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Changelog

Source: NEWS.md

photobiologyInOut 0.4.28

  • Track change in package ‘colorSpec’ to avoid an error by triggering a warning, instead. Affects functions spct_CRI and spct_CCT.

photobiologyInOut 0.4.27

CRAN release: 2023-07-20

  • Add functions 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.

photobiologyInOut 0.4.26

CRAN release: 2022-10-15

  • Add function read_spectrapen_csv() supporting PSI’s SpectraPen spectrometer.
  • Update for code-breaking changes in package ‘readr’.

photobiologyInOut 0.4.25

CRAN release: 2022-08-15

  • Fix bug in mspct2colorSpec() which affected also as.colorSpec.generic_mspct(). Attempts to convert collections containing spectra with inconsistent wavelength vectors would fail.
  • Improve compatibility with package ‘colorSpec’ (many thanks to Glenn Davis for his help!).

photobiologyInOut 0.4.24

CRAN release: 2022-05-14

  • Replace use of deprecated tidyr::gather_().
  • Add function read_cid_spectravue_csv() supporting data import from measurements CSV files output by CID Bio-Science’s SpectraVue CI-710s leaf spectrometer.
  • Add function read_foreign2mspct() to apply an import function to a list of files.
  • Add color-related functions 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.

photobiologyInOut 0.4.23

CRAN release: 2021-10-11

  • Add parameters na and ... to read_csi_data().
  • Add function 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.
  • Add function read_li180_txt() supporting data import from files saved by the LI-180 handheld array spectrometer from LI-COR.
  • Avoid spurious progress messages when reading files.
  • Track various changes in the tidyverse that deprecated functions used in this package.
  • Fix bugs in some imports from ‘photobiology’.
  • Move git repository from Bitbucket to Github.
  • Set up Github action for CRAN-checks on Windows, OS X and Ubuntu.

photobiologyInOut 0.4.22-1

CRAN release: 2020-04-14

  • Fix two bad test cases that passed with ‘photobiology’ (== 0.10.0) but not with ‘photobiology’ (>= 0.10.1).

photobiologyInOut 0.4.22

CRAN release: 2020-04-02

  • Revise read_fmi2mspct() adding flexibility to cope with variation in date and time formats used in headers of spectra.
  • Update for compatibility with ‘tibble’ (>= 3.0.0).
  • Update for compatibility with ‘photobiology’ (>= 0.10.0) which also provides compatibility with ‘dplyr’ (>= 1.0.0).
  • Depends now on ‘photobiology’ (>= 0.10.0).

photobiologyInOut 0.4.21-1

CRAN release: 2020-01-11

  • Package code unchanged.
  • Update test cases for ‘photobiology’ (>= 0.9.30).
  • Depends now on ‘photobiology’ (>= 0.9.30).

photobiologyInOut 0.4.21

CRAN release: 2019-08-20

  • Track changes in ‘tidyr’ (= 1.0.0).
  • Move packages ‘pavo’ and ‘hyperSpec’ to suggests.

photobiologyInOut 0.4.20

CRAN release: 2019-06-15

  • Track changes in ‘photobiology’ (= 0.9.28) and ‘dplyr’ (= 0.8.1).
  • Set “how.measured” attribute in file import functions.

photobiologyInOut 0.4.19

CRAN release: 2018-12-13

  • Add checks for non-ASCII characters in headers.
  • Track code breaking change in ‘readr’ (>= 1.3.0).

photobiologyInOut 0.4.18

CRAN release: 2018-11-24

  • Track code breaking change in ‘readr’ (>= 1.2.0).
  • Fix bug in read_oo_pidata() that was preventing reading of Ocean Optics “Raspberry Pi” Flame files with a sequence header line at the top.
  • Add decoding of file header to extract integration time and number of scans to read_oo_pidata().
  • Improve decoding of file header to extract instrument settings in read_oo_jazdata().

photobiologyInOut 0.4.17

  • Add new function to read transmittance and reflectance files from Ocean Optics’ Jaz modular spectrometer.
  • Fix bug in decoding of time and date in functions read_fmi2mspct(), read_tuv_usrout() and read_qtuv_txt(). Decoding failed under R 3.4.4 (oldrel) but worked under R 3.5.1 due to functions from ‘lubridate’ returning POSIXlt values instead of POSIXct values. Now we force conversion to POSIXct.

photobiologyInOut 0.4.16

CRAN release: 2018-08-31

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.

photobiologyInOut 0.4.15

CRAN release: 2018-08-10

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".

photobiologyInOut 0.4.14

CRAN release: 2018-04-03

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.

photobiologyInOut 0.4.13

CRAN release: 2017-03-20

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.

photobiologyInOut 0.4.12

CRAN release: 2016-10-22

Fix CITATION file. Add function read_uvspec_disort(), rename read_libradtran_vesa() to read_uvspec_disort_vesa().

photobiologyInOut 0.4.11

CRAN release: 2016-09-25

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.

photobiologyInOut 0.4.10

CRAN release: 2016-08-28

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).

photobiologyInOut 0.4.9

CRAN release: 2016-08-14

Fix LaTeX error in vignette.

photobiologyInOut 0.4.8

Replace a couple of NA returned by read functions with empty spectral objects. Improve handling of strict.range to avoid spurious warnings.

photobiologyInOut 0.4.7

CRAN release: 2016-08-03

Add functions mspct2matrix() and matrix2mspct for conversion of collections of spectra into R matrices and vice-versa.

photobiologyInOut 0.4.6

CRAN release: 2016-06-19

Fix bug introduced when attempting to make the package pass CRAN checks without triggering a note.

photobiologyInOut 0.4.5

CRAN release: 2016-06-18

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().

photobiologyInOut 0.4.4

CRAN release: 2016-05-24

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!

photobiologyInOut 0.4.3

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().