From 7d97e7db3d015f01a6a91f541ae49c11478b87a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vilmantas=20G=C4=97g=C5=BEna?= Date: Mon, 12 Jul 2021 19:00:32 +0300 Subject: [PATCH 1/2] Rename file to "DEPRECATED-read.jdx.R" --- hyperSpec/DESCRIPTION | 4 ++-- hyperSpec/R/{read.jdx.R => DEPRECATED-read.jdx.R} | 3 --- 2 files changed, 2 insertions(+), 5 deletions(-) rename hyperSpec/R/{read.jdx.R => DEPRECATED-read.jdx.R} (99%) diff --git a/hyperSpec/DESCRIPTION b/hyperSpec/DESCRIPTION index edeb21e7..12f4dc7c 100644 --- a/hyperSpec/DESCRIPTION +++ b/hyperSpec/DESCRIPTION @@ -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' @@ -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' @@ -177,6 +177,7 @@ Collate: 'merge.R' 'mergeextra.R' 'mvtnorm.R' + 'normalize01.R' 'palette_colorblind.R' 'palette_matlab.R' 'pearson_dist.R' @@ -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' diff --git a/hyperSpec/R/read.jdx.R b/hyperSpec/R/DEPRECATED-read.jdx.R similarity index 99% rename from hyperSpec/R/read.jdx.R rename to hyperSpec/R/DEPRECATED-read.jdx.R index ec7f4245..dbb09bbb 100644 --- a/hyperSpec/R/read.jdx.R +++ b/hyperSpec/R/DEPRECATED-read.jdx.R @@ -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 #' @@ -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:** #' From b677b31f298bdcbb53814c692451d6f490e82eba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vilmantas=20G=C4=97g=C5=BEna?= Date: Mon, 12 Jul 2021 19:31:47 +0300 Subject: [PATCH 2/2] Reorganize and update NEWS.md --- hyperSpec/NEWS.md | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/hyperSpec/NEWS.md b/hyperSpec/NEWS.md index dd667c9f..739fa0c4 100644 --- a/hyperSpec/NEWS.md +++ b/hyperSpec/NEWS.md @@ -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`. @@ -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