R: Read a General CTD File

read.ctd {oce} | R Documentation

## Read a General CTD File

### Description

Read a General CTD File

### Usage

    read.ctd(
      file,
      type = NULL,
      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.
`type` | If `NULL`, then the first line is studied, in order to determine the file type, and control is dispatched to a specialized function to handle that type. Otherwise, `type` must be a string. If `type="SBE19"` then a Seabird file format is assumed, and control is dispatched to `read.ctd.sbe()`. If `type="WOCE"` then a WOCE-exchange file is assumed, and control is dispatched to `read.ctd.woce()`. If `type="ITP"` then an ice-tethered profiler file is assumed, and control is dispatched to `read.ctd.itp()`. If `type="ODF"` then an ODF file (used by the Canadian Department of Fisheries and Ocean) is assumed, and control is dispatched to `read.ctd.odf()`. Finally, if `type="ODV"` then an ODV file (used by Ocean Data View software) is assumed, and control is dispatched to `read.ctd.odv()`.
`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.

### Value

a ctd object. 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 so widely.

### Author(s)

Dan Kelley

### See Also

Other things related to ctd data: `CTD_BCD2014666_008_1_DN.ODF.gz`, `[[,ctd-method`, `[[<-,ctd-method`, `as.ctd()`, `cnvName2oceName()`, `ctd-class`, `ctd.cnv`, `ctdDecimate()`, `ctdFindProfiles()`, `ctdRaw`, `ctdRepair()`, `ctdTrim()`, `ctd_aml.csv`, `ctd`, `d200321-001.ctd`, `d201211_0011.cnv`, `handleFlags,ctd-method`, `initialize,ctd-method`, `initializeFlagScheme,ctd-method`, `oceNames2whpNames()`, `oceUnits2whpUnits()`, `plot,ctd-method`, `plotProfile()`, `plotScan()`, `plotTS()`, `read.ctd.itp()`, `read.ctd.odf()`, `read.ctd.odv()`, `read.ctd.sbe()`, `read.ctd.woce.other()`, `read.ctd.woce()`, `setFlags,ctd-method`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames()`, `woceUnit2oceUnit()`, `write.ctd()`

Other functions that read ctd data: `read.ctd.aml()`, `read.ctd.itp()`, `read.ctd.odf()`, `read.ctd.sbe()`, `read.ctd.woce.other()`, `read.ctd.woce()`

[Package oce version 1.7-2 Index]