Merge branch 'develop' into update-gha-workflows

CONTRIBUTING.md

@@ -36,13 +36,13 @@ By contributing, you understand and agree that your work becomes the part of the
 
 * Use package [styler](http://styler.r-lib.org/) with RStudio add-in to easily re-style your code to comply with the guidelines.
 * When appropriate, prefer this naming scheme for the internal functions – `.<generic>_<x><y><...>` with `<x>`, `<y>`, etc. the first, second and later parameter/operand:
-    - _ ... missing
-    - a ... array
-    - d ... data frame
-    - f ... formula
-    - h ... hyperSpec object
-    - m ... matrix
-    - n ... numeric (scalar, vector, or matrix)
+  - _ ... missing
+  - a ... array
+  - d ... data frame
+  - f ... formula
+  - h ... hyperSpec object
+  - m ... matrix
+  - n ... numeric (scalar, vector, or matrix)
 
 * Each new function should be accompanied with appropriate unit tests.
 * If a unit test needs to be disabled temporarily, please use `skip("reason for switching off")`.
@@ -130,22 +130,24 @@ Every commit should be related to one feature only, but the commit should group
 
 The project adheres to the semantic versioning guidelines, as outlined at https://semver.org/ (Work in progress, see [#123](https://github.com/cbeleites/hyperSpec/issues/123)).
 
-Briefly, the version string has the form `x.y.z` (or `major.minor.patch`), where the major number gets incremeted if a release introduces breaking changes, the minor one after any changes in functionality (new features of bugfixes), and the patch number is increased after any trivial change. If a major or minor number is incremented, all subsequent ones are set to zero.
+Briefly, the version string has the form `x.y.z` (or `major.minor.patch`), where the major number gets incremented if a release introduces breaking changes, the minor one after any changes in functionality (new features of bugfixes), and the patch number is increased after any trivial change. If a major or minor number is incremented, all subsequent ones are set to zero.
 
 The version numbers refer only to commits in the `master` branch, and get incremented in one of two cases:
+
 * during the release preparation, when a `release/x.y.z` branch buds off `develop` and merges into `master`.
 * after a hotfix, which also results in a new commit on `master`.
 * development branches have version `x.x.x.9000` (or `.9001` and so on - but that is rarely needed).  
   This is important since **pkgdown** uses the `.9000` to distinguish between documentation for the released version vs. the development version.
 
 ### Release Process
+
 The process starts when the package is in a stable state that can be released to CRAN (release candidate). First, decide on a new version number `x.y.z` based on the severity of changes. Then:
 
 * Create a `release/x.y.z` branch using `git flow release start <x.y.z>` and push it with `git flow publish`
 * Open a pull request that merges into `master`
 * Update the version number in the `DESCRIPTION` file
 * Verify that the changes are listed in `NEWS.md`
-* Confirm that the package can be built for each plaftorm
+* Confirm that the package can be built for each platform
 * Ensure that all check are passed on the tarballs you build (either on your machine or using CI) with `R CMD check --as-cran <package.tar.gz>`. The checks must pass for `R` versions `R-oldrel`, `R-release`, `R-patched`, and `R-devel`.
 * If any bugs are found, they must be fixed in the very same branch (see [here](https://stackoverflow.com/a/57507373/6029703) for details)
 * Once everything works use `git flow release finish <x.y.z>`. It will merge the release branch into both `master` and `develop`, and will assign a tag to the newly created commit in the `master` branch.

DESCRIPTION

@@ -26,7 +26,7 @@ Description: Comfortable ways to work with hyperspectral data sets,
     of information associated with each of the spectra. The spectra can be data
     as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
     etc. More generally, any data that is recorded over a discretized variable,
-    e.g. absorbance = f (wavelength), stored as a vector of absorbance values
+    e.g. absorbance = f(wavelength), stored as a vector of absorbance values
     for discrete wavelengths is suitable.
 License: GPL (>= 3) + file LICENSE
 LazyLoad: yes

R/initialize.R

@@ -1,15 +1,14 @@
-
-#' Create a `hyperSpec` object
+#' Create a `hyperSpec` Object
 #'
-#' To create a new `hyperSpec` object, the following functions can be used:
+#' To create a new `hyperSpec` object, you can use one of the following functions:
 #' - [new()] (i.e., `new("hyperSpec", ...)`);
 #' - `new_hyperSpec()`.
 #'
 #' @note
 #'
-#' A `hyperSpec` object is an S4 object, so its initialization is carried out
-#' by calling `new("hyperSpec", ...)`. Function `new_hyperSpec()` is just
-#' a convenience function.
+#' A `hyperSpec` object is an S4 object, so its initialization is performed
+#' by calling `new("hyperSpec", ...)`. The function `new_hyperSpec()` is provided
+#' for convenience.
 #'
 #' @docType methods
 #'
@@ -29,30 +28,30 @@
 #'        A spectra matrix with spectra in rows and wavelength intensities in
 #'        columns.
 #'
-#'  The `spc` does not need to be an R `matrix`, but must be an object
+#'  The `spc` does not need to be an R `matrix`, but it must be an object
 #'  convertible to a matrix via `I(as.matrix(spc))`.
 #'
 #' @param data (`data.frame`)  \cr
 #'        A `data.frame` with extra (non-spectroscopic) data in columns.
 #'        The data frame may also contain a special column `spc` with a `matrix`
 #'        of spectroscopic data.
-#'        (Such single column that contains matrix can be created with
+#'        (Such a single column that contains a matrix can be created with
 #'        `data.frame(spc = I(as.matrix(spc)))`.
-#'        However, it will usually be more convenient if the spectra are given
-#'        via argument `spc`.)
+#'        However, it is usually more convenient to provide the spectra
+#'        via the `spc` argument.)
 #'
 #' @param wavelength (numeric vector)  \cr
 #'        The wavelengths corresponding to the columns of `spc`.
 #'
 #'  If no wavelengths are given, an appropriate vector is derived from the
-#'  column the column names of `data$spc`. If this is not possible,
+#'  column names of `data$spc`. If this is not possible,
 #'  `1:ncol(data$spc)` is used instead.
 #'
 #' @param labels A named `list`:
-#' - list's element names should containing one or more names of `data`
-#'   columns as well as special name `.wavelength` for `wavelength`s ).
+#' - list's element names should contain one or more names of `data`
+#'   columns as well as the special name `.wavelength` for `wavelength`s.
 #' - list's element values should contain the labels for the indicated
-#'   names usually either in a for of character strings or
+#'   names, usually in the form of character strings or
 #'   [plotmath][grDevices::plotmath()] expressions.
 #'   (The labels should be given in a form ready
 #'   for the text-drawing functions, see [grDevices::plotmath()]).
@@ -61,24 +60,26 @@
 #' columns of `data` and `wavelength` is used.
 #'
 #' @param gc (logical) \cr Use garbage collection.
-#'       If option `gc` is `TRUE`, the initialization will have frequent calls
-#'       to [base::gc()], which can help to avoid swapping or running out of
-#'       memory. The default value of `gc` can be set via [hy_set_options()].
+#'       If the option `gc` is set to `TRUE`, the initialization will have
+#'       frequent calls to [base::gc()], which can help avoid swapping or
+#'       running out of memory.
+#'       The default value of `gc` can be set via [hy_set_options()].
 #'
 #' @param log This parameter is currently **ignored**. It is present due to
-#'        backwards compatibility.
+#'        backward compatibility.
 #'
 #' @param .Object A new `hyperSpec` object.
 #'
 #'
-#' @author C.Beleites, V. Gegzna
+#' @author C. Beleites, V. Gegzna
 #' @seealso
 #'
 #' - [methods::new()] for more information on creating and initializing S4 objects.
-#' - [grDevices::plotmath()] on expressions for math annotations as for slot `label`.
-#' - [hy_set_options()] setting `hyperSpec` options.
+#' - [grDevices::plotmath()] for expressions used for math annotations as in the `label` slot.
+#' - [hy_set_options()] for setting `hyperSpec` options.
 #'
 #' @keywords methods datagen
+#'
 #' @concept hyperSpec conversion
 #'
 #' @examples
@@ -98,7 +99,7 @@
 #' colnames(spc) <- 600:603
 #' new("hyperSpec", spc = spc) # wavelength taken from colnames (spc)
 #'
-#' # given wavelengths precede over colnames of spc
+#' # given wavelengths take precedence over colnames of spc
 #' new("hyperSpec", spc = spc, wavelength = 700:703)
 #'
 #' # specifying labels
@@ -123,7 +124,7 @@ NULL
 .initialize <- function(.Object, spc = NULL, data = NULL, wavelength = NULL,
                         labels = NULL, gc = hy_get_option("gc"),
                         log = "ignored") {
-  # Do the small stuff first, so we need not be too careful about copies
+  # Handle the small stuff first, so we don't need to be too careful about copies
 
   # The wavelength axis
   if (!is.null(wavelength) && !is.numeric(wavelength)) {
@@ -197,7 +198,7 @@ NULL
   if (gc) base::gc()
 
   if (!is.null(data$spc) && !(is.null(spc))) {
-    warning("Spectra in data are overwritten by argument spc.")
+    warning("Spectra in data are overwritten by the argument spc.")
   }
 
   # Deal with spectra
@@ -216,7 +217,7 @@ NULL
     dim <- dim(spc)
     spc <- suppressWarnings(as.numeric(spc))
     if (all(is.na(spc))) {
-      stop("spectra matrix needs to be numeric or convertable to numeric")
+      stop("spectra matrix needs to be numeric or convertible to numeric")
     } else {
       warning("spectra matrix is converted from ", class(data$spc), " to numeric.")
     }
@@ -227,7 +228,7 @@ NULL
   if (gc) base::gc()
 
   if (!is.null(spc)) {
-    attr(spc, "class") <- "AsIs" # I seems to make more than one copy
+    attr(spc, "class") <- "AsIs" # It seems to make more than one copy
     if (gc) base::gc()
   }
 
@@ -254,7 +255,7 @@ NULL
 
   .Object <- .spc_fix_colnames(.Object) # For consistency with .wl<-
 
-  # Finally: check whether we got a valid hyperSpec object
+  # Finally, check whether we got a valid hyperSpec object
   validObject(.Object)
 
   .Object

R/write_txt_long.R

@@ -8,25 +8,25 @@
 #' @rdname write_txt
 #' @aliases write_txt_long
 #'
-#' @param file Filename or connection.
-#' @param object `hyperSpec` object.
-#' @param cols Column names specifying the column order.
-#' @param order Which columns should be [base::order()]ed? Parameter `order` is
-#'        used as index vector into a `data.frame` with columns given by `cols`.
-#' @param na.last Handed to [base::order()] by `write_txt_long`.
-#' @param quote,sep,col.names,row.names Have their usual meaning
-#'        (see [utils::write.table()]), but different default values.
-#'
-#' For file import, `row.names` should usually be `NULL` so that the first
-#'        column becomes a extra data column (as opposed to row names of the
-#'        extra data).
-#' @param col.labels Should the column labels be used rather than the
-#'        colnames?
+#' @param file Filename or connection to write the data.
+#' @param object A `hyperSpec` object to export.
+#' @param cols Column names specifying the order of columns in the output file.
+#' @param order Which columns should be sorted using [base::order()]? The `order`
+#'        parameter is used as an index vector into a `data.frame` with columns
+#'        specified by `cols`.
+#' @param na.last Passed to [base::order()] by `write_txt_long`.
+#' @param quote,sep,col.names,row.names These parameters have their usual meaning
+#'        as used in [utils::write.table()], but with different default values.
+#'
+#' For file import, `row.names` should usually be set to `NULL` so that the first
+#'        column becomes an extra data column (instead of row names of the extra data).
+#'
+#' @param col.labels Should the column labels be used rather than the colnames?
 #' @param append Should the output be appended to an existing file?
-#' @param decreasing logical vector giving the sort order.
-#' @param header.lines Toggle one or two line header (wavelengths in the
+#' @param decreasing A logical vector specifying the sort order for columns.
+#' @param header.lines Toggle one or two-line headers (wavelengths in the
 #'        second header line) for `write_txt_wide`.
-#' @param ... arguments handed to [utils::write.table()].
+#' @param ... Additional arguments passed to [utils::write.table()].
 #'
 #'
 #' @concept io
@@ -39,13 +39,13 @@
 #'
 #' ## Export & import Matlab files
 #' if (require(R.matlab)) {
-#'   # export to matlab file
+#'   # Export to a Matlab file
 #'   writeMat(paste0(tempdir(), "/test.mat"),
 #'     x = flu[[]], wavelength = flu@wavelength,
 #'     label = lapply(flu@label, as.character)
 #'   )
 #'
-#'   # reading a matlab file
+#'   # Read a Matlab file
 #'   data <- readMat(paste0(tempdir(), "/test.mat"))
 #'   print(data)
 #'   mat <- new("hyperSpec",
@@ -86,12 +86,12 @@
 #'
 #' read.txt.wide(
 #'   file = paste0(tempdir(), "/flu.txt"),
-#'   # give columns in same order as they are in the file
+#'   # Give columns in the same order as they are in the file
 #'   cols = list(
 #'     spc = "I / a.u",
 #'     c = expression("/"("c", "mg/l")),
 #'     filename = "filename",
-#'     # plus wavelength label last
+#'     # Plus wavelength label last
 #'     .wavelength = "lambda / nm"
 #'   ),
 #'   header = TRUE

README.md

@@ -5,9 +5,9 @@
 [![CRAN status](https://www.r-pkg.org/badges/version-last-release/hyperSpec)](https://cran.r-project.org/package=hyperSpec)
 [![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/hyperSpec)](https://cran.r-project.org/package=hyperSpec)
 [![metacran downloads](https://cranlogs.r-pkg.org/badges/hyperSpec)](https://cran.r-project.org/package=hyperSpec)
-[![R-CMD-check](https://github.com/r-hyperspec/hyperSpec/workflows/R-CMD-check/badge.svg?branch=develop)](https://github.com/r-hyperspec/hyperSpec/actions)
+[![R-CMD-check](https://github.com/r-hyperspec/hyperSpec/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-hyperspec/hyperSpec/actions/workflows/R-CMD-check.yaml)
 [![Codecov](https://codecov.io/gh/r-hyperspec/hyperSpec/branch/develop/graph/badge.svg)](https://codecov.io/gh/r-hyperspec/hyperSpec?branch=develop)
-![Website (pkgdown)](https://github.com/r-hyperspec/hyperSpec/workflows/Website%20(pkgdown)/badge.svg)
+[![Website (pkgdown)](https://github.com/r-hyperspec/hyperSpec/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/r-hyperspec/hyperSpec/actions/workflows/pkgdown.yaml)
 <!-- [![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) -->
 <!-- badges: end -->
 
@@ -21,7 +21,7 @@
 <font color="red" size=4>
 <b>Package `hyperSpec` is under overhaul now.</b>  
 So this website is still under construction and the contents as well as resources are not fully updated yet.  
-The documentation of version `0.100.0` is not present here too.
+The documentation of version <code>0.100.2</code> is not present here either.
 </font>
 </center>
 <br>
@@ -30,7 +30,7 @@ The documentation of version `0.100.0` is not present here too.
 
 [**R**](https://www.r-project.org/) package **hyperSpec** is the main package in the [**`r-hyperspec`**](https://r-hyperspec.github.io/) family of packages.
 The goal of **hyperSpec** (and whole **`r-hyperspec`**) is to make the work with hyperspectral data sets, (i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra) more comfortable.
-The spectra can be data as obtained during 
+The spectra can be data obtained during 
 [XRF](https://en.wikipedia.org/wiki/X-ray_fluorescence),
 [UV/VIS](https://en.wikipedia.org/wiki/Ultraviolet%E2%80%93visible_spectroscopy), 
 [Fluorescence](https://en.wikipedia.org/wiki/Fluorescence_spectroscopy),
@@ -59,7 +59,7 @@ The documentation of the other **`r-hyperspec`** family packages can be found at
 
 ## Issues, Bug Reports and Feature Requests
 
-Issues, bug reports and feature requests should go [here](https://github.com/r-hyperspec/hyperSpec/issues)!
+Issues, bug reports, and feature requests should go [here](https://github.com/r-hyperspec/hyperSpec/issues)!
 <!-- ---------------------------------------------------------------------- -->
 
 
@@ -96,7 +96,7 @@ remotes::install_github("r-hyperspec/hyperSpec")
 ```
 
 **NOTE 1:**
-Usually, "Windows" users need to download, install and properly configure **Rtools** (see [these instructions](https://cran.r-project.org/bin/windows/Rtools/)) to make the code above work.
+Usually, "Windows" users need to download, install, and properly configure **Rtools** (see [these instructions](https://cran.r-project.org/bin/windows/Rtools/)) to make the code above work.
 
 **NOTE 2:**
 This method will **not** install package's documentation (help pages and vignettes) into your computer.
@@ -115,14 +115,14 @@ So you can either use the [online documentation](https://r-hyperspec.github.io/)
 1. From the **hyperSpec**'s GitHub [repository](https://github.com/r-hyperspec/hyperSpec):
     - If you use Git, `git clone` the branch of interest.
       You may need to fork it before cloning.
-    - Or just chose the branch of interest (1 in Figure below), download a ZIP archive with the code (2, 3) and unzip it on your computer.  
+    - Or just choose the branch of interest (1 in Figure below), download a ZIP archive with the code (2, 3), and unzip it on your computer.  
 ![image](https://user-images.githubusercontent.com/12725868/89338263-ffa1dd00-d6a4-11ea-94c2-fa36ee026691.png)
 
 2. Open the downloaded directory in RStudio (preferably, as an RStudio project).
     - The code below works correctly only if your current working directory coincides with the root of the repository, i.e., if it is in the directory that contains file `README.md`.
     - If you open RStudio project correctly (e.g., by clicking `project.Rproj` icon ![image](https://user-images.githubusercontent.com/12725868/89340903-26621280-d6a9-11ea-8299-0ec5e9cf7e3e.png) in the directory), then the working directory is set correctly by default.
 
-3. In RStudio 'Console' window, run the code (provided below) to:
+3. In the RStudio 'Console' window, run the code (provided below) to:
     a. Install packages **remotes** and **devtools**.
     b. Install **hyperSpec**'s dependencies.
     c. Create **hyperSpec**'s documentation.
@@ -146,7 +146,7 @@ devtools::install(build_vignettes = TRUE)
 ```
 
 **NOTE 1:**
-Usually, "Windows" users need to download, install and properly configure **Rtools** (see [these instructions](https://cran.r-project.org/bin/windows/Rtools/)) to make the code above work.
+Usually, "Windows" users need to download, install, and properly configure **Rtools** (see [these instructions](https://cran.r-project.org/bin/windows/Rtools/)) to make the code above work.
 
 </details>
 

_pkgdown.yml

@@ -215,6 +215,7 @@ reference:
 - contents:
   - has_concept("labels")
 
+
 - title: '8. Other functions' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   desc: "Functions not mentioned above."
 - contents: