Skip to content
This repository has been archived by the owner on Jan 30, 2025. It is now read-only.

Commit

Permalink
Prepare for next release
Browse files Browse the repository at this point in the history
  • Loading branch information
nfrerebeau committed Jul 26, 2024
1 parent 2bec148 commit ecd85e4
Show file tree
Hide file tree
Showing 10 changed files with 106 additions and 121 deletions.
145 changes: 63 additions & 82 deletions CITATION.cff
Original file line number Diff line number Diff line change
@@ -1,23 +1,40 @@
# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
# --------------------------------------------

cff-version: 1.2.0
message: 'To cite package "alkahest" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'alkahest: Pre-Processing XY Data from Experimental Methods'
version: 1.1.1.9000
version: 1.2.0
doi: 10.5281/zenodo.7081524
identifiers:
- description: The concept DOI.
type: doi
value: 10.5281/zenodo.7081524
- description: The versioned DOI for version 1.0.0.
type: doi
value: 10.5281/zenodo.7081525
- description: The versioned DOI for version 1.1.0.
type: doi
value: 10.5281/zenodo.7947723
- description: The versioned DOI for version 1.1.1.
type: doi
value: 10.5281/zenodo.8031801
- description: The Software Heritage identifier for version 1.1.1.
type: swh
value: swh:1:rel:eb483bf44f6b883ee3c32e51fabd6fce0cb39fce
abstract: A lightweight, dependency-free toolbox for pre-processing XY data from experimental
methods (i.e. any signal that can be measured along a continuous variable). This
package provides methods for baseline estimation and correction, smoothing, normalization,
integration and peaks detection. Baseline correction methods includes polynomial
fitting as described in Lieber and Mahadevan-Jansen (2003) <doi:10.1366/000370203322554518>,
Rolling Ball algorithm after Kneen and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>,
SNIP algorithm after Ryan et al. (1988) <doi:10.1016/0168-583X(88)90063-8>, 4S Peak
Filling after Liland (2015) <doi:10.1016/j.mex.2015.02.009> and more.
fitting as described in Lieber and Mahadevan-Jansen (2003) <https://doi.org/10.1366/000370203322554518>,
Rolling Ball algorithm after Kneen and Annegarn (1996) <https://doi.org/10.1016/0168-583X(95)00908-6>,
SNIP algorithm after Ryan et al. (1988) <https://doi.org/10.1016/0168-583X(88)90063-8>,
4S Peak Filling after Liland (2015) <https://doi.org/10.1016/j.mex.2015.02.009>
and more.
authors:
- family-names: Frerebeau
given-names: Nicolas
Expand All @@ -33,14 +50,13 @@ preferred-citation:
email: nicolas.frerebeau@u-bordeaux-montaigne.fr
orcid: https://orcid.org/0000-0001-5759-4944
affiliation: Université Bordeaux Montaigne
year: '2023'
location:
name: Pessac, France
notes: R package version 1.1.1.9000
url: https://packages.tesselle.org/alkahest/
doi: 10.5281/zenodo.7081524
year: '2024'
institution:
name: Université Bordeaux Montaigne
address: Pessac, France
notes: R package version 1.2.0
url: https://packages.tesselle.org/alkahest/
doi: 10.5281/zenodo.7081524
repository: https://CRAN.R-project.org/package=alkahest
repository-code: https://github.com/tesselle/alkahest
url: https://packages.tesselle.org/alkahest/
Expand All @@ -61,56 +77,55 @@ references:
url: https://www.R-project.org/
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2024'
version: '>= 3.5.0'
- type: software
title: grDevices
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2024'
doi: 10.32614/CRAN.package.grDevices
- type: software
title: methods
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2024'
doi: 10.32614/CRAN.package.methods
- type: software
title: stats
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2024'
doi: 10.32614/CRAN.package.stats
- type: software
title: utils
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2024'
doi: 10.32614/CRAN.package.utils
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
Expand All @@ -122,7 +137,8 @@ references:
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2023'
year: '2024'
doi: 10.32614/CRAN.package.knitr
- type: software
title: Matrix
abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
Expand All @@ -140,72 +156,37 @@ references:
- family-names: Jagan
given-names: Mikael
orcid: https://orcid.org/0000-0002-3542-2938
year: '2023'
year: '2024'
doi: 10.32614/CRAN.package.Matrix
- type: software
title: rmarkdown
abstract: 'rmarkdown: Dynamic Documents for R'
title: markdown
abstract: 'markdown: Render Markdown with ''commonmark'''
notes: Suggests
url: https://pkgs.rstudio.com/rmarkdown/
repository: https://CRAN.R-project.org/package=rmarkdown
url: https://github.com/rstudio/markdown
repository: https://CRAN.R-project.org/package=markdown
authors:
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
- family-names: Dervieux
given-names: Christophe
email: cderv@posit.co
orcid: https://orcid.org/0000-0003-4474-2498
- family-names: McPherson
given-names: Jonathan
email: jonathan@posit.co
- family-names: Luraschi
given-names: Javier
- family-names: Ushey
given-names: Kevin
email: kevin@posit.co
- family-names: Atkins
given-names: Aron
email: aron@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Chang
given-names: Winston
email: winston@posit.co
- family-names: Iannone
given-names: Richard
email: rich@posit.co
orcid: https://orcid.org/0000-0003-3925-190X
year: '2023'
- family-names: Allaire
given-names: JJ
- family-names: Horner
given-names: Jeffrey
year: '2024'
doi: 10.32614/CRAN.package.markdown
- type: software
title: tinytest
abstract: 'tinytest: Lightweight and Feature Complete Unit Testing Framework'
notes: Suggests
url: https://github.com/markvanderloo/tinytest
repository: https://CRAN.R-project.org/package=tinytest
authors:
- family-names: van der Loo
- family-names: Loo
given-names: Mark
name-particle: van der
email: mark.vanderloo@gmail.com
orcid: https://orcid.org/0000-0002-9807-4686
year: '2023'
identifiers:
- description: The concept DOI.
type: doi
value: 10.5281/zenodo.7081524
- description: The versioned DOI for version 1.0.0.
type: doi
value: 10.5281/zenodo.7081525
- description: The versioned DOI for version 1.1.0.
type: doi
value: 10.5281/zenodo.7947723
- description: The versioned DOI for version 1.1.1.
type: doi
value: 10.5281/zenodo.8031801
year: '2024'
doi: 10.32614/CRAN.package.tinytest

6 changes: 3 additions & 3 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
Package: alkahest
Title: Pre-Processing XY Data from Experimental Methods
Version: 1.1.1.9000
Version: 1.2.0
Authors@R: c(
person("Nicolas", "Frerebeau", , "nicolas.frerebeau@u-bordeaux-montaigne.fr", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),
person("Brice", "Lebrun", , "brice.lebrun@u-bordeaux-montaigne.fr", role = "ctb",
comment = c(ORCID = "0000-0001-7503-8685")),
comment = c(ORCID = "0000-0001-7503-8685", "Logo designer")),
person("Université Bordeaux Montaigne", role = "fnd"),
person("CNRS", role = "fnd")
)
Expand Down Expand Up @@ -41,7 +41,7 @@ VignetteBuilder:
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
RoxygenNote: 7.3.2
Collate:
'AllGenerics.R'
'alkahest-internal.R'
Expand Down
2 changes: 1 addition & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# alkahest 1.1.1.9000
# alkahest 1.2.0
## New classes and methods
* Add baseline estimation with asymmetric least squares smoothing (Eilers and Boelens, 2005).
* Add Standard Normal Variate (SNV) transformation (Barnes et al., 1989).
Expand Down
2 changes: 1 addition & 1 deletion R/alkahest-package.R
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
#' \tabular{ll}{
#' **Package:** \tab alkahest \cr
#' **Type:** \tab Package \cr
#' **Version:** \tab 1.1.1 \cr
#' **Version:** \tab 1.2.0 \cr
#' **License:** \tab GPL-3 \cr
#' **Zenodo:** \tab \doi{10.5281/zenodo.7081524} \cr
#' }
Expand Down
8 changes: 6 additions & 2 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -37,10 +37,14 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale

**alkahest** is a lightweight, dependency-free toolbox for pre-processing XY data from experimental methods (i.e. any signal that can be measured along a continuous variable). It provides methods for baseline estimation and correction, smoothing, normalization, integration and peaks detection.

```{r citation, echo=FALSE, comment=''}
utils::citation("alkahest")
* Baseline estimation methods: Linear, Polynomial [@lieber2003], Asymmetric Least Squares [@eilers2005], Rolling Ball [@kneen1996], Rubberband, SNIP [@morhac1997; @morhac2008; @ryan1988], 4S Peak Filling [@liland2015].
* Smoothing methods: Rectangular, Triangular, Loess, Savitzky-Golay Filter [@gorry1990; @savitzky1964], Whittaker [@eilers2003], Penalized Likelihood [@derooi2014]

---

```{r citation, echo=FALSE, comment='', results='asis'}
cite <- utils::citation("alkahest")
print(cite, bibtex = FALSE)
```

## Installation
Expand Down
32 changes: 11 additions & 21 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ can be measured along a continuous variable). It provides methods for
baseline estimation and correction, smoothing, normalization,
integration and peaks detection.

To cite alkahest in publications use:
- Baseline estimation methods: Linear, Polynomial (Lieber and
Mahadevan-Jansen 2003), Asymmetric Least Squares (Eilers and Boelens
2005), Rolling Ball (Kneen and Annegarn 1996), Rubberband, SNIP
Expand All @@ -51,26 +50,17 @@ integration and peaks detection.
Filter (Gorry 1990; Savitzky and Golay 1964), Whittaker (Eilers 2003),
Penalized Likelihood (De Rooi et al. 2014)

Frerebeau N (2023). _alkahest: Pre-Processing XY Data from
Experimental Methods_. Université Bordeaux Montaigne, Pessac, France.
doi:10.5281/zenodo.7081524 <https://doi.org/10.5281/zenodo.7081524>,
R package version 1.1.1, <https://packages.tesselle.org/alkahest/>.

A BibTeX entry for LaTeX users is

@Manual{,
author = {Nicolas Frerebeau},
title = {{alkahest: Pre-Processing XY Data from Experimental Methods}},
year = {2023},
organization = {Université Bordeaux Montaigne},
address = {Pessac, France},
note = {R package version 1.1.1},
url = {https://packages.tesselle.org/alkahest/},
doi = {10.5281/zenodo.7081524},
}

This package is a part of the tesselle project
<https://www.tesselle.org>.
------------------------------------------------------------------------

To cite alkahest in publications use:

Frerebeau N (2024). *alkahest: Pre-Processing XY Data from Experimental
Methods*. Université Bordeaux Montaigne, Pessac, France.
<doi:10.5281/zenodo.7081524> <https://doi.org/10.5281/zenodo.7081524>, R
package version 1.2.0, <https://packages.tesselle.org/alkahest/>.

This package is a part of the tesselle project
<https://www.tesselle.org>.

## Installation

Expand Down
Loading

0 comments on commit ecd85e4

Please sign in to comment.