Nothing
R/convert.respirometry.R
In FishResp: Analytical Tool for Aquatic Respirometry
Defines functions
convert.respirometry
Documented in
convert.respirometry
#' Convert Raw Respirometry Data (respirometry)
#'
#' This function is the modification of the function \code{\link[respirometry]{conv_o2}} from the R package \pkg{respirometry} allowing to convert raw respirometry data from one DO unit to another obtained in multichannel respirometry systems.
#'
#' @usage
#' convert.respirometry(import.file, export.file,
#' n.chamber = c(1,2,3,4,5,6,7,8),
#' logger = c("AutoResp", "FishResp", "QboxAqua"),
#' from, to, sal = 0, atm_pres = 1013.25)
#'
#' @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 from string: dissolved oxygen unit in an imported file (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#' @param to string: dissolved oxygen unit in an exported file (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#' @param sal string: salinity is measured in ppm (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#' @param atm_pres string: ambient atmospheric pressure value (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#'
#' @return The function exports a data frame with converted DO units.
#'
#' @importFrom respirometry conv_o2
#' @importFrom utils write.table write.csv
#'
#' @examples
#' \dontrun{
#' # Import raw data for standard metabolic rate
#' SMR.path = system.file("extdata/stickleback/SMR_raw.txt.xz", package = "FishResp")
#'
#' convert.respirometry(import.file = SMR.path,
#' export.file = "converted_SMR_raw.txt",
#' n.chamber = 1, logger = "AutoResp",
#' from = "mg_per_l", to = "mmol_per_l",
#' sal = 0, atm_pres = 1013.25)
#' }
#' @export
convert.respirometry <- function(import.file, export.file,
n.chamber = c(1,2,3,4,5,6,7,8),
logger = c("AutoResp", "FishResp", "QboxAqua"),
from, to, sal = 0,
atm_pres = 1013.25){
### 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] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 2){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 3){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 4){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 5){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 6){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
MR.data.body[,22] <- conv_o2(o2 = MR.data.body[,22],
from = from,
to = to,
temp = MR.data.body[,21],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 7){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
MR.data.body[,22] <- conv_o2(o2 = MR.data.body[,22],
from = from,
to = to,
temp = MR.data.body[,21],
sal = sal, atm_pres = atm_pres)
MR.data.body[,25] <- conv_o2(o2 = MR.data.body[,25],
from = from,
to = to,
temp = MR.data.body[,24],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 8){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
MR.data.body[,22] <- conv_o2(o2 = MR.data.body[,22],
from = from,
to = to,
temp = MR.data.body[,21],
sal = sal, atm_pres = atm_pres)
MR.data.body[,25] <- conv_o2(o2 = MR.data.body[,25],
from = from,
to = to,
temp = MR.data.body[,24],
sal = sal, atm_pres = atm_pres)
MR.data.body[,28] <- conv_o2(o2 = MR.data.body[,28],
from = from,
to = to,
temp = MR.data.body[,27],
sal = sal, atm_pres = atm_pres)
}
## 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 [", to, "]", 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] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 2){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 3){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 4){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 5){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 6){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
MR.data.body[,14] <- conv_o2(o2 = MR.data.body[,14],
from = from,
to = to,
temp = MR.data.body[,13],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 7){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
MR.data.body[,14] <- conv_o2(o2 = MR.data.body[,14],
from = from,
to = to,
temp = MR.data.body[,13],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 8){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
MR.data.body[,14] <- conv_o2(o2 = MR.data.body[,14],
from = from,
to = to,
temp = MR.data.body[,13],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,18] <- conv_o2(o2 = MR.data.body[,18],
from = from,
to = to,
temp = MR.data.body[,17],
sal = sal, atm_pres = atm_pres)
}
## 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, " [", to, "]", 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)] <- conv_o2(o2 = MR.data.body[, ncol(MR.data.body)],
from = from,
to = to,
temp = MR.data.body[,4],
sal = sal, atm_pres = atm_pres)
}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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Defines functions convert.respirometry
Documented in convert.respirometry
#' Convert Raw Respirometry Data (respirometry)
#'
#' This function is the modification of the function \code{\link[respirometry]{conv_o2}} from the R package \pkg{respirometry} allowing to convert raw respirometry data from one DO unit to another obtained in multichannel respirometry systems.
#'
#' @usage
#' convert.respirometry(import.file, export.file,
#' n.chamber = c(1,2,3,4,5,6,7,8),
#' logger = c("AutoResp", "FishResp", "QboxAqua"),
#' from, to, sal = 0, atm_pres = 1013.25)
#'
#' @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 from string: dissolved oxygen unit in an imported file (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#' @param to string: dissolved oxygen unit in an exported file (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#' @param sal string: salinity is measured in ppm (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#' @param atm_pres string: ambient atmospheric pressure value (more information can be found in the documentation of the function \code{\link{conv_o2}}, R package \pkg{respirometry})
#'
#' @return The function exports a data frame with converted DO units.
#'
#' @importFrom respirometry conv_o2
#' @importFrom utils write.table write.csv
#'
#' @examples
#' \dontrun{
#' # Import raw data for standard metabolic rate
#' SMR.path = system.file("extdata/stickleback/SMR_raw.txt.xz", package = "FishResp")
#'
#' convert.respirometry(import.file = SMR.path,
#' export.file = "converted_SMR_raw.txt",
#' n.chamber = 1, logger = "AutoResp",
#' from = "mg_per_l", to = "mmol_per_l",
#' sal = 0, atm_pres = 1013.25)
#' }
#' @export
convert.respirometry <- function(import.file, export.file,
n.chamber = c(1,2,3,4,5,6,7,8),
logger = c("AutoResp", "FishResp", "QboxAqua"),
from, to, sal = 0,
atm_pres = 1013.25){
### 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] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 2){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 3){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 4){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 5){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 6){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
MR.data.body[,22] <- conv_o2(o2 = MR.data.body[,22],
from = from,
to = to,
temp = MR.data.body[,21],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 7){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
MR.data.body[,22] <- conv_o2(o2 = MR.data.body[,22],
from = from,
to = to,
temp = MR.data.body[,21],
sal = sal, atm_pres = atm_pres)
MR.data.body[,25] <- conv_o2(o2 = MR.data.body[,25],
from = from,
to = to,
temp = MR.data.body[,24],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 8){
MR.data.body[,7] <- conv_o2(o2 = MR.data.body[,7],
from = from,
to = to,
temp = MR.data.body[,6],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,13] <- conv_o2(o2 = MR.data.body[,13],
from = from,
to = to,
temp = MR.data.body[,12],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,19] <- conv_o2(o2 = MR.data.body[,19],
from = from,
to = to,
temp = MR.data.body[,18],
sal = sal, atm_pres = atm_pres)
MR.data.body[,22] <- conv_o2(o2 = MR.data.body[,22],
from = from,
to = to,
temp = MR.data.body[,21],
sal = sal, atm_pres = atm_pres)
MR.data.body[,25] <- conv_o2(o2 = MR.data.body[,25],
from = from,
to = to,
temp = MR.data.body[,24],
sal = sal, atm_pres = atm_pres)
MR.data.body[,28] <- conv_o2(o2 = MR.data.body[,28],
from = from,
to = to,
temp = MR.data.body[,27],
sal = sal, atm_pres = atm_pres)
}
## 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 [", to, "]", 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] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 2){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 3){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 4){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 5){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 6){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
MR.data.body[,14] <- conv_o2(o2 = MR.data.body[,14],
from = from,
to = to,
temp = MR.data.body[,13],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 7){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
MR.data.body[,14] <- conv_o2(o2 = MR.data.body[,14],
from = from,
to = to,
temp = MR.data.body[,13],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
}
else if (n.chamber == 8){
MR.data.body[,4] <- conv_o2(o2 = MR.data.body[,4],
from = from,
to = to,
temp = MR.data.body[,3],
sal = sal, atm_pres = atm_pres)
MR.data.body[,6] <- conv_o2(o2 = MR.data.body[,6],
from = from,
to = to,
temp = MR.data.body[,5],
sal = sal, atm_pres = atm_pres)
MR.data.body[,8] <- conv_o2(o2 = MR.data.body[,8],
from = from,
to = to,
temp = MR.data.body[,7],
sal = sal, atm_pres = atm_pres)
MR.data.body[,10] <- conv_o2(o2 = MR.data.body[,10],
from = from,
to = to,
temp = MR.data.body[,9],
sal = sal, atm_pres = atm_pres)
MR.data.body[,12] <- conv_o2(o2 = MR.data.body[,12],
from = from,
to = to,
temp = MR.data.body[,11],
sal = sal, atm_pres = atm_pres)
MR.data.body[,14] <- conv_o2(o2 = MR.data.body[,14],
from = from,
to = to,
temp = MR.data.body[,13],
sal = sal, atm_pres = atm_pres)
MR.data.body[,16] <- conv_o2(o2 = MR.data.body[,16],
from = from,
to = to,
temp = MR.data.body[,15],
sal = sal, atm_pres = atm_pres)
MR.data.body[,18] <- conv_o2(o2 = MR.data.body[,18],
from = from,
to = to,
temp = MR.data.body[,17],
sal = sal, atm_pres = atm_pres)
}
## 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, " [", to, "]", 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)] <- conv_o2(o2 = MR.data.body[, ncol(MR.data.body)],
from = from,
to = to,
temp = MR.data.body[,4],
sal = sal, atm_pres = atm_pres)
}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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