Changelog

Source: NEWS.md

hyperSpec 1.0.0 2022-xx-xx

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

• The GitHub repository of this package was moved to https://github.com/r-hyperspec/hyperSpec
• Documentation now available in pkgdown sites (https://r-hyperspec.github.io/).
• NEWS.md (this file) added so that users can readily see changes that may affect the use of the package.
• Introductory vignette reorganized and enhanced, thanks to Bryan Hanson.
• Dataset faux_cell and function generate_faux_cell() replace chondro dataset (cbeleites/hyperSpec#125, cbeleites/hyperSpec#156, cbeleites/hyperSpec#180, cbeleites/hyperSpec#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()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#302
  .fix_spc_colnames()	.spc_fix_colnames()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  alois.palette()	palette_alois()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#299, @sangttruong
  chk.hy()	assert_hyperSpec()	#34
  fitraster()	raster_fit()	#47
  guess.wavelength()	extract_numbers()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#309
  hy.getOption()	hy_get_option()	#21
  hy.getOptions()	hy_get_options()	#21
  hy.setOptions()	hy_set_options()	#21
  makeraster()	raster_make()	#47
  mark.dendrogram()	mark_groups_in_dendrogram()	#43
  markpeak()	mark_peak()	#44
  matlab.dark.palette()	palette_matlab_dark()	cbeleites/hyperSpec#299, cbeleites/hyperSpec#299, @sangttruong
  matlab.palette()	palette_matlab()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#299, @sangttruong
  mergeextra()	merge_data()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#302
  orderwl()	wl_sort()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#309
  normalize01()	normalize_01()	#50
  pearson.dist()	dist_pearson()	#19
  plotc()	plot_c()	#48
  plotmap()	plot_map()	#48
  plotmat()	plot_matrix()	#48
  plotspc()	plot_spc()	#48
  plotvoronoi()	plot_voronoi()	#48
  pooled.cov()	cov_pooled()	#51
  spc.bin()	spc_bin()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  spc.fit.poly()	spc_fit_poly()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  spc.fit.poly.below()	spc_fit_poly_below()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  spc.identify()	identify_spc()	#40
  spc.label.default()	format_label_ispc_wl()	#39
  spc.label.wlonly()	format_label_wl_only()	#39
  spc.loess()	spc_loess()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  spc.NA.approx()	spc_na_approx()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  spc.point.default()	locate_spc_point_clicked()	#46
  spc.point.max()	locate_spc_point_max()	#46
  spc.point.min()	locate_spc_point_min()	#46
  spc.point.sqr()	locate_spc_point_parabola_max()	#46
  spc.rubberband()	spc_rubberband()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  spc.smooth.spline()	spc_smooth_spline()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#301
  stacked.offsets()	calculate_offsets()	#41
  wl.eval()	wl_eval()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#309
  wlconv()	wl_convert_units()	cbeleites/hyperSpec#208, cbeleites/hyperSpec#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() (cbeleites/hyperSpec#300).
• Function wl_convert_units() converted to S3 generic. Default and hyperSpec methods were added (#29).
• Function spc.NA.linapprox(), which was deprecated for long time, is now completely removed (cbeleites/hyperSpec#239).
• Column names in spectra matrix ($spc column of hyperSpec object) are now returned correctly by functions spc.bin() (cbeleites/hyperSpec#237), and spc.loess() (cbeleites/hyperSpec#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, cbeleites/hyperSpec#219).
• Changes related to function as.hyperSpec():
  • New method as.hyperSpec(<hyperSpec>) was created (cbeleites/hyperSpec#282).
  • The default value of argument wl is now set to wl = NULL (cbeleites/hyperSpec#297).
  • wl = NULL now means that the default values of wavelengths should be calculated inside the methods of as.hyperSpec() (cbeleites/hyperSpec#297).
• Possibility to initialize hyperSpec object by providing wavelengths only (cbeleites/hyperSpec#288).
• Function wl.eval() is converted into S3 generic. Methods wl.eval(<hyperSpec>) and wl.eval(<numeric>) for numeric vectors were added (cbeleites/hyperSpec#287).
• New function new_hyperSpec() that initializes hyperSpec object in a similar way as new("hyperSpec") does but has autocompletion possibilities in RStudio (cbeleites/hyperSpec#283).
• Functions show() and print() give more concise default output now (@GegznaV, cbeleites/hyperSpec#211).
• The default output of function summary() was changed (@GegznaV, cbeleites/hyperSpec#211).
• New color palette palette_colorblind introduced (@bryanhanson).
• Function sample() gains new argument index; sample(..., index = TRUE) replaced function isample() (@GegznaV, #17).
• New function wl_create_label_from_units() that creates labels for wavelength axis (@GegznaV).

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 (cbeleites/hyperSpec#228).