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nexus

Sourcing Archaeological Materials by Chemical Composition - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/nexus

https://github.com/tesselle/nexus

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 11 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.6%) to scientific vocabulary

Keywords

archaeological-science archaeology archaeometry compositional-data provenance-studies r-package
Last synced: 4 months ago · JSON representation ·

Repository

Sourcing Archaeological Materials by Chemical Composition - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/nexus

Basic Info
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 4
Topics
archaeological-science archaeology archaeometry compositional-data provenance-studies r-package
Created about 6 years ago · Last pushed 5 months ago
Metadata Files
Readme Changelog License Citation Codemeta

README.Rmd 

---
output: github_document
bibliography: vignettes/bibliography.bib
nocite: '@*'
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = NULL
)
Sys.setenv(LANGUAGE = "en") # Force locale
```

# nexus 


[![Code coverage](https://packages.tesselle.org/nexus/coverage/badge.svg)](https://packages.tesselle.org/nexus/coverage/){.pkgdown-devel}
[![Code coverage](https://packages.tesselle.org/nexus/coverage/badge.svg)](https://packages.tesselle.org/nexus/coverage/){.pkgdown-devel}
[![Dependencies](https://tinyverse.netlify.app/badge/nexus)](https://cran.r-project.org/package=nexus){.pkgdown-devel}

[![r-universe](https://tesselle.r-universe.dev/badges/nexus)](https://tesselle.r-universe.dev/nexus){.pkgdown-devel}
[![CRAN Version](https://www.r-pkg.org/badges/version/nexus)](https://cran.r-project.org/package=nexus){.pkgdown-release}
[![CRAN checks](https://badges.cranchecks.info/worst/nexus.svg)](https://cran.r-project.org/web/checks/check_results_nexus.html){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/nexus)](https://cran.r-project.org/package=nexus){.pkgdown-release}

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10225630.svg)](https://doi.org/10.5281/zenodo.10225630)


## Overview

Exploration and analysis of compositional data in the framework of @aitchison1986. **nexus** provides tools for chemical fingerprinting and source tracking of ancient materials. This package provides methods for compositional data analysis:

* Compositional statistics: `covariance()`, `mean()`, `pip()`, `quantile()`, `variance()`, `variation()`.
* Compositional data visualization: `barplot()`, `boxplot()`, `pairs()`, `plot()`.
* Logratio transformations: `transform_lr()`, `transform_clr()`, `transform_alr()`, `transform_ilr()`, `transform_plr()`.
* Zero and missing value replacement.
* Outlier detection: `detect_outlier()`.

This package also includes methods for provenance studies:

* Multivariate analysis: `pca()`.
* Mixed-mode analysis using geochemical and petrographic data [@baxter2008]: `mix()`.

[**isopleuros**](https://packages.tesselle.org/isopleuros/) is a companion package to **nexus** that allows to create ternary plots.

---

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

## Installation

You can install the released version of **nexus** from [CRAN](https://CRAN.R-project.org) with:

```{r cran-installation, eval=FALSE}
install.packages("nexus")
```

And the development version from [Codeberg](https://codeberg.org/) with:

```{r gh-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_git("https://codeberg.org/tesselle/nexus")
```

## Usage

```{r packages}
## Install extra packages (if needed)
# install.packages("folio")

## Load the package
library(nexus)
```

**nexus** provides a set of S4 classes that represent different special types of matrix (see `vignette("nexus")`). The most basic class represents a compositional data matrix, i.e. quantitative (nonnegative) descriptions of the parts of some whole, carrying relative, rather than absolute, information [@aitchison1986].

*It assumes that you keep your data tidy*: each variable must be saved in its own column and each observation (sample) must be saved in its own row.
  
```{r groups}
## Data from Wood and Liu 2023
data("bronze", package = "folio")

## Coerce to compositional data
coda <- as_composition(bronze, parts = 4:11)

## Use dynasties as groups
coda <- group(coda, by = bronze$dynasty)
```

```{r barplot, fig.width=5, fig.height=7}
## Select major elements
major <- coda[, is_element_major(coda)]

## Compositional barplot
barplot(major, order_rows = "Cu", names = FALSE, border = NA, space = 0)
```

```{r lra, fig.width=7, fig.height=7, out.width='50%', fig.show='hold'}
## Log-ratio analysis
## (PCA of centered log-ratio; outliers should be removed first)
clr <- transform_clr(coda, weights = TRUE)
lra <- pca(clr)

## Visualize results
viz_individuals(
  x = lra, 
  extra_quali = group_names(clr),
  color = c("#004488", "#DDAA33", "#BB5566"),
  hull = TRUE
)

viz_variables(lra)
```

## Translation

This package provides translations of user-facing communications, like messages, warnings and errors, and graphical elements (axis labels). The preferred language is by default taken from the locale. This can be overridden by setting of the environment variable `LANGUAGE` (you only need to do this once per session):

``` r
Sys.setenv(LANGUAGE = "")
```

Languages currently available are English (`en`) and French (`fr`).

## Contributing

Please note that the **nexus** project is released with a [Contributor Code of Conduct](https://www.tesselle.org/conduct.html). By contributing to this project, you agree to abide by its terms.

## References

```{r metadata, include=FALSE}
## Update codemeta.json
codemetar::write_codemeta(verbose = FALSE)

## Update CITATION.cff
cff_keys <- list(
  # message = format(citation("nexus")[[1]], style = "text"),
  identifiers = list(
    list(description = "The concept DOI.",
         type = "doi",
         value = "10.5281/zenodo.10225630"),
    list(description = "The versioned DOI for version 0.1.0.",
         type = "doi",
         value = "10.5281/zenodo.10225631"),
    list(description = "The versioned DOI for version 0.2.0.",
         type = "doi",
         value = "10.5281/zenodo.10711236"),
    list(description = "The versioned DOI for version 0.3.0.",
         type = "doi",
         value = "10.5281/zenodo.13646482"),
    list(description = "The versioned DOI for version 0.4.0.",
         type = "doi",
         value = "10.5281/zenodo.14645055"),
    list(description = "The versioned DOI for version 0.5.0.",
         type = "doi",
         value = "10.5281/zenodo.15167099"),
    list(description = "The versioned DOI for version 0.6.0.",
         type = "doi",
         value = "10.5281/zenodo.15577213"),
    list(description = "The CRAN DOI",
         type = "doi",
         value = "10.32614/cran.package.nexus")
  )
)
cff <- cffr::cff_create("DESCRIPTION", keys = cff_keys)
if (cffr::cff_validate(cff)) cffr::cff_write(cff, outfile = "CITATION.cff")
```

Owner

  • Name: tesselle
  • Login: tesselle
  • Kind: organization
  • Location: France

A collection of R packages for archaeological research and teaching

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
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: 0.6.0
doi: 10.5281/zenodo.10225630
identifiers:
- description: The concept DOI.
  type: doi
  value: 10.5281/zenodo.10225630
- description: The versioned DOI for version 0.1.0.
  type: doi
  value: 10.5281/zenodo.10225631
- description: The versioned DOI for version 0.2.0.
  type: doi
  value: 10.5281/zenodo.10711236
- description: The versioned DOI for version 0.3.0.
  type: doi
  value: 10.5281/zenodo.13646482
- description: The versioned DOI for version 0.4.0.
  type: doi
  value: 10.5281/zenodo.14645055
- description: The versioned DOI for version 0.5.0.
  type: doi
  value: 10.5281/zenodo.15167099
- description: The versioned DOI for version 0.6.0.
  type: doi
  value: 10.5281/zenodo.15577213
- description: The CRAN DOI
  type: doi
  value: 10.32614/cran.package.nexus
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
  and source tracking of ancient materials.'
authors:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
- family-names: Philippe
  given-names: Anne
  email: anne.philippe@univ-nantes.fr
  orcid: https://orcid.org/0000-0002-5331-5087
preferred-citation:
  type: manual
  title: 'nexus: Sourcing Archaeological Materials by Chemical Composition'
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  - family-names: Philippe
    given-names: Anne
    email: anne.philippe@univ-nantes.fr
    orcid: https://orcid.org/0000-0002-5331-5087
  year: '2025'
  institution:
    name: Université Bordeaux Montaigne
    address: Pessac, France
  notes: R package version 0.6.0
  url: https://packages.tesselle.org/nexus/
  doi: 10.5281/zenodo.10225630
repository: https://CRAN.R-project.org/package=nexus
repository-code: https://codeberg.org/tesselle/nexus
url: https://packages.tesselle.org/nexus/
contact:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
keywords:
- archaeology
- archaeological-science
- archaeometry
- compositional-data
- provenance-studies
- r-package
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 3.5'
- type: software
  title: dimensio
  abstract: 'dimensio: Multivariate Data Analysis'
  notes: Depends
  url: https://packages.tesselle.org/dimensio/
  repository: https://tesselle.r-universe.dev
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  doi: 10.32614/CRAN.package.dimensio
  version: '>= 0.14.0'
- 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
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  doi: 10.32614/CRAN.package.arkhe
  version: '>= 1.11.0'
- type: software
  title: graphics
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: grDevices
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: isopleuros
  abstract: 'isopleuros: Ternary Plots'
  notes: Imports
  url: https://packages.tesselle.org/isopleuros/
  repository: https://CRAN.R-project.org/package=isopleuros
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  doi: 10.32614/CRAN.package.isopleuros
  version: '>= 1.4.0'
- type: software
  title: khroma
  abstract: 'khroma: Colour Schemes for Scientific Data Visualization'
  notes: Imports
  url: https://packages.tesselle.org/khroma/
  repository: https://CRAN.R-project.org/package=khroma
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  doi: 10.32614/CRAN.package.khroma
  version: '>= 1.16.0'
- type: software
  title: MASS
  abstract: 'MASS: Support Functions and Datasets for Venables and Ripley''s MASS'
  notes: Imports
  url: http://www.stats.ox.ac.uk/pub/MASS4/
  repository: https://CRAN.R-project.org/package=MASS
  authors:
  - family-names: Ripley
    given-names: Brian
    email: Brian.Ripley@R-project.org
  - family-names: Venables
    given-names: Bill
  year: '2025'
  doi: 10.32614/CRAN.package.MASS
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: cluster
  abstract: 'cluster: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw
    et al.'
  notes: Suggests
  url: https://svn.r-project.org/R-packages/trunk/cluster/
  repository: https://CRAN.R-project.org/package=cluster
  authors:
  - family-names: Maechler
    given-names: Martin
    email: maechler@stat.math.ethz.ch
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Rousseeuw
    given-names: Peter
    email: peter.rousseeuw@kuleuven.be
    orcid: https://orcid.org/0000-0002-3807-5353
  - family-names: Struyf
    given-names: Anja
  - family-names: Hubert
    given-names: Mia
    email: Mia.Hubert@uia.ua.ac.be
    orcid: https://orcid.org/0000-0001-6398-4850
  year: '2025'
  doi: 10.32614/CRAN.package.cluster
- type: software
  title: folio
  abstract: 'folio: Datasets for Teaching Archaeology and Paleontology'
  notes: Suggests
  url: https://packages.tesselle.org/folio/
  repository: https://CRAN.R-project.org/package=folio
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  doi: 10.32614/CRAN.package.folio
  version: '>= 1.5.0'
  year: '2025'
- type: software
  title: fontquiver
  abstract: 'fontquiver: Set of Installed Fonts'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=fontquiver
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.fontquiver
- type: software
  title: igraph
  abstract: 'igraph: Network Analysis and Visualization'
  notes: Suggests
  url: https://r.igraph.org/
  repository: https://CRAN.R-project.org/package=igraph
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
    orcid: https://orcid.org/0000-0001-7098-9676
  - family-names: Nepusz
    given-names: Tamás
    email: ntamas@gmail.com
    orcid: https://orcid.org/0000-0002-1451-338X
  - family-names: Traag
    given-names: Vincent
    orcid: https://orcid.org/0000-0003-3170-3879
  - family-names: Horvát
    given-names: Szabolcs
    email: szhorvat@gmail.com
    orcid: https://orcid.org/0000-0002-3100-523X
  - family-names: Zanini
    given-names: Fabio
    email: fabio.zanini@unsw.edu.au
    orcid: https://orcid.org/0000-0001-7097-8539
  - family-names: Noom
    given-names: Daniel
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2025'
  doi: 10.32614/CRAN.package.igraph
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: markdown
  abstract: 'markdown: Render Markdown with ''commonmark'''
  notes: Suggests
  url: https://github.com/rstudio/markdown
  repository: https://CRAN.R-project.org/package=markdown
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Allaire
    given-names: JJ
  - family-names: Horner
    given-names: Jeffrey
  year: '2025'
  doi: 10.32614/CRAN.package.markdown
- type: software
  title: rsvg
  abstract: 'rsvg: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
    Bitmap Arrays'
  notes: Suggests
  url: https://docs.ropensci.org/rsvg/
  repository: https://CRAN.R-project.org/package=rsvg
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  year: '2025'
  doi: 10.32614/CRAN.package.rsvg
- type: software
  title: svglite
  abstract: 'svglite: An ''SVG'' Graphics Device'
  notes: Suggests
  url: https://svglite.r-lib.org
  repository: https://CRAN.R-project.org/package=svglite
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: jake@apache.org
  - family-names: Decorde
    given-names: Matthieu
    email: matthieu.decorde@ens-lyon.fr
  - family-names: Lise
    given-names: Vaudor
    email: lise.vaudor@ens-lyon.fr
  year: '2025'
  doi: 10.32614/CRAN.package.svglite
- type: software
  title: tinysnapshot
  abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'
  notes: Suggests
  url: https://github.com/vincentarelbundock/tinysnapshot
  repository: https://CRAN.R-project.org/package=tinysnapshot
  authors:
  - family-names: Arel-Bundock
    given-names: Vincent
    email: vincent.arel-bundock@umontreal.ca
    orcid: https://orcid.org/0000-0003-2042-7063
  year: '2025'
  doi: 10.32614/CRAN.package.tinysnapshot
- 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: Loo
    given-names: Mark
    name-particle: van der
    email: mark.vanderloo@gmail.com
    orcid: https://orcid.org/0000-0002-9807-4686
  year: '2025'
  doi: 10.32614/CRAN.package.tinytest

CodeMeta (codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "nexus",
  "description": "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 and source tracking of ancient materials.",
  "name": "nexus: Sourcing Archaeological Materials by Chemical Composition",
  "relatedLink": [
    "https://packages.tesselle.org/nexus/",
    "https://tesselle.r-universe.dev/nexus",
    "https://CRAN.R-project.org/package=nexus"
  ],
  "codeRepository": "https://codeberg.org/tesselle/nexus",
  "issueTracker": "https://codeberg.org/tesselle/nexus/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "0.6.0",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.5.0 (2025-04-11)",
  "provider": {
    "@id": "https://cran.r-project.org",
    "@type": "Organization",
    "name": "Comprehensive R Archive Network (CRAN)",
    "url": "https://cran.r-project.org"
  },
  "author": [
    {
      "@type": "Person",
      "givenName": "Nicolas",
      "familyName": "Frerebeau",
      "email": "nicolas.frerebeau@u-bordeaux-montaigne.fr",
      "@id": "https://orcid.org/0000-0001-5759-4944"
    },
    {
      "@type": "Person",
      "givenName": "Anne",
      "familyName": "Philippe",
      "email": "anne.philippe@univ-nantes.fr",
      "@id": "https://orcid.org/0000-0002-5331-5087"
    }
  ],
  "funder": [
    {
      "@type": "Organization",
      "name": "Universit Bordeaux Montaigne"
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