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Add support for StellarNet, Brewer, and Bentham spectrometers (examples of data files are welcome for these and other instruments).
qtuv_m_s.e.irrad() adding support for
collections of simulated spectral irradiance for multiple altidues.spct_CRI(), spct_CCT(), and
spct_SSI().read_qtuv_txt()
not to add by default variables angle and date
to the returned source_spct object. Support addition on
user request of variables sun.elevation,
zenith.angle, time, and ozone.du,
and for backwards compatibility, but deprecated, date and
angle, individually and in any combination.read_qtuv_txt() to handle text/HTML files from
Quick TUV saved with embedded new line escapes (`“”) instead of
actual new lines. This seems to be a change in the output from the
on-line Quick TUV calculator and/or in how web browsers handle it.qtuv_s.e.irrad() to directly obtain
simulated spectral irradiance from the Quick TUV calculator.qtuv_m_s.e.irrad() to directly obtain
collections of simulated spectral irradiance for multiple values of
arguments for input parameters.read_CIE_csv() to read the CSV and JSON
files from CIE, recently published at the CIE Datasets page.mspct2fdata() and
spct2fdata() to export spectra as fdata
objects for use with package ‘fda.usc’, and functions
fdata2spct() and fdata2mspct() to import the
‘fdata’ objects with functional data analysis results back into objects
of one of the classes from package ‘photobiology’. Currently classes
source_spct, response_spct,
filter_spct, and reflector_spct and the
matching ‘mspct’ collections are recognized automatically in both
directions.read_spectrapen_csv() supporting PSI’s
SpectraPen spectrometer.mspct2colorSpec() which affected also
as.colorSpec.generic_mspct(). Attempts to convert
collections containing spectra with inconsistent wavelength vectors
would fail.tidyr::gather_().read_cid_spectravue_csv() supporting data
import from measurements CSV files output by CID Bio-Science’s
SpectraVue CI-710s leaf spectrometer.read_foreign2mspct() to apply an import
function to a list of files.spct_CRI(),
spct_CCT() and spct_SSI() implemented as
wrappers to functions in package ‘colorSpec’ that accept
source_spct objects as arguments. CRI, CCT and SSI are
quantities used to describe light used for illumination, photography,
cinematography and video.na and ... to
read_csi_data().read_wasatch_csv() supporting data import
from long form CSV spectrum files saved by Wasatch’s Enlighten program.
Metadata parsed and added to spectral object. Session and JSON files not
yet supported.read_fmi2mspct() adding flexibility to cope with
variation in date and time formats used in headers of spectra.read_oo_pidata() that was preventing reading
of Ocean Optics “Raspberry Pi” Flame files with a sequence header line
at the top.read_oo_pidata().read_oo_jazdata().Revise read_fmi_dat() to extract date from file header and save the
file header to the spectral object as a comment. Add
read_fmi2mspct() for reading spectral irradiance. Bug fix:
decoding of dates in fmi import functions for daily data not always
returned POSIXct objects triggering errors in downstream code.
Add read_yoctopuce_csv() to read CSV files from
YoctoPuce modules. Add read_qtuv_txt() to read spectral
data output files from the on-line Quick TUV calculator. Add
read_tuv_usrout2mspct() wrapper of
read_tuv_usrout() and subset2mspct(). Revise
read_tuv_usrout() with new formal parameter ozone.du and
fix a bug in the setting of "where.measured" attribute.
Revise all read functions so that they store the header of the imported
file as a vector of character strings to attribute
"file.header".
Implement class coercion methods (“as.” methods) to complement earlier functions, tracking ‘photobiology’ 0.9.20. Move coercion methods from and to matrix objects to ‘photobiology’ 0.9.20. Update to track API changes in ‘colorSpec’ 0.7-3. Translate vignette to Rmarkdown.
Add function read_FReD_csv() (read files flower
reflectance database). Add function read_ASTER_txt() (read
files ASTER materials reflectance database). Revise function
read_licor_prn() to accept transmittance and reflectance
spectra in addition to energy and photon irradiance spectra. Improve
handling of 'label' by using only the base name of files
and appending user supplied label text. Change location of external data
used in vignettes.
Fix CITATION file. Add function read_uvspec_disort(),
rename read_libradtran_vesa() to
read_uvspec_disort_vesa().
Edit read_licor_prn() to work around a bug in readr::read_table()
that results in missread data (wrong numbers). Add
read_csi_dat() to read data saved from modern Campbell
Scientific loggers.
Make compatible with upcoming version of package ‘lubridate’ (pull
request by vspinu NA). Add function read_avaspec_xls()
which can import spectral data from Excel files exported from Avantes
software. Fix code to avoid partial matches of function parameter names
(tz -> tzone).
Fix LaTeX error in vignette.
Replace a couple of NA returned by read functions with empty spectral objects. Improve handling of strict.range to avoid spurious warnings.
Add functions mspct2matrix() and
matrix2mspct for conversion of collections of spectra into
R matrices and vice-versa.
Fix bug introduced when attempting to make the package pass CRAN checks without triggering a note.
Fix for compatibility with ‘dplyr’ (> 0.4.3). Add functions to
exchange data with package ‘colorSpec’: colorSpec2spct(),
colorSpec2chroma_spct(), colorSpec2mspct(),
spct2colorSpec(), chroma_spct2colorSpec(), and
mspct2colorSpec(). Add or revise functions to exchange data
with package ‘hyperSpec’: spct2hyperSpec(),
mspct2hyperSpec(), hyperSpec2spct() and
hyperSpec2mspct(). Add import function for raw counts from
Ocean Optics instruments accessed through server running on a Raspberry
Pi board: read_oo_pidata().
Add ‘readr::locale’ support to all functions that could make use of it. Add ‘label’ parameter to all file import functions. Add function read_oo_ssdata() for reading SpectraSuite files containing raw counts. Add function read_libradtran_vesa() for reading libRadtran output file with multiple solar spectrum simulations (as preprocessed by Vesa’s script). Add metadata as consistently as possible to the objects returned by all the file import functions. Update dependencies. Edit the user Guide. WARNING: from version 0.4.4 the time zone (tz) is by default “UTC” for decoding dates and times in files imported. In most cases you will need to pass the tz (or the locale) where the file was created as an argument to the functions!
Update for compatibility with ‘lubridate’ (>= 1.5.6) Add function
read_oo_jazdata() to read Jaz files containing raw counts. Add
preliminary versions of functions to exchange data with package
‘hyperSpec’: mspct2hyperSpec() and
hyperSpec2mspct(). Add preliminary version of function to
import data from package ‘pavo’: rspec2mspct().
Fix bug in read_fmi_cum(). Update dependencies.
Update vignette. Fix docs.
This is a major update, not backwards compatible, as names and formal parameters of all functions have changed. Trimming is no longer supported (should be done as a separate operation).
The functions for Ocean Optics files now read the number of pixels from the file header, and hopefully will better adjust to different instruments and settings.
Functions for reading multiple spectra now return collections of spectra. (Functions that saved the spectral objects constructed from the data read from text files on disk back to disk as R data files have been removed.)
New functions for reading daily spectral exposure data from files returned by models from FMI have been added.
New function for reading .csv file from Avantes’ AvaSpec spectrometers added.
Add "use.hinges" argument to functions, and default to
not adding hinges when trimming input.
Remove dependency on data.table.
Corrected some bugs in read_licor_files().
Added function to read spectral irradiance files generated by the Jaz spectrometer from Ocean Optics.
Functions names shortened.
Expanded the User Guide.
Edited read_licor_prn_files() drastically. The new version is functionally equivalent but formal arguments have changed. In addition it is now implemented by calling read_licor_prn_file().
New functions read_licor_prn_file(),
read_macam_dta_file(), read_ooss_txt_file()
and read_tuv_file() returning source.spct
objects.
Function read_xlsx() removed as there are other packages
available for Excel file import.
Added function read.xlsx() for reading data from Excel
workbook files saved as .xlsx (zipped XML format).
Added parameter unit.out and cleaned code.
First version containing only one function for importing data measured with a LI-COR LI-1800 spectroradiometer from .PRN text files produced by the PC1800 MS-DOS program from LI-COR.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.