FishResp (version 1.1.1)

prepare.data: Prepare Raw Respirometry Data

Description

This function is used for preparation of raw data in the FishResp format before the actual respirometry analysis. As namely, the function will create measurement points for each second (the required FishResp format) if the time interval between two measurement points is more than one second. In addition, low and high thresold for both dissolved oxygen and water temperature might be applied here. The measurement points beyond the threshold(s) will be transformed to NA (be careful if use the 'parallel' method for background respiration correction as it might transform DO or Temp to NA as well).

Usage

prepare.data(import.file, export.file,
             date.format = c("DMY", "MDY", "YMD"),
             DO.low = NA, DO.high = NA,
             Temp.low = NA, Temp.high = NA)

Value

The function exports a data file with one second interval between measurement points and excluded data beyond the defined threshold(s)

Arguments

import.file

the name of a file with raw respirometry data which should be imported for raw data preparation

export.file

the name of a file with results of raw data preparation

date.format

string: date format (DMY, MDY or YMD), where D = day, M = month, Y - year.

DO.low

numeric: the low threshold defining a minimum accepted value for dissolved oxygen (DO)

DO.high

numeric: the high threshold defining a maximum accepted value for dissolved oxygen (DO)

Temp.low

numeric: the low threshold defining a minimum accepted value for water temperature (Temp)

Temp.high

numeric: the high threshold defining a maximum accepted value for water temperature (Temp)

Examples

if (FALSE) {
amphipod.path = system.file("extdata/amphipod/amphipod.txt",
                 package = "FishResp")

prepare.data(import.file = amphipod.path,
             export.file = "amphipod_corrected.txt",
             date.format = "DMY",
             DO.low = 0.5,
             DO.high = 12)
}