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Read OO irradiance calibration.

Source: R/oo-calibration.R
read_oo_caldata.Rd

Reads a calibration data file as supplied by Ocean Optics. Wavelength and calibration values are stored as data and the metadata parsed from the header or supplied as arguments as attributes of the same object, including the time and date of the calibration. The whole file header is in addition stored as a comment.

Usage

read_oo_caldata(
  file,
  time = NULL,
  geocode = NULL,
  label = NULL,
  descriptor = NULL,
  tz = NULL,
  locale = NULL,
  verbose = getOption("photobiology.verbose", default = FALSE)
)

Arguments

file

character string Path or file to read.

time

a POSIXct object, but if NULL the date stored in file is used, and if NA the when.measured attribute is set to NA.

geocode

A one row data frame with numeric columns lon and lat, and optionally a character column address.

label

character string, but if NULL the value of file is used, and if NA the "what.measured" attribute is set to NA.

descriptor

list A list describing the instrument, used to set attribute instr.descriptor.

tz

character Time zone is by default read from the file.

locale

The locale controls defaults that vary from place to place. The default locale is US-centric (like R), but you can use locale to create your own locale that controls things like the default time zone, encoding, decimal mark, big mark, and day/month names.

verbose

Logical indicating the level of warnings wanted.

Value

A generic_spct object, with columns w.length and oo.cal.

Details

The format of the data used by Ocean Optics seems to have remained consistent in time and with spectrometer model, but not the header. In particular, the format of the date and whether time is included or not varies. The function is able to decode three different date formats that I have come across. If decoding fails with a message indicating that parsing has failed, the problem can be overcome by passing the date as an argument to parameter time when calling the function, as in this case no decoding of the date is attempted. The easiest approach is to use function dmy or similar from package 'lubridate'. When no time zone information is included in the file header, the local time zone is used, which in many cases will shift the date by one day. If you know where the calibration was done, the correct TZ can be passed as an argument. Anyway as calibrations are usually considered valid for one or two years, this shift is only rarely important,

See also

oo_calib2irrad_mult