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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 words
SKELETON
andhySpc.skeleton
with the new package name in:DESCRIPTION
NEWS.md
README.md
LICENSE
tests/testthat.R
tests/testthat/test_attached.R
- other files
- update
DESCRIPTION
:- title
- description
- the list of authors and contributors
- license
- other fields
- update licensing information in
DESCRIPTION
LICENSE
README.md
- elswhere
- update
README
:- update badges
- update installation instructions (e.g., instead of
devtools::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 (in
github-helpers/
), - delete
github-helpers/
- apply github labels (in
- Code & Vignettes:
- Be sure to review
CONTRIBUTING.md
which describes the standard operating procedures for ther-hyperspec
project. - Copy the code needed for this new package from the original
hyperSpec
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 original
hyperSpec
. 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 in
CONTRIBUTING.md
. - Rinse and repeat to reach perfection!
- Be sure to review
- 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 the branches in
- update this list of TODOs
- Delete this TODO section.
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
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 should go to an appopriate package's 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 (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 (details)
From thehySpc.skeleton's GitHubrepository:
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
iconin the directory), then the working directory is set correctly by default.
- 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
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.
Developers can find information about automatic deployment from this repo topkg-repo
here inCONTRIBUTING.md
.
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Spike removal algortithms for Raman spectra
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