presens.aquaresp: Convert Respirometry Data from PreSens and AquaResp Software...

Description Usage Arguments Value Examples

View source: R/presens.aquaresp.R

Description

The function is used to convert raw data from 'OxyView' (PreSens) 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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presens.aquaresp(presens.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

presens.file

the name of a file which contains raw data obtained from the 'OxyView' software (PreSens)

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 'OxyView' 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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presens.path.1 = system.file("extdata/presens/presens-ch1.txt",
                 package = "FishResp")
presens.path.2 = system.file("extdata/presens/presens-ch2.txt",
                 package = "FishResp")
presens.path.3 = system.file("extdata/presens/presens-ch3.txt",
                 package = "FishResp")
presens.path.4 = system.file("extdata/presens/presens-ch4.txt",
                 package = "FishResp")
aquaresp.path = system.file("extdata/presens/presens-aquaresp.txt",
                 package = "FishResp")

presens.aquaresp(presens.file = c(presens.path.1, presens.path.2,
                                  presens.path.3, presens.path.4),
                 aquaresp.file = aquaresp.path,
                 fishresp.file = "fishresp.txt",
                 date.format = "DMY",
                 n.chamber = 4,
                 wait.phase = 60,
                 measure.phase = 240)

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