Changelog

Source: NEWS.md

hyperSpec 1.0.0 2021-xx-xx Unreleased

Acknowledgements

• The hyperSpec team gratefully acknowledges support from the Google Summer of Code program, which sponsored student Erick Oduniyi during summer 2020. Erick and the team carried out a significant overhaul of hyperSpec which led to this major release.

User-Facing Changes from 0.99 Series

• NEWS.md (this file) added so that users can readily see changes that may affect the use of the package.
• Documentation now available in pkgdown sites (https://r-hyperspec.github.io/).
• Introductory vignette reorganized and enhanced, thanks to Bryan Hanson.
• Dataset faux_cell and function generate_faux_cell() replace chondro dataset (#125, #156, #180, #229).
• Portions of hyperSpec were spun out into their own packages for ease of maintenance. — ELABORATE —
  • Dataset chondro was moved to package hySpc.chondro (https://r-hyperspec.github.io/hySpc.chondro/).
  • Functions qplotspc(), qplotmap(), qplotc(), qplotmixmap(), legendright(), qmixtile(), normalize.colrange(), normalize.range(), normalize.null(), normalize.minmax(), qmixlegend(), colmix.rgb() were deprecated due analogous functionality in package hySpc.ggplot2 (https://r-hyperspec.github.io/hySpc.ggplot2/).
  • Functions read.ENVI(), read.ENVI.HySpex(), read.ENVI.Nicolet() were deprecated due to analogous functionality in package hySpc.read.ENVI (https://r-hyperspec.github.io/hySpc.read.ENVI/).
  • Functions read.spc(), read.spc.Kaiser(), read.spc.KaiserMap(), read.spc.KaiserLowHigh() were deprecated due to analogous functionality in package hySpc.read.spc (https://r-hyperspec.github.io/hySpc.read.spc/).
  • Functions read.spe(), spe.showcalpoints() were deprecated due to analogous functionality in package hySpc.read.spe (https://r-hyperspec.github.io/hySpc.read.spe/).
  • Functions read.mat.Cytospec(), read.mat.Witec() were deprecated due to analogous functionality in package hySpc.read.mat (https://r-hyperspec.github.io/hySpc.read.mat/).
  • Function read.jdx() was deprecated due to analogous functionality in package hySpc.read.jdx (https://r-hyperspec.github.io/hySpc.read.jdx/).
  • Functions read.asc.Andor(), read.asc.PerkinElmer(), read.txt.Horiba(), read.txt.Horiba.xy(), read.txt.Horiba.t(), read.txt.long(), read.txt.Renishaw(), read.zip.Renishaw(), read.txt.Shimadzu(), read.txt.wide(), read.txt.Witec(), read.txt.Witec.Graph(), read.dat.Witec(), wc(), count_lines() were deprecated due analogous functionality in package hySpc.read.txt (https://r-hyperspec.github.io/hySpc.read.txt/).
  • The following functions were renamed or replaced by new ones (see table below).

  Deprecated function	New (replacement) function	Related issues
  .fileio.optional()	.spc_io_postprocess_optional()	#208, #302
  .fix_spc_colnames()	.spc_fix_colnames()	#208, #301
  alois.palette()	palette_alois()	#208, #299, @sangttruong
  guess.wavelength()	extract_numbers()	#208, #309
  matlab.dark.palette()	palette_matlab_dark()	#299, #299, @sangttruong
  matlab.palette()	palette_matlab()	#208, #299, @sangttruong
  mergeextra()	merge_data()	#208, #302
  orderwl()	wl_sort()	#208, #309
  spc.bin()	spc_bin()	#208, #301
  spc.fit.poly()	spc_fit_poly()	#208, #301
  spc.fit.poly.below()	spc_fit_poly_below()	#208, #301
  spc.loess()	spc_loess()	#208, #301
  spc.NA.approx()	spc_na_approx()	#208, #301
  spc.rubberband()	spc_rubberband()	#208, #301
  spc.smooth.spline()	spc_smooth_spline()	#208, #301
  wl.eval()	wl_eval()	#208, #309
  wlconv()	wl_convert_units()	#208, #309

  • Wavelength unit conversion functions ev2freq(), ev2invcm(), ev2nm(), ev2raman(), freq2ev(), freq2invcm(), freq2nm(), freq2raman(), invcm2ev(), invcm2freq(), invcm2nm(), invcm2raman(), nm2ev(), nm2freq(), nm2invcm(), nm2raman(), raman2ev(), raman2freq(), raman2invcm(), raman2nm() are deprecated in favor of wl_convert_units() (#300).
• Function spc.NA.linapprox(), which was deprecated for long time, is now completely removed (#239).
• Column names in spectra matrix ($spc column of hyperSpec object) are now returned correctly by functions spc.bin() (#237), and spc.loess() (#245).
• New function hy_list_available_hySpc_packages() lists packages, that are available in GitHub organization r-hyperSpec.
• New function hy_browse_homepage() opens the homepage of R hyperSpec in a web browser.
• New function hy_list_installed_hySpc_packages() lists and function hy_attach() conveniently loads and attaches all installed r-hyperspec family packages (@cbeleites, @GegznaV, #219).
• Changes related to function as.hyperSpec():
  • New method as.hyperSpec(<hyperSpec>) was created (#282).
  • The default value of argument wl is now set to wl = NULL (#297).
  • wl = NULL now means that the default values of wavelengths should be calculated inside the methods of as.hyperSpec() (#297).
• Possibility to initialize hyperSpec object by providing wavelengths only (#288).
• Function wl.eval() is converted into S3 generic. Methods wl.eval(<hyperSpec>) and wl.eval(<numeric>) for numeric vectors were added (#287).
• New function new_hyperSpec() that initializes hyperSpec object in a similar way as new("hyperSpec") does but has autocompletion possibilities in RStudio (#283).
• Functions show() and print() give more concise default output now (@GegznaV, #211).
• The default output of function summary() was changed (@GegznaV, #211).
• New color palette palette_colorblind introduced (@bryanhanson).

Non-User-Facing Changes from 0.99 Series

• Note: this listing is for the benefit of developers, and should summarize significant infrastructure changes.
• Vignettes converted to .Rmd and formatted consistently, thanks to @GegznaV.
• Package hySpc.testthat is now used for unit testing (#228).