read_licor_prn {photobiologyInOut}

Read '.PRN' File(s) Saved by LI-COR's PC1800 Program.

Description

Read and parse the header of a processed data file as output by the PC1800 program to extract the whole header remark field and also decode whether data is irradiance in photon or energy based units, transmittance, reflectance or absorbance and then extract the wavelength and spectral data. PC1800 is an MS-DOS program provided for use with the LI-1800 spectrometer. This instrument was released in the 1980's and was sold until the early 2000's. It was very popular and several of them remain in use. (It should not be confused with the LI-180, a new spectrometer released released in 2020.)

Usage

read_licor_prn(
  file,
  date = NULL,
  geocode = NULL,
  label = NULL,
  tz = NULL,
  locale = readr::default_locale(),
  s.qty = NULL
)

read_m_licor_prn(
  files,
  date = NULL,
  geocode = NULL,
  label = NULL,
  tz = Sys.timezone(),
  locale = readr::default_locale(),
  s.qty = NULL
)

Arguments

file

Path to file as a character string.

date

a POSIXct object to use to set the "when.measured" attribute. If NULL, the default, the date is extracted from the file header.

geocode

A data frame with columns lon and lat used to set attribute "where.measured".

label

character string, but if NULL the value of file is used, and if NA the "what.measured" attribute is not set.

tz

character Time zone used for interpreting times saved in the file header.

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.

s.qty

character The name of the spectral quantity to be read. One of "s.irrad", "Tfr", or "Rfr".

files

A list or vector of character strings.

Details

Function read_m_licor_prn() calls red_licor_prn() for each file in files. See read_table for a description of valid arguments for files.

Value

read_licor_prn() returns a source_spct object with time.unit attribute set to "second" and when.measured attribute set to the date-time extracted from the file name, or supplied.

Function read_m_licor_prn() returns a source_mspct object containing one spectrum per file read.

Note

The LI-1800 spectroradiometer does not store the year as part of the data, only month, day, and time of day. Because of this, in the current version, if NULL is the argument to date, year is set to 0000.

References

LI-COR Biosciences, Environmental. https://www.licor.com/env/

Examples

 file.name <- 
   system.file("extdata", "spectrum.PRN", 
               package = "photobiologyInOut", mustWork = TRUE)
                
 licor.spct <- read_licor_prn(file = file.name)
 
 licor.spct
 getWhenMeasured(licor.spct)
 getWhatMeasured(licor.spct)
 cat(comment(licor.spct))