├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── 1_bug_report.md │ ├── 2_feature_request.md │ └── 3_other.md └── workflows │ ├── R-CMD-check.yaml │ ├── drat--insert-package.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── NEWS.md ├── R ├── Arith.R ├── Compare.R ├── DEPRECATED-chk.hy.R ├── DEPRECATED-count_lines.R ├── DEPRECATED-dist_pearson.R ├── DEPRECATED-extract_numbers.R ├── DEPRECATED-ggplot2.R ├── DEPRECATED-hy_options.R ├── DEPRECATED-isample.R ├── DEPRECATED-mark.dendrogram.R ├── DEPRECATED-markpeak.R ├── DEPRECATED-normalize01.R ├── DEPRECATED-plotc.R ├── DEPRECATED-plotmap.R ├── DEPRECATED-plotmat.R ├── DEPRECATED-plotspc.R ├── DEPRECATED-plotvoronoi.R ├── DEPRECATED-pooled.cov.R ├── DEPRECATED-raster.R ├── DEPRECATED-read.ENVI.HySpex.R ├── DEPRECATED-read.ENVI.Nicolet.R ├── DEPRECATED-read.ENVI.R ├── DEPRECATED-read.asc.Andor.R ├── DEPRECATED-read.asc.PerkinElmer.R ├── DEPRECATED-read.ini.R ├── DEPRECATED-read.jdx.R ├── DEPRECATED-read.mat.Cytospec.R ├── DEPRECATED-read.mat.Witec.R ├── DEPRECATED-read.spc.Kaiser.R ├── DEPRECATED-read.spc.R ├── DEPRECATED-read.spe.R ├── DEPRECATED-read.txt.Horiba.R ├── DEPRECATED-read.txt.Renishaw.R ├── DEPRECATED-read.txt.Shimadzu.R ├── DEPRECATED-read.txt.Witec.R ├── DEPRECATED-read.txt.long.R ├── DEPRECATED-read.txt.wide.R ├── DEPRECATED-scan.R ├── DEPRECATED-spc.identify.R ├── DEPRECATED-spc_bin.R ├── DEPRECATED-spc_fit_poly.R ├── DEPRECATED-spc_fix_colnames.R ├── DEPRECATED-spc_loess.R ├── DEPRECATED-spc_na_approx.R ├── DEPRECATED-spc_rubberband.R ├── DEPRECATED-spc_spline.R ├── DEPRECATED-stacked.offsets.R ├── DEPRECATED-wc.R ├── DEPRECATED-wl_convert_units.R ├── DEPRECATED-wl_eval.R ├── DEPRECATED-wl_sort.R ├── DEPRECATED-write_txt_long.R ├── DEPRECATED-write_txt_wide.R ├── Math.R ├── Summary.R ├── aggregate.R ├── all.equal.R ├── apply.R ├── as.data.frame.R ├── as_hyperSpec.R ├── barbiturates.R ├── bind.R ├── colMeans.R ├── collapse.R ├── constants-regexps.R ├── cov_pooled.R ├── decomposition.R ├── dim.R ├── dimnames.R ├── dist_pearson.R ├── droplevels.R ├── empty.R ├── expand.R ├── extract.R ├── extract_numbers.R ├── faux_cell.R ├── flu.R ├── generate-test-data.R ├── hy_attach.R ├── hy_auto_completion.R ├── hy_browse_homepage.R ├── hy_deprecation-messages.R ├── hy_list_available_hySpc_packages.R ├── hy_list_installed_hySpc_packages.R ├── hy_options.R ├── hy_paste_names.R ├── hy_validate.R ├── hyperspec-class.R ├── hyperspec-package.R ├── identify_spc.R ├── initialize.R ├── labels.R ├── laser.R ├── levelplot.R ├── map_identify.R ├── mark_groups_in_dendrogram.R ├── mark_peak.R ├── mean_sd.R ├── merge.R ├── mergeextra.R ├── normalize_01.R ├── palette_colorblind.R ├── palette_matlab.R ├── paracetamol.R ├── paste_row.R ├── plot.R ├── plot_and_get.R ├── plot_c.R ├── plot_map.R ├── plot_mat.R ├── plot_spc.R ├── plot_voronoi.R ├── quantile.R ├── raster.R ├── rbind.fill.R ├── read_txt_long.R ├── read_txt_wide.R ├── replace.R ├── rmmvnorm.R ├── sample.R ├── scale.R ├── seq.R ├── show.R ├── spc_bin.R ├── spc_fit_poly.R ├── spc_fix_colnames.R ├── spc_io_postprocess_optional.R ├── spc_loess.R ├── spc_na_approx.R ├── spc_rubberband.R ├── spc_spline.R ├── split.R ├── subset.R ├── sweep.R ├── sysdata.rda ├── trellis_factor_key.R ├── vandermonde.R ├── wl.R ├── wl2i.R ├── wl_convert_units.R ├── wl_create_label_from_units.R ├── wl_eval.R ├── wl_fix_unit_name.R ├── wl_sort.R ├── write_txt_long.R ├── write_txt_wide.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data-raw ├── barbiturates.R ├── flu.R ├── fluNA.R ├── laser.R └── paracetamol.R ├── data ├── barbiturates.rda ├── flu.rda ├── laser.rda ├── palette_colorblind.rda └── paracetamol.rda ├── inst ├── CITATION ├── extdata │ ├── BARBITUATES.SPC │ ├── README.txt │ ├── chondro_mini.rds │ ├── flu │ │ ├── flu1.txt │ │ ├── flu2.txt │ │ ├── flu3.txt │ │ ├── flu4.txt │ │ ├── flu5.txt │ │ └── flu6.txt │ ├── laser.txt.gz │ └── paracetamol.txt └── schemes │ └── r-hyperspec-family.gv ├── pkgdown └── extra.css ├── tests ├── interactive.tests ├── test.spc ├── testthat.R └── testthat │ ├── _snaps │ └── attached │ │ ├── plot-1-fill.svg │ │ ├── plot-1-rev.svg │ │ ├── plot-c.svg │ │ ├── plot-depth.svg │ │ ├── plot-map.svg │ │ ├── plot-mat-contour.svg │ │ ├── plot-mat.svg │ │ ├── plot-spc.svg │ │ ├── plot-spcmeansd.svg │ │ ├── plot-spcprctile.svg │ │ ├── plot-spcprctl5.svg │ │ ├── plot-ts.svg │ │ ├── plot-voronoi-01.svg │ │ ├── plot.svg │ │ ├── plotc.svg │ │ ├── plotmap.svg │ │ ├── plotmat.svg │ │ ├── plotspc.svg │ │ └── plotvoronoi.svg │ └── test-attached.R └── vignettes ├── .gitignore ├── .install_extras ├── baseline.Rmd ├── elsevier-with-titles.csl ├── fileio--fileformats.txt ├── fileio.Rmd ├── fileio.bib ├── flu.Rmd ├── hyperSpec.Rmd ├── intro--structure--hyperSpec--objects.png ├── laser--rgl-3d.png ├── laser.Rmd ├── list-of-vignettes.md ├── plotting--fig-3D-01.png ├── plotting.Rmd ├── read.ENVI.Nicolet.R ├── 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