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Spike removal algortithms for Raman spectra

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r-hyperspec/hySpc.remove.Raman.spikes

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RepositoryhySpc.skeleton is a package template ("skeleton") forr-hyperspec family packages.

When creating a new package (repository):

  • replace wordsSKELETON andhySpc.skeleton with the new package name in:
    • DESCRIPTION
    • NEWS.md
    • README.md
    • LICENSE
    • tests/testthat.R
    • tests/testthat/test_attached.R
    • other files
  • updateDESCRIPTION:
    • title
    • description
    • the list of authors and contributors
    • license
    • other fields
  • update licensing information in
    • DESCRIPTION
    • LICENSE
    • README.md
    • elswhere
  • updateREADME:
    • update badges
    • update installation instructions (e.g., instead ofdevtools::install(build_vignettes = TRUE) the following code might be more appropriate if no vignettes are includeddevtools::install())
    • update other information, if needed.
  • create issue labels:
    • apply github labels (ingithub-helpers/),
    • deletegithub-helpers/
  • Code & Vignettes:
    • Be sure to reviewCONTRIBUTING.md which describes the standard operating procedures for ther-hyperspec project.
    • Copy the code needed for this new package from the originalhyperSpec files. Leave the old code untouched for now, ashyperSpec has to continue to operate.
    • Update the code and write new code as needed.
    • Update unit tests as needed.
    • Update examples as needed.
    • Build and check locally. Chase out the demons.
    • Create a new vignette for this package, starting from the relevant vignette in originalhyperSpec. The support files are already present. If you don't want a vignette, delete the entire vignette folder.
    • Build and check locally again, fixing any remaining problems.
    • Create a pull request as described inCONTRIBUTING.md.
    • Rinse and repeat to reach perfection!
  • Workflows:
    • Update the branches in.github/workflows/drat--insert-package.yaml. Triggering branches are set to NONE inpkg-skeleton because we don't wantpkg-skeleton to be deployed to the repo.
  • update this list of TODOs
  • Delete this TODO section.

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.CRAN statusR-CMD-checkWebsite (pkgdown)Codecov

R PackagehySpc.skeleton


This package is still under construction. So this website is not fully updated yet.

R packagehySpc.skeleton is a member of ther-hyperspec packages family, which ...
WRITE THE PURPOSE OF THIS PACKAGE

Documentation

There are two versions ofhySpc.skeleton online documentation:

a. for thereleased version of package,
b. for thedevelopment version of package.

The documentation of the otherr-hyperspec family packages can be found atr-hyperspec.github.io.

Issues, Bug Reports and Feature Requests

Issues, bug reports and feature requests should go to an appopriate package's repository:

Installation

Install from CRAN-like Repository

Therecommended way to install the in-development version:

repos<- c("https://r-hyperspec.github.io/pkg-repo/", getOption("repos"))install.packages("hySpc.skeleton",repos=repos)

Install from GitHub

Install from GitHub (details)

You can install the in-development version of the package fromGitHub too:

if (!require(remotes)) {install.packages("remotes")}remotes::install_github("r-hyperspec/hySpc.skeleton")

NOTE 1:Usually, "Windows" users need to download, install and properly configureRtools (seethese instructions) to make the code above work.

NOTE 2:This method willnot install package's documentation (help pages and vignettes) into your computer.So you can either use theonline documentation or build the package from source (see the next section).

Install from Source

Install from Source (details)
  1. From thehySpc.skeleton's GitHubrepository:

    • 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.
      image
  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 fileREADME.md.
    • If you open RStudio project correctly (e.g., by clickingproject.Rproj iconimage in the directory), then the working directory is set correctly by default.
  3. In RStudio 'Console' window, run the code (provided below) to:a. Install packagesremotes anddevtools.b. InstallhySpc.skeleton's dependencies.c. CreatehySpc.skeleton's documentation.d. Install packagehySpc.skeleton.

# Do not abort installation even if some packages are not availableSys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")# Install packages remotes and devtoolsinstall.packages(c("remotes","devtools"))# Install hySpc.skeleton's dependenciesremotes::install_deps(dependencies=TRUE)# Create hySpc.skeleton's documentationdevtools::document()# Install package hySpc.skeletondevtools::install(build_vignettes=TRUE)

NOTE 1:Usually, "Windows" users need to download, install and properly configureRtools (seethese instructions) to make the code above work.

For Developers

Developers can find information about automatic deployment from this repo topkg-repohere inCONTRIBUTING.md.

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