R: Read a CTD file in ODF format

read.ctd.odf {oce} | R Documentation

## Read a CTD file in ODF format

### Description

Read a CTD file in ODF format

### Usage

    read.ctd.odf(
      file,
      columns = NULL,
      station = NULL,
      missingValue,
      deploymentType = "unknown",
      monitor = FALSE,
      exclude = NULL,
      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.
`exclude` | either a character value holding a regular expression that is used with `grep()` to remove lines from the header before processing, or `NULL` (the default), meaning not to exclude any such lines. The purpose of this argument is to solve problems with some files, which can have thousands of lines that indicate details that are may be of little value in processing. For example, some files have thousands of lines that would be excluded by using `exclude="PROCESS='Nulled the .* value"` in the function call.
`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.odf` reads files stored in Ocean Data Format, used in some Canadian hydrographic databases.

### 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.

### Caution

Lacking detailed documentation of the ODF file format, the `read.odf()` and `read.ctd.odf()` functions were crafted based on inspection of data files, and so some guesses had to be made.

The `PARAMETER_HEADER` chunks describing quality-control flags are a case in point. These contain `NAME` components that refer to other `PARAMETER_HEADER` chunks that hold measured data. However, those references are not always matched well with the data names, and even if they do match, the cross-reference syntax used by the Bedford Institute of Oceanography differs from that used by l’Institut Maurice-Lamontagne. To simplify coding, it was assumed that each quality-control sequence applies to the data sequence immediately preceding it. (This assumption is made in other analysis systems.)

It is also prudent to pay attention to the units decoding, which `read.odf()` handles by calling `unitFromString()`. Be on the lookout for incorrect temperature scales, which are sometimes reported with nonstandard strings in ODF files. Also, note that you may see warnings about conductivity ratios, which some ODF files incorrectly suggest have dimensions.

### Author(s)

Dan Kelley

### References

For sources that describe the ODF format, see the documentation for the odf class.

### 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.odv()`, `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()`

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.odv()`, `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()`

Other things related to odf data: `CTD_BCD2014666_008_1_DN.ODF.gz`, `ODF2oce()`, `ODFListFromHeader()`, `ODFNames2oceNames()`, `[[,odf-method`, `[[<-,odf-method`, `odf-class`, `plot,odf-method`, `read.odf()`, `subset,odf-method`, `summary,odf-method`

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

[Package oce version 1.7-2 Index]