NEWS.md (this file) added so that users can readily see changes that may affect the use of the package..Rmd and formatted consistently, thanks to @GegznaV.hyperSpec.Rmd reorganized and enhanced, thanks to Bryan Hanson (@bryanhanson).pkgdown sites at https://r-hyperspec.github.io/palette_colorblind introduced (@bryanhanson).hy_browse_homepage() opens the homepage of R hyperSpec in a web browser.hy_list_available_hySpc_packages() lists packages, that are available in GitHub organization r-hyperSpec.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).hyperSpec() that initializes hyperSpec object in a similar way as new("hyperSpec") does but has autocompletion possibilities in RStudio (cbeleites/hyperSpec#283, #129).wl_convert_units() (cbeleites/hyperSpec#300).wl_create_label_from_units() that creates labels for wavelength axis (@GegznaV).as.hyperSpec(<hyperSpec>) (cbeleites/hyperSpec#282).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).show(<hyperSpec>) and print(<hyperSpec>) give more concise default output now (@GegznaV, cbeleites/hyperSpec#211).summary(<hyperSpec>) was changed (@GegznaV, cbeleites/hyperSpec#211).wl.eval() is converted into S3 generic. Methods wl.eval(<hyperSpec>) and wl.eval(<numeric>) for numeric vectors were added (cbeleites/hyperSpec#287).sample() gains new argument index; sample(..., index = TRUE) replaced function isample() (@GegznaV, #17).wl_convert_units() converted into S3 generic. Default and hyperSpec methods were added (#29).faux_cell and function generate_faux_cell() replace chondro dataset (cbeleites/hyperSpec#125, cbeleites/hyperSpec#156, cbeleites/hyperSpec#180, cbeleites/hyperSpec#229).hyperSpec(), and to refer to the package, package?hyperSpec should be used (#129).hyperSpec object by providing wavelengths only (cbeleites/hyperSpec#288).$spc column of hyperSpec object) are now returned correctly by functions spc.bin() (cbeleites/hyperSpec#237), and spc.loess() (cbeleites/hyperSpec#245Portions of package hyperSpec were partitioned into individual packages to facilitate maintenance.
chondro was moved to package hySpc.chondro (https://r-hyperspec.github.io/hySpc.chondro/).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/).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/).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/).read.spe(), spe.showcalpoints() were deprecated due to analogous functionality in package hySpc.read.spe (https://r-hyperspec.github.io/hySpc.read.spe/).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/).read.jdx() was deprecated due to analogous functionality in package hySpc.read.jdx (https://r-hyperspec.github.io/hySpc.read.jdx/).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 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.
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
spc.NA.linapprox(), which was deprecated for long time, is now completely removed (cbeleites/hyperSpec#239).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.