NEWS.md

In r-hyperspec/hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

hyperSpec 0.101.0 (2024-05-01)

User-Facing Changes from Previous Versions

Repository

• The GitHub repository of this package was moved to https://github.com/r-hyperspec/hyperSpec

Documentation

• NEWS.md (this file) added so that users can readily see changes that may affect the use of the package.
• Vignettes converted to .Rmd and formatted consistently, thanks to @GegznaV.
• Introductory vignette hyperSpec.Rmd reorganized and enhanced, thanks to Bryan Hanson (@bryanhanson).
• Documentation is now available in the form of pkgdown sites at https://r-hyperspec.github.io/

New Functions and Methods

• New color palette palette_colorblind introduced (@bryanhanson).
• New function hy_browse_homepage() opens the homepage of R hyperSpec in a web browser.
• New function hy_list_available_hySpc_packages() lists packages, that are available in GitHub organization r-hyperSpec.
• 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).
• New function hyperSpec() that initializes hyperSpec object in a similar way as new("hyperSpec") does but has autocompletion possibilities in RStudio (cbeleites/hyperSpec#283, #129).
• New function wl_convert_units() (cbeleites/hyperSpec#300).
• New function wl_create_label_from_units() that creates labels for wavelength axis (@GegznaV).
• New method as.hyperSpec(<hyperSpec>) (cbeleites/hyperSpec#282).

Changes

• as.hyperSpec(): The default value of argument wl is now set to wl = NULL (cbeleites/hyperSpec#297).
• as.hyperSpec(): wl = NULL now means that the default values of wavelengths should be calculated inside the methods of as.hyperSpec() (cbeleites/hyperSpec#297).
• Methods show(<hyperSpec>) and print(<hyperSpec>) give more concise default output now (@GegznaV, cbeleites/hyperSpec#211).
• The default output of method summary(<hyperSpec>) was changed (@GegznaV, cbeleites/hyperSpec#211).
• Function wl.eval() is converted into S3 generic. Methods wl.eval(<hyperSpec>) and wl.eval(<numeric>) for numeric vectors were added (cbeleites/hyperSpec#287).
• Function sample() gains new argument index; sample(..., index = TRUE) replaced function isample() (@GegznaV, #17).
• Function wl_convert_units() converted into S3 generic. Default and hyperSpec methods were added (#29).
• Dataset faux_cell and function generate_faux_cell() replace chondro dataset (cbeleites/hyperSpec#125, cbeleites/hyperSpec#156, cbeleites/hyperSpec#180, cbeleites/hyperSpec#229).
• Documentation aliases have been updated. Now, ?hyperSpec points to the function hyperSpec(), and to refer to the package, package?hyperSpec should be used (#129).

Bugfixes

• Possibility to initialize hyperSpec object by providing wavelengths only (cbeleites/hyperSpec#288).
• 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

Soft Deprecation: Functions That Will Be Moved to Other Packages

Portions of package hyperSpec were partitioned into individual packages to facilitate maintenance.

• 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 to 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/).

Soft Deprecation: Function Name Standardization

The names of functions in hyperSpec started to be standardized to (a) have more self-explanatory names which reflect the essence of the functions and (b) to be more in alignment with the Tidyverse style. The following functions were renamed (see the table and the list below). In the current version of package, both old and new functions exist. But gradually the old functions will go through the deprecation phases and finally will be removed in the future versions of the package.

• 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 to Deprecate | 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

Defunct/Removed Features

• Function spc.NA.linapprox(), which was deprecated for long time, is now completely removed (cbeleites/hyperSpec#239).

Non-User-Facing Changes from 0.99 Series

• Code style improved to be more aligned with the Tidyverse style.
• Package hySpc.testthat is now used for unit testing (cbeleites/hyperSpec#228).
• Unit testing improved to cover more cases.

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 release.

r-hyperspec/hyperSpec documentation built on May 31, 2024, 5:53 p.m.