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R/convert.rMR.R
In FishResp: Analytical Tool for Aquatic Respirometry
Defines functions
convert.rMR
Documented in
convert.rMR
#' Convert Raw Respirometry Data (rMR)
#'
#' This function is the modification of the function \code{\link[rMR]{DO.unit.convert}} from the R package \pkg{rMR} allowing to convert raw respirometry data from one DO unit to another obtained in multichannel respirometry systems.
#'
#' @usage
#' convert.rMR(import.file, export.file,
#' n.chamber = c(1,2,3,4,5,6,7,8),
#' logger = c("AutoResp", "FishResp", "QboxAqua"),
#' DO.units.in, DO.units.out, salinity = 0,
#' bar.press = 101.325, bar.units.in = "kpa")
#'
#' @param import.file the name of a file with raw respirometry data which should be imported to convert DO units
#' @param export.file the name of a file with results of the DO unit conversion
#' @param n.chamber integer: the number of chambers used in an experiment (including empty ones)
#' @param 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 \code{\link{presens.aquaresp}} or \code{\link{pyroscience.aquaresp}}, respectively).
#' @param DO.units.in string: dissolved oxygen unit in an imported file (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param DO.units.out string: dissolved oxygen unit in an exported file (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param salinity string: salinity is measured in ppm (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param bar.press string: ambient barometric pressure value (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param bar.units.in string: barometric pressure unit (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#'
#' @return The function exports a data frame with converted DO units.
#'
#' @importFrom rMR DO.unit.convert
#' @importFrom utils write.table write.csv
#'
#' @examples
#' \dontrun{
#' # Import raw data for active metabolic rate
#' AMR.path = system.file("extdata/stickleback/AMR_raw.txt.xz", package = "FishResp")
#'
#' convert.rMR(import.file = AMR.path,
#' export.file = "converted_AMR_raw.txt",
#' n.chamber = 2, logger = "AutoResp", salinity = 0,
#' DO.units.in = "mg/L", DO.units.out = "PP",
#' bar.press = 101.325, bar.units.in = "kpa")
#' }
#' @export
convert.rMR <- function(import.file, export.file,
n.chamber = c(1,2,3,4,5,6,7,8),
logger = c("AutoResp", "FishResp", "QboxAqua"),
DO.units.in, DO.units.out,
salinity = 0,
bar.press = 101.325,
bar.units.in = "kpa"){
### AutoResp format ###
if (logger == "AutoResp"){
MR.data.head <- readLines(import.file, 37)
MR.data.body <- read.table(import.file, sep = "\t", skip=37,
header=T, check.names=FALSE, strip.white=T)
if (n.chamber == 1){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 2){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 3){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 4){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 5){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 6){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,22] <- DO.unit.convert(x = MR.data.body[,22],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,21],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 7){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,22] <- DO.unit.convert(x = MR.data.body[,22],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,21],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,25] <- DO.unit.convert(x = MR.data.body[,25],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,24],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 8){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,22] <- DO.unit.convert(x = MR.data.body[,22],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,21],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,25] <- DO.unit.convert(x = MR.data.body[,25],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,24],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,28] <- DO.unit.convert(x = MR.data.body[,28],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,27],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
## rename columns ##
col.DO <- c(7,10,13,16,19,22,25,28)
ch=1
for(i in col.DO){
names(MR.data.body)[i] <- paste("CH", ch, " O2 [", DO.units.out, "]", sep = "")
ch = ch + 1
}
write.table(MR.data.head,
file = export.file,
append = F,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
MR.data.name <- data.frame()
MR.data.name <- rbind(MR.data.name, names(MR.data.body))
write.table(MR.data.name,
file = export.file,
append = T,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
names(MR.data.body) <- NULL
write.table(MR.data.body,
file = export.file,
append = T,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
}
else if (logger == "FishResp"){
MR.data.body <- read.table(import.file, sep = "\t", header=T,
check.names=FALSE, strip.white=T)
if (n.chamber == 1){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 2){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 3){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 4){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 5){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 6){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,14] <- DO.unit.convert(x = MR.data.body[,14],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,13],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 7){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,14] <- DO.unit.convert(x = MR.data.body[,14],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,13],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 8){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,14] <- DO.unit.convert(x = MR.data.body[,14],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,13],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,18] <- DO.unit.convert(x = MR.data.body[,18],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,17],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
## rename columns ##
col.DO <- c(4,6,8,10,12,14,16,18)
col.DO <- col.DO[1:n.chamber]
ch=1
for(i in col.DO){
names(MR.data.body)[i] <- paste("Ox.", ch, " [", DO.units.out, "]", sep = "")
ch = ch + 1
}
MR.data.name <- data.frame()
MR.data.name <- rbind(MR.data.name, names(MR.data.body))
write.table(MR.data.name,
file = export.file,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
names(MR.data.body) <- NULL
write.table(MR.data.body,
file = export.file,
append = T,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
}
else if (logger == "QboxAqua"){
MR.data.body <- read.table(import.file, sep = ",", header=T,
check.names=FALSE, strip.white=T)
if (n.chamber == 1){
MR.data.body[, ncol(MR.data.body)] <- DO.unit.convert(x = MR.data.body[, ncol(MR.data.body)],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,4],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}else{
print("If 'Qubit Systems' starts producing multi-chamber systems for aquatic respirometry, please contact us via email: fishresp@gmail.com")
}
MR.data.name <- data.frame()
MR.data.name <- rbind(MR.data.name, names(MR.data.body))
write.table(MR.data.name,
file = export.file,
sep = ",",
row.names = F,
col.names = F,
quote = F)
names(MR.data.body) <- NULL
write.table(MR.data.body,
file = export.file,
append = T,
sep = ",",
row.names = F,
col.names = F,
quote = F)
}
}
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FishResp documentation built on Sept. 18, 2022, 5:06 p.m.
R Package Documentation
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Defines functions convert.rMR
Documented in convert.rMR
#' Convert Raw Respirometry Data (rMR)
#'
#' This function is the modification of the function \code{\link[rMR]{DO.unit.convert}} from the R package \pkg{rMR} allowing to convert raw respirometry data from one DO unit to another obtained in multichannel respirometry systems.
#'
#' @usage
#' convert.rMR(import.file, export.file,
#' n.chamber = c(1,2,3,4,5,6,7,8),
#' logger = c("AutoResp", "FishResp", "QboxAqua"),
#' DO.units.in, DO.units.out, salinity = 0,
#' bar.press = 101.325, bar.units.in = "kpa")
#'
#' @param import.file the name of a file with raw respirometry data which should be imported to convert DO units
#' @param export.file the name of a file with results of the DO unit conversion
#' @param n.chamber integer: the number of chambers used in an experiment (including empty ones)
#' @param 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 \code{\link{presens.aquaresp}} or \code{\link{pyroscience.aquaresp}}, respectively).
#' @param DO.units.in string: dissolved oxygen unit in an imported file (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param DO.units.out string: dissolved oxygen unit in an exported file (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param salinity string: salinity is measured in ppm (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param bar.press string: ambient barometric pressure value (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#' @param bar.units.in string: barometric pressure unit (more information can be found in the documentation of the function \code{\link{DO.unit.convert}}, R package \pkg{rMR})
#'
#' @return The function exports a data frame with converted DO units.
#'
#' @importFrom rMR DO.unit.convert
#' @importFrom utils write.table write.csv
#'
#' @examples
#' \dontrun{
#' # Import raw data for active metabolic rate
#' AMR.path = system.file("extdata/stickleback/AMR_raw.txt.xz", package = "FishResp")
#'
#' convert.rMR(import.file = AMR.path,
#' export.file = "converted_AMR_raw.txt",
#' n.chamber = 2, logger = "AutoResp", salinity = 0,
#' DO.units.in = "mg/L", DO.units.out = "PP",
#' bar.press = 101.325, bar.units.in = "kpa")
#' }
#' @export
convert.rMR <- function(import.file, export.file,
n.chamber = c(1,2,3,4,5,6,7,8),
logger = c("AutoResp", "FishResp", "QboxAqua"),
DO.units.in, DO.units.out,
salinity = 0,
bar.press = 101.325,
bar.units.in = "kpa"){
### AutoResp format ###
if (logger == "AutoResp"){
MR.data.head <- readLines(import.file, 37)
MR.data.body <- read.table(import.file, sep = "\t", skip=37,
header=T, check.names=FALSE, strip.white=T)
if (n.chamber == 1){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 2){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 3){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 4){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 5){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 6){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,22] <- DO.unit.convert(x = MR.data.body[,22],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,21],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 7){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,22] <- DO.unit.convert(x = MR.data.body[,22],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,21],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,25] <- DO.unit.convert(x = MR.data.body[,25],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,24],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 8){
MR.data.body[,7] <- DO.unit.convert(x = MR.data.body[,7],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,6],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,13] <- DO.unit.convert(x = MR.data.body[,13],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,12],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,19] <- DO.unit.convert(x = MR.data.body[,19],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,18],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,22] <- DO.unit.convert(x = MR.data.body[,22],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,21],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,25] <- DO.unit.convert(x = MR.data.body[,25],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,24],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,28] <- DO.unit.convert(x = MR.data.body[,28],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,27],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
## rename columns ##
col.DO <- c(7,10,13,16,19,22,25,28)
ch=1
for(i in col.DO){
names(MR.data.body)[i] <- paste("CH", ch, " O2 [", DO.units.out, "]", sep = "")
ch = ch + 1
}
write.table(MR.data.head,
file = export.file,
append = F,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
MR.data.name <- data.frame()
MR.data.name <- rbind(MR.data.name, names(MR.data.body))
write.table(MR.data.name,
file = export.file,
append = T,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
names(MR.data.body) <- NULL
write.table(MR.data.body,
file = export.file,
append = T,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
}
else if (logger == "FishResp"){
MR.data.body <- read.table(import.file, sep = "\t", header=T,
check.names=FALSE, strip.white=T)
if (n.chamber == 1){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 2){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 3){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 4){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 5){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 6){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,14] <- DO.unit.convert(x = MR.data.body[,14],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,13],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 7){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,14] <- DO.unit.convert(x = MR.data.body[,14],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,13],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
else if (n.chamber == 8){
MR.data.body[,4] <- DO.unit.convert(x = MR.data.body[,4],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,3],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,6] <- DO.unit.convert(x = MR.data.body[,6],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,5],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,8] <- DO.unit.convert(x = MR.data.body[,8],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,7],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,10] <- DO.unit.convert(x = MR.data.body[,10],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,9],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,12] <- DO.unit.convert(x = MR.data.body[,12],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,11],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,14] <- DO.unit.convert(x = MR.data.body[,14],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,13],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,16] <- DO.unit.convert(x = MR.data.body[,16],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,15],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
MR.data.body[,18] <- DO.unit.convert(x = MR.data.body[,18],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,17],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}
## rename columns ##
col.DO <- c(4,6,8,10,12,14,16,18)
col.DO <- col.DO[1:n.chamber]
ch=1
for(i in col.DO){
names(MR.data.body)[i] <- paste("Ox.", ch, " [", DO.units.out, "]", sep = "")
ch = ch + 1
}
MR.data.name <- data.frame()
MR.data.name <- rbind(MR.data.name, names(MR.data.body))
write.table(MR.data.name,
file = export.file,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
names(MR.data.body) <- NULL
write.table(MR.data.body,
file = export.file,
append = T,
sep = "\t",
row.names = F,
col.names = F,
quote = F)
}
else if (logger == "QboxAqua"){
MR.data.body <- read.table(import.file, sep = ",", header=T,
check.names=FALSE, strip.white=T)
if (n.chamber == 1){
MR.data.body[, ncol(MR.data.body)] <- DO.unit.convert(x = MR.data.body[, ncol(MR.data.body)],
DO.units.in = DO.units.in,
DO.units.out = DO.units.out,
temp.C = MR.data.body[,4],
salinity = salinity,
salinity.units = "pp.thou",
bar.press = bar.press,
bar.units.in = bar.units.in,
bar.units.out = bar.units.in)
}else{
print("If 'Qubit Systems' starts producing multi-chamber systems for aquatic respirometry, please contact us via email: fishresp@gmail.com")
}
MR.data.name <- data.frame()
MR.data.name <- rbind(MR.data.name, names(MR.data.body))
write.table(MR.data.name,
file = export.file,
sep = ",",
row.names = F,
col.names = F,
quote = F)
names(MR.data.body) <- NULL
write.table(MR.data.body,
file = export.file,
append = T,
sep = ",",
row.names = F,
col.names = F,
quote = F)
}
}
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