

pyroscience.file

the name of a file which contains raw data obtained from the 'Pyro Oxygen Logger' software (PyroScience)

aquaresp.file

the name of a file which contains summary data obtained from the 'AquaResp' software (free software)

fishresp.file

the name of an exported file containing raw data in the 'FishResp' format

n.chamber

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

date.format

string: date format (DMY, MDY or YMD) used in raw data obtained from the 'Pyro Oxygen Logger' software

wait.phase

integer: duration of the wait phase (in seconds), see the 'AquaResp' summary file (row #5)

measure.phase

integer: duration of the measure phase (in seconds), see the 'AquaResp' summary file (row #6)

Value

The function exports a file containing raw data in the 'FishResp' format

Examples

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pyroscience.path = system.file("extdata/pyroscience/pyroscience.txt",
                 package = "FishResp")
aquaresp.path = system.file("extdata/pyroscience/pyroscience-aquaresp.txt",
                 package = "FishResp")

pyroscience.aquaresp(pyroscience.file = pyroscience.path,
                     aquaresp.file = aquaresp.path,
                     fishresp.file = "fishresp.txt",
                     date.format = "MDY",
                     n.chamber = 1,
                     wait.phase = 120,
                     measure.phase = 600)

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