diff --git a/CITATION.cff b/CITATION.cff index e8c4ed1..c811a9f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,7 +8,7 @@ message: 'To cite package "nexus" in publications use:' type: software license: GPL-3.0-or-later title: 'nexus: Sourcing Archaeological Materials by Chemical Composition' -version: 0.1.0 +version: 0.2.0 doi: 10.5281/zenodo.10225630 abstract: 'Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting @@ -38,10 +38,10 @@ preferred-citation: email: anne.philippe@univ-nantes.fr orcid: https://orcid.org/0000-0002-5331-5087 affiliation: Université de Nantes - year: '2023' + year: '2024' location: name: Pessac, France - notes: R package version 0.1.0 + notes: R package version 0.2.0 url: https://packages.tesselle.org/nexus/ doi: 10.5281/zenodo.10225630 institution: @@ -71,38 +71,38 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing version: '>= 3.5' - type: software - title: arkhe - abstract: 'arkhe: Tools for Cleaning Rectangular Data' - notes: Imports - url: https://packages.tesselle.org/arkhe/ - repository: https://CRAN.R-project.org/package=arkhe + title: dimensio + abstract: 'dimensio: Multivariate Data Analysis' + notes: Depends + url: https://packages.tesselle.org/dimensio/ + repository: https://CRAN.R-project.org/package=dimensio authors: - family-names: Frerebeau given-names: Nicolas email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - year: '2023' - version: '>= 1.4.0' + year: '2024' + version: '>= 0.6.0' - type: software - title: dimensio - abstract: 'dimensio: Multivariate Data Analysis' + title: arkhe + abstract: 'arkhe: Tools for Cleaning Rectangular Data' notes: Imports - url: https://packages.tesselle.org/dimensio/ - repository: https://CRAN.R-project.org/package=dimensio + url: https://packages.tesselle.org/arkhe/ + repository: https://CRAN.R-project.org/package=arkhe authors: - family-names: Frerebeau given-names: Nicolas email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - year: '2023' - version: '>= 0.5.0' + year: '2024' + version: '>= 1.6.0' - type: software title: graphics abstract: 'R: A Language and Environment for Statistical Computing' @@ -111,7 +111,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -122,7 +122,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -137,8 +137,8 @@ references: email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - year: '2023' - version: '>= 1.0.0' + year: '2024' + version: '>= 1.2.0' - type: software title: methods abstract: 'R: A Language and Environment for Statistical Computing' @@ -147,7 +147,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -160,7 +160,7 @@ references: - family-names: Ripley given-names: Brian email: ripley@stats.ox.ac.uk - year: '2023' + year: '2024' - type: software title: stats abstract: 'R: A Language and Environment for Statistical Computing' @@ -169,7 +169,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -180,7 +180,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -205,7 +205,7 @@ references: given-names: Mia email: Mia.Hubert@uia.ua.ac.be orcid: https://orcid.org/0000-0001-6398-4850 - year: '2023' + year: '2024' - type: software title: folio abstract: 'folio: Datasets for Teaching Archaeology and Paleontology' @@ -218,7 +218,8 @@ references: email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - year: '2023' + year: '2024' + version: '>= 1.4.0' - type: software title: igraph abstract: 'igraph: Network Analysis and Visualization' @@ -251,7 +252,7 @@ references: given-names: Kirill email: kirill@cynkra.com orcid: https://orcid.org/0000-0002-1416-3412 - year: '2023' + year: '2024' - type: software title: knitr abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R' @@ -263,50 +264,23 @@ references: given-names: Yihui email: xie@yihui.name orcid: https://orcid.org/0000-0003-0645-5666 - year: '2023' + year: '2024' - 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' - type: software title: rsvg abstract: 'rsvg: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or @@ -319,7 +293,7 @@ references: given-names: Jeroen email: jeroen@berkeley.edu orcid: https://orcid.org/0000-0002-4035-0289 - year: '2023' + year: '2024' - type: software title: svglite abstract: 'svglite: An ''SVG'' Graphics Device' @@ -346,7 +320,7 @@ references: - family-names: Lise given-names: Vaudor email: lise.vaudor@ens-lyon.fr - year: '2023' + year: '2024' - type: software title: tinysnapshot abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework' @@ -358,7 +332,7 @@ references: given-names: Vincent email: vincent.arel-bundock@umontreal.ca orcid: https://orcid.org/0000-0003-2042-7063 - year: '2023' + year: '2024' - type: software title: tinytest abstract: 'tinytest: Lightweight and Feature Complete Unit Testing Framework' @@ -370,7 +344,7 @@ references: given-names: Mark email: mark.vanderloo@gmail.com orcid: https://orcid.org/0000-0002-9807-4686 - year: '2023' + year: '2024' identifiers: - description: The concept DOI. type: doi diff --git a/DESCRIPTION b/DESCRIPTION index c876821..a846d14 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: nexus Title: Sourcing Archaeological Materials by Chemical Composition -Version: 0.1.0.9000 +Version: 0.2.0 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")), diff --git a/NEWS.md b/NEWS.md index ee59a64..7b9e857 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# nexus 0.1.0.9000 +# nexus 0.2.0 ## New classes and methods * Add `hist()` methods to plot ILR histograms. * Add `quantile()` methods for compositional data matrix. diff --git a/R/nexus-package.R b/R/nexus-package.R index 0935939..c7d40aa 100644 --- a/R/nexus-package.R +++ b/R/nexus-package.R @@ -2,9 +2,9 @@ #' \tabular{ll}{ #' **Package:** \tab nexus \cr #' **Type:** \tab Package \cr -#' **Version:** \tab 0.1.0 \cr +#' **Version:** \tab 0.2.0 \cr #' **License:** \tab GPL-3 \cr -#' **Zenodo:** \tab \cr +#' **Zenodo:** \tab \doi{10.5281/zenodo.10225630} \cr #' } #' #' @section Package options: diff --git a/README.Rmd b/README.Rmd index f5c100d..071ff9c 100644 --- a/README.Rmd +++ b/README.Rmd @@ -94,7 +94,7 @@ head(coda) **nexus** allows to specify whether an observation belongs to a specific group (or not). Additionally, the presence of repeated measurements can be specified by giving several observations the same sample name: -```{r groups} +```{r groups, fig.width=7, fig.height=5, fig.align='center'} ## Mineral compositions of five slides as reported by five analysts ## Data from Aitchison 1986 data("slides") @@ -103,6 +103,9 @@ head(slides) ## Coerce to compositional data coda <- as_composition(slides, sample = 2, group = 1) head(coda) + +## Grouped compositional barplots +barplot(coda, order = 1) ``` ## Contributing diff --git a/README.md b/README.md index ce3f2a3..f80a409 100644 --- a/README.md +++ b/README.md @@ -57,10 +57,10 @@ companion package to **nexus** that allows to create ternary plots. To cite nexus in publications use: - Frerebeau N, Philippe A (2023). _nexus: Sourcing Archaeological + Frerebeau N, Philippe A (2024). _nexus: Sourcing Archaeological Materials by Chemical Composition_. Université Bordeaux Montaigne, Pessac, France. doi:10.5281/zenodo.10225630 - , R package version 0.1.0, + , R package version 0.2.0, . A BibTeX entry for LaTeX users is @@ -68,10 +68,10 @@ companion package to **nexus** that allows to create ternary plots. @Manual{, author = {Nicolas Frerebeau and Anne Philippe}, title = {{nexus: Sourcing Archaeological Materials by Chemical Composition}}, - year = {2023}, + year = {2024}, organization = {Université Bordeaux Montaigne}, address = {Pessac, France}, - note = {R package version 0.1.0}, + note = {R package version 0.2.0}, url = {https://packages.tesselle.org/nexus/}, doi = {10.5281/zenodo.10225630}, } @@ -100,6 +100,7 @@ remotes::install_github("tesselle/nexus") ``` r ## Load the package library(nexus) +#> Loading required package: dimensio ``` **nexus** provides a set of S4 classes that represent different special @@ -183,8 +184,13 @@ head(coda) #> 4 0.005000000 #> 5 0.003000000 #> 6 0.003000000 + +## Grouped compositional barplots +barplot(coda, order = 1) ``` + + ## Contributing Please note that the **nexus** project is released with a [Contributor diff --git a/codemeta.json b/codemeta.json index bb46489..8de1851 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,7 +8,7 @@ "codeRepository": "https://github.com/tesselle/nexus", "issueTracker": "https://github.com/tesselle/nexus/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.1.0", + "version": "0.2.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -44,6 +44,13 @@ "familyName": "Lebrun", "email": "brice.lebrun@u-bordeaux-montaigne.fr", "@id": "https://orcid.org/0000-0001-7503-8685" + }, + { + "@type": "Person", + "givenName": "Arthur", + "familyName": "Leck", + "email": "arthur.leck@u-bordeaux-montaigne.fr", + "@id": "https://orcid.org/0009-0004-8819-9970" } ], "funder": [ @@ -82,6 +89,7 @@ "@type": "SoftwareApplication", "identifier": "folio", "name": "folio", + "version": ">= 1.4.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -116,15 +124,15 @@ }, { "@type": "SoftwareApplication", - "identifier": "rmarkdown", - "name": "rmarkdown", + "identifier": "markdown", + "name": "markdown", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://CRAN.R-project.org/package=rmarkdown" + "sameAs": "https://CRAN.R-project.org/package=markdown" }, { "@type": "SoftwareApplication", @@ -184,29 +192,29 @@ }, "2": { "@type": "SoftwareApplication", - "identifier": "arkhe", - "name": "arkhe", - "version": ">= 1.4.0", + "identifier": "dimensio", + "name": "dimensio", + "version": ">= 0.6.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://CRAN.R-project.org/package=arkhe" + "sameAs": "https://CRAN.R-project.org/package=dimensio" }, "3": { "@type": "SoftwareApplication", - "identifier": "dimensio", - "name": "dimensio", - "version": ">= 0.5.0", + "identifier": "arkhe", + "name": "arkhe", + "version": ">= 1.6.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://CRAN.R-project.org/package=dimensio" + "sameAs": "https://CRAN.R-project.org/package=arkhe" }, "4": { "@type": "SoftwareApplication", @@ -222,7 +230,7 @@ "@type": "SoftwareApplication", "identifier": "isopleuros", "name": "isopleuros", - "version": ">= 1.0.0", + "version": ">= 1.2.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -260,11 +268,11 @@ }, "SystemRequirements": null }, - "fileSize": "505.098KB", + "fileSize": "588.788KB", "citation": [ { "@type": "SoftwareSourceCode", - "datePublished": "2023", + "datePublished": "2024", "author": [ { "@type": "Person", @@ -280,7 +288,7 @@ "name": "{nexus: Sourcing Archaeological Materials by Chemical Composition}", "identifier": "10.5281/zenodo.10225630", "url": "https://packages.tesselle.org/nexus/", - "description": "R package version 0.1.0", + "description": "R package version 0.2.0", "@id": "https://doi.org/10.5281/zenodo.10225630", "sameAs": "https://doi.org/10.5281/zenodo.10225630" } diff --git a/cran-comments.md b/cran-comments.md index bd86a3f..932b418 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -8,6 +8,11 @@ 0 errors | 0 warnings | 1 note -* This is a resubmission: - * References in the description of the DESCRIPTION file have been properly formatted. - * Replace `\dontrun{}` with `\donttest{}` in examples. +* Some links in the documentation point to articles behind paywalls that may return an error. + +## revdepcheck results + +We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 0 new problems + * We failed to check 0 packages diff --git a/inst/CITATION b/inst/CITATION index e8732c5..bee6640 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -5,7 +5,7 @@ bibentry( author = c(person("Nicolas", "Frerebeau", role = "aut"), person("Anne", "Philippe", role = "aut")), title = "{nexus: Sourcing Archaeological Materials by Chemical Composition}", - year = "2023", + year = "2024", organization = "Université Bordeaux Montaigne", address = "Pessac, France", note = sprintf("R package version %s", meta$Version), diff --git a/man/figures/README-groups-1.png b/man/figures/README-groups-1.png new file mode 100644 index 0000000..a6c1270 Binary files /dev/null and b/man/figures/README-groups-1.png differ diff --git a/man/nexus-package.Rd b/man/nexus-package.Rd index 3725115..1eea2f3 100644 --- a/man/nexus-package.Rd +++ b/man/nexus-package.Rd @@ -14,9 +14,9 @@ Exploration and analysis of compositional data in the framework of Aitchison (19 \tabular{ll}{ \strong{Package:} \tab nexus \cr \strong{Type:} \tab Package \cr -\strong{Version:} \tab 0.1.0 \cr +\strong{Version:} \tab 0.2.0 \cr \strong{License:} \tab GPL-3 \cr -\strong{Zenodo:} \tab \cr +\strong{Zenodo:} \tab \doi{10.5281/zenodo.10225630} \cr } } \section{Package options}{ diff --git a/revdep/.gitignore b/revdep/.gitignore new file mode 100644 index 0000000..31f6c40 --- /dev/null +++ b/revdep/.gitignore @@ -0,0 +1,6 @@ +checks +library +checks.noindex +library.noindex +data.sqlite +*.html diff --git a/revdep/README.md b/revdep/README.md new file mode 100644 index 0000000..c5898c2 --- /dev/null +++ b/revdep/README.md @@ -0,0 +1,27 @@ +# Platform + +|field |value | +|:--------|:----------------------------------------------------------------------------| +|version |R version 4.3.2 (2023-10-31) | +|os |Ubuntu 22.04.3 LTS | +|system |x86_64, linux-gnu | +|ui |RStudio | +|language |(EN) | +|collate |fr_FR.UTF-8 | +|ctype |fr_FR.UTF-8 | +|tz |Europe/Paris | +|date |2024-02-26 | +|rstudio |2023.12.1+402 Ocean Storm (desktop) | +|pandoc |3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) | + +# Dependencies + +|package |old |new |Δ | +|:----------|:-----|:-----|:--| +|nexus |0.1.0 |0.2.0 |* | +|arkhe |1.6.0 |1.6.0 | | +|dimensio |0.6.0 |0.6.0 | | +|isopleuros |1.2.0 |1.2.0 | | + +# Revdeps + diff --git a/revdep/cran.md b/revdep/cran.md new file mode 100644 index 0000000..782ef68 --- /dev/null +++ b/revdep/cran.md @@ -0,0 +1,7 @@ +## revdepcheck results + +We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 0 new problems + * We failed to check 0 packages + diff --git a/revdep/failures.md b/revdep/failures.md new file mode 100644 index 0000000..9a20736 --- /dev/null +++ b/revdep/failures.md @@ -0,0 +1 @@ +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/revdep/problems.md b/revdep/problems.md new file mode 100644 index 0000000..9a20736 --- /dev/null +++ b/revdep/problems.md @@ -0,0 +1 @@ +*Wow, no problems at all. :)* \ No newline at end of file