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Rename file, update NEWS.md #336

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Jul 12, 2021
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Rename file, update NEWS.md #336

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7d97e7d
Rename file to "DEPRECATED-read.jdx.R"
GegznaV Jul 12, 2021
b677b31
Reorganize and update NEWS.md
GegznaV Jul 12, 2021
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4 changes: 2 additions & 2 deletions hyperSpec/DESCRIPTION
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Expand Up @@ -101,6 +101,7 @@ Collate:
'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'
Expand All @@ -124,7 +125,6 @@ Collate:
'DEPRECATED-spc_spline.R'
'DEPRECATED-wc.R'
'DEPRECATED-wl_convert_units.R'
'normalize01.R'
'wl_eval.R'
'DEPRECATED-wl_eval.R'
'DEPRECATED-wl_sort.R'
Expand Down Expand Up @@ -177,6 +177,7 @@ Collate:
'merge.R'
'mergeextra.R'
'mvtnorm.R'
'normalize01.R'
'palette_colorblind.R'
'palette_matlab.R'
'pearson_dist.R'
Expand All @@ -187,7 +188,6 @@ Collate:
'plotvoronoi.R'
'quantile.R'
'rbind.fill.R'
'read.jdx.R'
'read_txt_long.R'
'read_txt_wide.R'
'replace.R'
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33 changes: 17 additions & 16 deletions hyperSpec/NEWS.md
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Expand Up @@ -10,35 +10,39 @@
* `NEWS.md` (this file) added so that users can readily see changes that may affect the use of the package.
* Documentation now available in `pkgdown` sites (https://r-hyperspec.github.io/).
* Introductory vignette reorganized and enhanced, thanks to Bryan Hanson.
* Dataset `faux_cell` and function `generate_faux_cell()` replace `chondro` dataset (#125, #156, #180, #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/).
- Functions `read.mat.Witec()`, **--- ELABORATE ---** were deprecated due analogous functionality in package **hySpc.read.mat** (https://r-hyperspec.github.io/hySpc.read.mat/).
- The following functions were renamed or replaced by new ones (see table below).

Deprecated function | New (replacement) function | Related issues
-------------------------|------------------------------- | ----------------
`matlab.dark.palette` | `palette_matlab_dark` | #208, #299
`matlab.palette` | `palette_matlab` | #208, #299
`alois.palette` | `palette_alois` | #208, #299
`spc.NA.approx()` | `spc_na_approx()` | #208, #301
`.fileio.optional()` | `.spc_io_postprocess_optional()` | #208, #302
`.fix_spc_colnames()` | `.spc_fix_colnames()` | #208, #301
`alois.palette()` | `palette_alois()` | #208, #299, @sangttruong
`guess.wavelength()` | `extract_numbers()` | #208, #309
`matlab.dark.palette()` | `palette_matlab_dark()` | #299, #299, @sangttruong
`matlab.palette()` | `palette_matlab()` | #208, #299, @sangttruong
`mergeextra()` | `merge_data()` | #208, #302
`orderwl()` | `wl_sort()` | #208, #309
`spc.bin()` | `spc_bin()` | #208, #301
`spc.fit.poly()` | `spc_fit_poly()` | #208, #301
`spc.fit.poly.below()` | `spc_fit_poly_below()` | #208, #301
`spc.loess()` | `spc_loess()` | #208, #301
`spc.smooth.spline()` | `spc_smooth_spline()` | #208, #301
`spc.NA.approx()` | `spc_na_approx()` | #208, #301
`spc.rubberband()` | `spc_rubberband()` | #208, #301
`.fix_spc_colnames()` | `.spc_fix_colnames()` | #208, #301
`mergeextra()` | `merge_data()` | #208, #302
`.fileio.optional()` | `.spc_io_postprocess_optional()` | #208, #302
`guess.wavelength()` | `extract_numbers()` | #208, #309
`orderwl()` | `wl_sort()` | #208, #309
`spc.smooth.spline()` | `spc_smooth_spline()` | #208, #301
`wl.eval()` | `wl_eval()` | #208, #309
`wlconv()` | `wl_convert_units()` | #208, #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()` (#300).
* Dataset `faux_cell` and function `generate_faux_cell()` replace `chondro` dataset (#125, #156, #180, #229).
* Function `spc.NA.linapprox()`, which was deprecated for long time, is now completely removed (#239).
* Column names in spectra matrix (`$spc` column of `hyperSpec` object) are now returned correctly by functions `spc.bin()` (#237), and `spc.loess()` (#245).
* New function `hy_list_available_hySpc_packages()` lists packages, that are available in GitHub organization `r-hyperSpec`.
Expand All @@ -54,10 +58,7 @@
* Functions `show()` and `print()` give more concise default output now (@GegznaV, #211).
* The default output of function `summary()` was changed (@GegznaV, #211).
* New color palette `palette_colorblind` introduced (@bryanhanson).
* Changing name of color palette functions with prefix palette_ (@sangttruong, #299):
- Change matlab.dark.palette() to palette_matlab_dark().
- Change matlab.palette() to palette_matlab().
- Change alois.palette() to palette_alois().



## Non-User-Facing Changes from 0.99 Series
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3 changes: 0 additions & 3 deletions hyperSpec/R/read.jdx.R → hyperSpec/R/DEPRECATED-read.jdx.R
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@@ -1,5 +1,3 @@
# TODO: rename this file to "DEPRECATED-read.jdx.R" in a separate pull request.

#' @name DEPRECATED-read.jdx
#' @concept moved to hySpc.read.jdx
#'
Expand All @@ -13,7 +11,6 @@
#' More on functions in package \pkg{hySpc.read.jdx}
#' [here (link)](https://r-hyperspec.github.io/hySpc.read.jdx/reference/index.html).
#'
#' ***
#'
#' **Old description:**
#'
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