import.meas: Import Raw Data of Metabolic Rate Measurements

Description Usage Arguments Details Value Examples

View source: R/import.meas.R

Description

The function is used to import raw data of metabolic rate measurements to R environment.

Usage

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import.meas(file, info.data,
            n.chamber = c(1,2,3,4,5,6,7,8),
            logger = c("AutoResp", "FishResp", "QboxAqua"),
            date.format = c("DMY", "MDY", "YMD"),
            start.measure = "00:00:00",
            stop.measure = "23:59:59",
            set.date.time = NA,
            meas.to.wait = 0,
            plot.temperature = TRUE,
            plot.oxygen = TRUE)

Arguments

file

the name of a file which raw data of metabolic rate measurements are to be read from

info.data

a data frame obtained by using the function input.info

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

  • 'AutoResp' if you use commercial software by 'Loligo Systems'

  • 'FishResp' if you use free software 'AquaResp' in combination with equipment produced by 'PreSens' or 'Pyroscience', please convert data to the 'FishResp' format using the functions presens.aquaresp or pyroscience.aquaresp, respectively.
    If you do not use commercial software or 'AquaResp' for running intermittent-flow respirometry, adjust raw data manually to the 'FishResp' format (see Details below).

  • 'QboxAqua' if you use commercial software by 'Qubit Systems'

date.format

string: date format (DMY, MDY or YMD)

start.measure

chron: time when metabolic rate measurements are started

stop.measure

chron: time when metabolic rate measurements are finished

set.date.time

chron: this parameter is turned off by default and needed to be specified only if raw data were recorded by 'Q-box Aqua' logger software. Specifically, input the date and time when .cmbl file was built in one of the following formats: "dd/mm/yyyy/hh:mm:ss", "mm/dd/yyyy/hh:mm:ss", or "yyyy/mm/dd/hh:mm:ss" (in accourdance to the chosen date.format parameter).

meas.to.wait

integer: the number of first rows for each measurement phase (M) which should be reassigned to the wait phase (W). The parameter should be used when the wait phase (W) is absent (e.g. in 'Q-box Aqua' logger software) or not long enough to eliminate non-linear change in DO concentration over time from the measurement phase (M) after shutting off water supply from the ambient water source.

plot.temperature

logical: if TRUE then the graph of raw temperature data is plotted

plot.oxygen

logical: if TRUE then the graph of raw oxygen data is plotted

Details

If you use closed respirometry approach, please standardize raw data. The example of "FishResp" format for 4-channel respirometry system is shown here:

Date&Time Phase Temp.1 Ox.1 Temp.2 Ox.2 Temp.3 Ox.3 Temp.4 Ox.4
19/08/2016/18:47:20 F1 24.49 7.78 24.56 7.73 24.49 7.78 24.56 7.73
19/08/2016/18:47:21 F1 24.49 7.78 24.56 7.73 24.49 7.78 24.56 7.73
19/08/2016/18:47:22 M1 24.49 7.77 24.56 7.72 24.49 7.78 24.56 7.73
19/08/2016/18:47:23 M1 24.49 7.76 24.56 7.72 24.49 7.78 24.56 7.73

where the items are:

Value

The function returns a data frame containing standardized raw data of metabolic rate measurements. The data frame should be used in the function correct.meas to correct metabolic rate measurements for background respiration.

Examples

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# Import raw data for standard and active metabolic
# rate measurements (SMR and AMR, respectively)

# if the data have been already loaded to R,
# skip the first line of the code:
data(info)
## Not run: 
SMR.path = system.file("extdata/stickleback/SMR_raw.txt.xz", package = "FishResp")
SMR.raw <- import.meas(file = SMR.path,
                       info.data = info,
                       logger = "AutoResp",
                       n.chamber = 4,
                       date.format = "DMY",
                       start.measure = "22:00:00",
                       stop.measure = "06:00:00",
                       plot.temperature = TRUE,
                       plot.oxygen = TRUE)

## End(Not run)
AMR.path = system.file("extdata/stickleback/AMR_raw.txt.xz", package = "FishResp")
AMR.raw <- import.meas(file = AMR.path,
                       info.data = info,
                       logger = "AutoResp",
                       n.chamber = 4,
                       date.format = "DMY",
                       plot.temperature = TRUE,
                       plot.oxygen = TRUE)

# an example for importing raw data recorded by 'Q-box Aqua'
qbox.path = system.file("extdata/qboxaqua/qboxaqua.csv", package = "FishResp")
RMR.raw <- import.meas(file = qbox.path,
                        info.data = info,
                        logger = "QboxAqua",
                        n.chamber = 1,
                        date.format = "DMY",
                        start.measure = "23:30:00",
                        stop.measure = "01:00:00",
                        set.date.time = "23/02/2014/23:30:22",
                        meas.to.wait = 200,
                        plot.temperature = TRUE,
                        plot.oxygen = TRUE)

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