R: Read an ITP-type CTD File

read.ctd.itp {oce} | R Documentation

## Read an ITP-type CTD File

### Description

Read an ITP-type CTD File

### Usage

    read.ctd.itp(file, columns = NULL, station = NULL, missingValue,
      deploymentType = "unknown", monitor = FALSE,
      debug = getOption("oceDebug"), processingLog, ...)

### Arguments

`file` | A connection or a character string giving the name of the file to load. For `read.ctd.sbe()` and `read.ctd.woce()`, this may be a wildcard (e.g. `"*.cnv"` or `"*.csv"`) in which case the return value is a vector containing CTD objects created by reading the files from `list.files` with `pattern` set to the specified wildcard pattern.
`columns` | An optional `list` that can be used to convert unrecognized data names to resultant variable names. This is used only by `read.ctd.sbe` and `read.ctd.odf`. For example, if a data file named salinity as `"SAL"`, then using
    d <- read.ctd(f, columns=list(
        salinity=list(name="SAL",
                      unit=list(unit=expression(),
                      scale="PSS-78"))))
would assign the `"SAL"` column to the `salinity` entry in the data slot of the CTD object returned by the `read.*` function.
`station` | Optional character string containing an identifying name or number for the station. This can be useful if the routine cannot determine the name automatically, or if another name is preferred.
`missingValue` | Optional missing-value flag; data matching this value will be set to `NA` upon reading. If this is provided, then it overrules any missing-value flag found in the data. For Seabird (`.cnv`) files, there is usually no need to set `missingValue`, because it can be inferred from the header (typically as -9.990e-29). Set `missingValue=NULL` to turn off missing-value detection, even in `.cnv` files that contain missing-value codes in their headers. If `missingValue` is not specified, then an attempt is made to infer such a value from the data, by testing whether salinity and/or temperature has a minimum that is under -8 in value; this should catch common values in files, without false positives. A warning will be issued in this case, and a note inserted in the processing log of the return value.
`deploymentType` | character string indicating the type of deployment. Use `"unknown"` if this is not known, `"profile"` for a profile (in which the data were acquired during a downcast, while the device was lowered into the water column, perhaps also including an upcast; `"moored"` if the device is installed on a fixed mooring, `"thermosalinograph"` (or `"tsg"`) if the device is mounted on a moving vessel, to record near-surface properties, or `"towyo"` if the device is repeatedly lowered and raised.
`monitor` | Boolean, set to `TRUE` to provide an indication of progress. This is useful if `filename` is a wildcard.
`debug` | An integer specifying whether debugging information is to be printed during the processing. This is a general parameter that is used by many `oce` functions. Generally, setting `debug=0` turns off the printing, while higher values suggest that more information be printed.
`processingLog` | If provided, the action item to be stored in the log. This is typically only provided for internal calls; the default that it provides is better for normal calls by a user.
`...` | additional arguments, passed to called routines.

### Details

`read.ctd.itp()` reads ice-tethered-profiler data that are stored in a format files used by WHOI servers as of 2016-2017. Lacking documentation on the format, the author constructed this function to work with some files that were on-hand. Whether the function will prove robust is an open question.

### Value

An object of `ctd-class`. The details of the contents depend on the source file. The `metadata` slot is particularly variable across data formats, because the meta-information provided in those formats varies widely.

### Author(s)

Dan Kelley

### References

Information about ice-tethered profile data is provided at http://www.whoi.edu/page.do?pid=23096, which also provides a link for downloading data. Note that the present version only handles data in profiler-mode, not fixed-depth mode.

### See Also

Other things related to ctd data: `[[,ctd-method`, `[[<-,ctd-method`, `as.ctd`, `cnvName2oceName`, `ctd-class`, `ctdDecimate`, `ctdFindProfiles`, `ctdRaw`, `ctdTrim`, `ctd`, `handleFlags,ctd-method`, `initialize,ctd-method`, `initializeFlagScheme,ctd-method`, `oceNames2whpNames`, `oceUnits2whpUnits`, `plot,ctd-method`, `plotProfile`, `plotScan`, `plotTS`, `read.ctd.odf`, `read.ctd.sbe`, `read.ctd.woce.other`, `read.ctd.woce`, `read.ctd`, `setFlags,ctd-method`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames`, `woceUnit2oceUnit`, `write.ctd`

[Package oce version 1.1-1 Index]