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56 changes: 43 additions & 13 deletions CITATION.cff
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Expand Up @@ -10,6 +10,16 @@ license: GPL-3.0-or-later
title: 'nexus: Sourcing Archaeological Materials by Chemical Composition'
version: 0.3.0
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
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.'
Expand Down Expand Up @@ -86,7 +96,8 @@ references:
orcid: https://orcid.org/0000-0001-5759-4944
affiliation: Université Bordeaux Montaigne
year: '2024'
version: '>= 0.8.0'
doi: 10.32614/CRAN.package.dimensio
version: '>= 0.9.0'
- type: software
title: arkhe
abstract: 'arkhe: Tools for Cleaning Rectangular Data'
Expand All @@ -100,7 +111,8 @@ references:
orcid: https://orcid.org/0000-0001-5759-4944
affiliation: Université Bordeaux Montaigne
year: '2024'
version: '>= 1.6.0'
doi: 10.32614/CRAN.package.arkhe
version: '>= 1.7.0'
- type: software
title: graphics
abstract: 'R: A Language and Environment for Statistical Computing'
Expand Down Expand Up @@ -134,7 +146,23 @@ references:
orcid: https://orcid.org/0000-0001-5759-4944
affiliation: Université Bordeaux Montaigne
year: '2024'
doi: 10.32614/CRAN.package.isopleuros
version: '>= 1.2.0'
- 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
affiliation: Université Bordeaux Montaigne
year: '2024'
doi: 10.32614/CRAN.package.khroma
version: '>= 1.14.0'
- type: software
title: methods
abstract: 'R: A Language and Environment for Statistical Computing'
Expand All @@ -155,7 +183,10 @@ references:
- family-names: Ripley
given-names: Brian
email: ripley@stats.ox.ac.uk
- family-names: Venables
given-names: Bill
year: '2024'
doi: 10.32614/CRAN.package.MASS
- type: software
title: stats
abstract: 'R: A Language and Environment for Statistical Computing'
Expand Down Expand Up @@ -199,6 +230,7 @@ references:
email: Mia.Hubert@uia.ua.ac.be
orcid: https://orcid.org/0000-0001-6398-4850
year: '2024'
doi: 10.32614/CRAN.package.cluster
- type: software
title: folio
abstract: 'folio: Datasets for Teaching Archaeology and Paleontology'
Expand All @@ -212,7 +244,8 @@ references:
orcid: https://orcid.org/0000-0001-5759-4944
affiliation: Université Bordeaux Montaigne
year: '2024'
version: '>= 1.4.0'
doi: 10.32614/CRAN.package.folio
version: '>= 1.5.0'
- type: software
title: igraph
abstract: 'igraph: Network Analysis and Visualization'
Expand Down Expand Up @@ -246,6 +279,7 @@ references:
email: kirill@cynkra.com
orcid: https://orcid.org/0000-0002-1416-3412
year: '2024'
doi: 10.32614/CRAN.package.igraph
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
Expand All @@ -258,6 +292,7 @@ references:
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2024'
doi: 10.32614/CRAN.package.knitr
- type: software
title: markdown
abstract: 'markdown: Render Markdown with ''commonmark'''
Expand All @@ -274,6 +309,7 @@ references:
- family-names: Horner
given-names: Jeffrey
year: '2024'
doi: 10.32614/CRAN.package.markdown
- type: software
title: rsvg
abstract: 'rsvg: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
Expand All @@ -287,6 +323,7 @@ references:
email: jeroen@berkeley.edu
orcid: https://orcid.org/0000-0002-4035-0289
year: '2024'
doi: 10.32614/CRAN.package.rsvg
- type: software
title: svglite
abstract: 'svglite: An ''SVG'' Graphics Device'
Expand Down Expand Up @@ -314,6 +351,7 @@ references:
given-names: Vaudor
email: lise.vaudor@ens-lyon.fr
year: '2024'
doi: 10.32614/CRAN.package.svglite
- type: software
title: tinysnapshot
abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'
Expand All @@ -326,6 +364,7 @@ references:
email: vincent.arel-bundock@umontreal.ca
orcid: https://orcid.org/0000-0003-2042-7063
year: '2024'
doi: 10.32614/CRAN.package.tinysnapshot
- type: software
title: tinytest
abstract: 'tinytest: Lightweight and Feature Complete Unit Testing Framework'
Expand All @@ -339,14 +378,5 @@ references:
email: mark.vanderloo@gmail.com
orcid: https://orcid.org/0000-0002-9807-4686
year: '2024'
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
doi: 10.32614/CRAN.package.tinytest

2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: nexus
Title: Sourcing Archaeological Materials by Chemical Composition
Version: 0.2.0.9000
Version: 0.3.0
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")),
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -112,9 +112,11 @@ importFrom(methods,.valueClassTest)
importFrom(methods,as)
importFrom(methods,callGeneric)
importFrom(methods,callNextMethod)
importFrom(methods,cbind2)
importFrom(methods,initialize)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,rbind2)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
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2 changes: 1 addition & 1 deletion NEWS.md
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@@ -1,4 +1,4 @@
# nexus 0.2.0.9000
# nexus 0.3.0
## New classes and methods
* Add transformation methods for `LogRatio` objects (clr <-> alr, clr -> ilr, alr -> ilr).
* Add `condense()` to compute compositional mean of data subsets.
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4 changes: 2 additions & 2 deletions R/nexus-package.R
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Expand Up @@ -39,8 +39,8 @@

#' @import arkhe
#' @importFrom isopleuros ternary_pairs
#' @importFrom methods as as<- callGeneric callNextMethod
#' .hasSlot initialize is new setClass setGeneric setMethod slot slot<-
#' @importFrom methods as as<- cbind2 callGeneric callNextMethod
#' .hasSlot initialize is new rbind2 setClass setGeneric setMethod slot slot<-
#' slotNames validObject .valueClassTest
#' @importFrom MASS cov.rob
#' @importFrom stats as.dist contr.helmert cov dist hclust mahalanobis ppoints
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -20,7 +20,7 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale

<!-- badges: start -->
[![R-CMD-check](https://github.com/tesselle/nexus/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/nexus/actions)
[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://codecov.io/gh/tesselle/nexus)
[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://app.codecov.io/gh/tesselle/nexus)
[![CodeFactor](https://www.codefactor.io/repository/github/tesselle/nexus/badge/main)](https://www.codefactor.io/repository/github/tesselle/nexus/overview/main)
[![Dependencies](https://tinyverse.netlify.app/badge/nexus)](https://cran.r-project.org/package=nexus)

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -6,7 +6,7 @@
<!-- badges: start -->

[![R-CMD-check](https://github.com/tesselle/nexus/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/nexus/actions)
[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://codecov.io/gh/tesselle/nexus)
[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://app.codecov.io/gh/tesselle/nexus)
[![CodeFactor](https://www.codefactor.io/repository/github/tesselle/nexus/badge/main)](https://www.codefactor.io/repository/github/tesselle/nexus/overview/main)
[![Dependencies](https://tinyverse.netlify.app/badge/nexus)](https://cran.r-project.org/package=nexus)

Expand Down Expand Up @@ -68,7 +68,7 @@ To cite nexus in publications use:
Frerebeau N, Philippe A (2024). *nexus: Sourcing Archaeological
Materials by Chemical Composition*. Université Bordeaux Montaigne,
Pessac, France. <doi:10.5281/zenodo.10225630>
<https://doi.org/10.5281/zenodo.10225630>, R package version 0.2.0.9000,
<https://doi.org/10.5281/zenodo.10225630>, R package version 0.3.0,
<https://packages.tesselle.org/nexus/>.

This package is a part of the tesselle project
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31 changes: 22 additions & 9 deletions codemeta.json
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Expand Up @@ -14,7 +14,7 @@
"name": "R",
"url": "https://r-project.org"
},
"runtimePlatform": "R version 4.4.0 (2024-04-24)",
"runtimePlatform": "R version 4.4.1 (2024-06-14)",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
Expand Down Expand Up @@ -89,7 +89,7 @@
"@type": "SoftwareApplication",
"identifier": "folio",
"name": "folio",
"version": ">= 1.4.0",
"version": ">= 1.5.0",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
Expand Down Expand Up @@ -194,7 +194,7 @@
"@type": "SoftwareApplication",
"identifier": "dimensio",
"name": "dimensio",
"version": ">= 0.8.0",
"version": ">= 0.9.0",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
Expand All @@ -207,7 +207,7 @@
"@type": "SoftwareApplication",
"identifier": "arkhe",
"name": "arkhe",
"version": ">= 1.6.0",
"version": ">= 1.7.0",
"provider": {
"@id": "https://cran.r-project.org",
"@type": "Organization",
Expand Down Expand Up @@ -240,11 +240,24 @@
"sameAs": "https://CRAN.R-project.org/package=isopleuros"
},
"7": {
"@type": "SoftwareApplication",
"identifier": "khroma",
"name": "khroma",
"version": ">= 1.14.0",
"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=khroma"
},
"8": {
"@type": "SoftwareApplication",
"identifier": "methods",
"name": "methods"
},
"8": {
"9": {
"@type": "SoftwareApplication",
"identifier": "MASS",
"name": "MASS",
Expand All @@ -256,19 +269,19 @@
},
"sameAs": "https://CRAN.R-project.org/package=MASS"
},
"9": {
"10": {
"@type": "SoftwareApplication",
"identifier": "stats",
"name": "stats"
},
"10": {
"11": {
"@type": "SoftwareApplication",
"identifier": "utils",
"name": "utils"
},
"SystemRequirements": null
},
"fileSize": "804.818KB",
"fileSize": "992.587KB",
"citation": [
{
"@type": "SoftwareSourceCode",
Expand All @@ -295,7 +308,7 @@
],
"releaseNotes": "https://github.com/tesselle/nexus/blob/master/NEWS.md",
"readme": "https://github.com/tesselle/nexus/blob/main/README.md",
"contIntegration": ["https://github.com/tesselle/nexus/actions", "https://app.codecov.io/gh/tesselle/nexus"],
"contIntegration": ["https://github.com/tesselle/nexus/actions", "https://codecov.io/gh/tesselle/nexus"],
"developmentStatus": "https://www.repostatus.org/#wip",
"keywords": ["archaeology", "archaeological-science", "archaeometry", "provenance-studies", "compositional-data", "r-package"]
}
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39 changes: 20 additions & 19 deletions revdep/README.md
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@@ -1,27 +1,28 @@
# 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) |
|field |value |
|:--------|:------------------------------------------------------------------------------------|
|version |R version 4.4.1 (2024-06-14) |
|os |Ubuntu 22.04.4 LTS |
|system |x86_64, linux-gnu |
|ui |RStudio |
|language |(EN) |
|collate |fr_FR.UTF-8 |
|ctype |fr_FR.UTF-8 |
|tz |Europe/Paris |
|date |2024-09-03 |
|rstudio |2024.04.2+764 Chocolate Cosmos (desktop) |
|pandoc |3.1.11 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (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 | |
|package |old |new |Δ |
|:----------|:------|:------|:--|
|nexus |0.2.0 |0.3.0 |* |
|arkhe |1.7.0 |1.7.0 | |
|dimensio |0.9.0 |0.9.0 | |
|isopleuros |1.2.0 |1.2.0 | |
|khroma |1.14.0 |1.14.0 | |

# Revdeps

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