readTDR: Read comma-delimited file with "TDR" data

In diveMove: Dive analysis and calibration

Description

Read a delimited (*.csv) file containing time-depth recorder (TDR) data from various TDR models. Return a TDR or TDRspeed object. createTDR creates an object of one of these classes from other objects.

Usage

readTDR(file, dateCol=1, timeCol=2, depthCol=3, speed=FALSE,
        subsamp=5, concurrentCols=4:6,
        dtformat="%d/%m/%Y %H:%M:%S", tz="GMT", ...)
createTDR(time, depth,
          concurrentData=data.frame(matrix(ncol=0, nrow=length(time))),
          speed=FALSE, dtime, file)

Arguments

file	character: a string indicating the path to the file to read. This can also be a text-mode connection, as allowed in read.csv.
dateCol	integer: column number containing dates, and optionally, times.
timeCol	integer: column number with times.
depthCol	integer: column number containing depth readings.
speed	logical: whether speed is included in one of the columns of concurrentCols.
subsamp	numeric scalar: subsample rows in file with subsamp interval, in s.
concurrentCols	integer vector of column numbers to include as concurrent data collected.
dtformat	character: a string specifying the format in which the date and time columns, when pasted together, should be interpreted (see strptime).
tz	character: a string indicating the time zone assumed for the date and time readings.
...	Passed to read.csv
time	A POSIXct object with date and time readings for each reading.
depth	numeric vector with depth readings.
concurrentData	data.frame with additional, concurrent data collected.
dtime	numeric scalar: sampling interval used in seconds. If missing, it is calculated from the time argument.

Details

The input file is assumed to have a header row identifying each field, and all rows must be complete (i.e. have the same number of fields). Field names need not follow any convention. However, depth and speed are assumed to be in m, and m/s, respectively, for further analyses.

If speed is TRUE and concurrentCols contains a column named speed or velocity, then an object of class TDRspeed is created, where speed is considered to be the column matching this name.

Value

An object of class TDR or TDRspeed.

Note

Although TDR and TDRspeed classes check that time stamps are in increasing order, the integrity of the input must be thoroughly verified for common errors present in text output from TDR devices such as duplicate records, missing time stamps and non-numeric characters in numeric fields. These errors are much more efficiently dealt with outside of GNU R using tools like GNU awk or GNU sed, so diveMove does not currently attempt to fix these errors.

Author(s)

Sebastian P. Luque [e-mail]

Examples

## Do example to define object zz with location of dataset
utils::example("dives", package="diveMove",
               ask=FALSE, echo=FALSE)
srcfn <- basename(zz)
readTDR(zz, speed=TRUE, sep=";", na.strings="", as.is=TRUE)

## Or more pedestrian
tdrX <- read.csv(zz, sep=";", na.strings="", as.is=TRUE)
date.time <- paste(tdrX$date, tdrX$time)
tdr.time <- as.POSIXct(strptime(date.time, format="%d/%m/%Y %H:%M:%S"),
                       tz="GMT")
createTDR(tdr.time, tdrX$depth, concurrentData=data.frame(speed=tdrX$speed),
          file=srcfn, speed=TRUE)

diveMove documentation built on May 2, 2019, 4:47 p.m.