- The GitHub repository of this package was moved to https://github.com/r-hyperspec/hyperSpec
NEWS.md(this file) added so that users can readily see changes that may affect the use of the package.- Vignettes converted to
.Rmdand formatted consistently, thanks to @GegznaV. - Introductory vignette
hyperSpec.Rmdreorganized and enhanced, thanks to Bryan Hanson (@bryanhanson). - Documentation is now available in the form of
pkgdownsites at https://r-hyperspec.github.io/
- New color palette
palette_colorblindintroduced (@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 organizationr-hyperSpec. - New function
hy_list_installed_hySpc_packages()lists and functionhy_attach()conveniently loads and attaches all installedr-hyperspecfamily packages (@cbeleites, @GegznaV, cbeleites/hyperSpec#219). - New function
hyperSpec()that initializeshyperSpecobject in a similar way asnew("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).
as.hyperSpec(): The default value of argumentwlis now set towl = NULL(cbeleites/hyperSpec#297).as.hyperSpec():wl = NULLnow means that the default values of wavelengths should be calculated inside the methods ofas.hyperSpec()(cbeleites/hyperSpec#297).- Methods
show(<hyperSpec>)andprint(<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. Methodswl.eval(<hyperSpec>)andwl.eval(<numeric>)for numeric vectors were added (cbeleites/hyperSpec#287). - Function
sample()gains new argumentindex;sample(..., index = TRUE)replaced functionisample()(@GegznaV, #17). - Function
wl_convert_units()converted into S3 generic. Default and hyperSpec methods were added (#29). - Dataset
faux_celland functiongenerate_faux_cell()replacechondrodataset (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?hyperSpecshould be used (#129).
- Possibility to initialize
hyperSpecobject by providing wavelengths only (cbeleites/hyperSpec#288). - Column names in spectra matrix (
$spccolumn ofhyperSpecobject) are now returned correctly by functionsspc.bin()(cbeleites/hyperSpec#237), andspc.loess()(cbeleites/hyperSpec#245
Portions of package hyperSpec were partitioned into individual packages to facilitate maintenance.
- Dataset
chondrowas 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/).
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 ofwl_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 |
- Function
spc.NA.linapprox(), which was deprecated for long time, is now completely removed (cbeleites/hyperSpec#239).
- 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.
- The
hyperSpecteam 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 ofhyperSpecwhich led to this release.