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dimensio

Multivariate Data Analysis - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/dimensio

https://github.com/tesselle/dimensio

Science Score: 77.0%

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 25 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.8%) to scientific vocabulary

Keywords

data-analysis multivariate-analysis r-package
Last synced: 4 months ago · JSON representation ·

Repository

Multivariate Data Analysis - :exclamation: This is a read-only mirror from https://codeberg.org/tesselle/dimensio

Basic Info
Statistics
  • Stars: 10
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 17
Topics
data-analysis multivariate-analysis r-package
Created almost 5 years ago · Last pushed 4 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
```

# dimensio 


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

[![r-universe](https://tesselle.r-universe.dev/badges/dimensio)](https://tesselle.r-universe.dev/dimensio){.pkgdown-devel}
[![CRAN Version](https://www.r-pkg.org/badges/version/dimensio)](https://cran.r-project.org/package=dimensio){.pkgdown-release}
[![CRAN checks](https://badges.cranchecks.info/worst/dimensio.svg)](https://cran.r-project.org/web/checks/check_results_dimensio.html){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/dimensio)](https://cran.r-project.org/package=dimensio){.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.4478530.svg)](https://doi.org/10.5281/zenodo.4478530)


## Overview

Simple Principal Components Analysis (PCA; see `vignette("pca")`) and (Multiple) Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation.

There are many very good packages for multivariate data analysis (such as [**FactoMineR**](http://factominer.free.fr/), [**ade4**](https://pbil.univ-lyon1.fr/ade4/), [**vegan**](https://rpubs.com/brouwern/veganpca) or [**ca**](https://cran.r-project.org/package=ca), all extended by [**FactoExtra**](https://rpkgs.datanovia.com/factoextra/)). **dimensio** is designed to be as simple as possible, providing all the necessary tools to explore the results of the analysis.

---

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

## Installation

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

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

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/dimensio")
```

## Usage

```{r packages-load}
## Load package
library(dimensio)
```

### Compute

```{r pca}
## Load data
data(iris)

## Compute PCA
X <- pca(iris, center = TRUE, scale = TRUE, sup_quali = "Species")
```

### Extract

**dimensio** provides several methods to extract the results: 

* `get_data()` returns the original data.
* `get_contributions()` returns the contributions to the definition of the principal dimensions.
* `get_coordinates()` returns the principal or standard coordinates.
* `get_correlations()` returns the correlations between variables and dimensions.
* `get_cos2()` returns the cos^2^ values (i.e. the quality of the representation of the points on the factor map).
* `get_eigenvalues()` returns the eigenvalues, the percentages of variance and the cumulative percentages of variance.

### Visualize

The package allows to quickly visualize the results:

* `biplot()` produces a biplot.
* `screeplot()` produces a scree plot.
* `viz_rows()`/`viz_individuals()` displays row/individual principal coordinates.
* `viz_columns()`/`viz_variables()` displays columns/variable principal coordinates. `viz_variables()` depicts the variables by rays emanating from the origin (both their lengths and directions are important to the interpretation).
* `viz_contributions()` displays (joint) contributions. 
* `viz_cos2()` displays (joint) cos^2^.

The `viz_*()` functions allow to highlight additional information by varying different graphical elements (color, transparency, shape and size of symbols...).

```{r seed, echo=FALSE}
set.seed(12345)
```

```{r biplot, fig.width=7, fig.height=7, fig.align='center'}
## Form biplot
biplot(X, type = "form")
```

```{r plot-ind, fig.width=7, fig.height=7, out.width='50%', fig.show='hold'}
## Highlight species
viz_individuals(
  x = X, 
  extra_quali = iris$Species,
  color = c("#004488", "#DDAA33", "#BB5566"),
  ellipse = list(type = "tolerance", level = 0.95) # Add ellipses
)

## Highlight petal length
viz_individuals(
  x = X,
  extra_quanti = iris$Petal.Length,
  color = color("iridescent")(255), 
  size = c(1, 3)
)
```

```{r plot-var, fig.width=7, fig.height=7, out.width='50%', fig.show='hold'}
## Plot variables factor map
viz_variables(X)

## Scree plot
screeplot(X, eigenvalues = FALSE, cumulative = TRUE)
```

## 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 **dimensio** 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(
  identifiers = list(
    list(description = "The concept DOI.",
         type = "doi",
         value = "10.5281/zenodo.4478530"),
    list(description = "The versioned DOI for version 0.1.0.",
         type = "doi",
         value = "10.5281/zenodo.4478531"),
    list(description = "The versioned DOI for version 0.2.0.",
         type = "doi",
         value = "10.5281/zenodo.4709122"),
    list(description = "The versioned DOI for version 0.2.1.",
         type = "doi",
         value = "10.5281/zenodo.4769401"),
    list(description = "The versioned DOI for version 0.2.2.",
         type = "doi",
         value = "10.5281/zenodo.5515458"),
    list(description = "The versioned DOI for version 0.3.0.",
         type = "doi",
         value = "10.5281/zenodo.6993004"),
    list(description = "The versioned DOI for version 0.3.1.",
         type = "doi",
         value = "10.5281/zenodo.7798592"),
    list(description = "The versioned DOI for version 0.4.0.",
         type = "doi",
         value = "10.5281/zenodo.8277200"),
    list(description = "The versioned DOI for version 0.4.1.",
         type = "doi",
         value = "10.5281/zenodo.10022325"),
    list(description = "The versioned DOI for version 0.5.0.",
         type = "doi",
         value = "10.5281/zenodo.10207582"),
    list(description = "The versioned DOI for version 0.6.0.",
         type = "doi",
         value = "10.5281/zenodo.10696035"),
    list(description = "The versioned DOI for version 0.7.0.",
         type = "doi",
         value = "10.5281/zenodo.10948604"),
    list(description = "The versioned DOI for version 0.8.0.",
         type = "doi",
         value = "10.5281/zenodo.11518715"),
    list(description = "The versioned DOI for version 0.8.1.",
         type = "doi",
         value = "10.5281/zenodo.13135650"),
    list(description = "The versioned DOI for version 0.9.0",
         type = "doi",
         value = "10.5281/zenodo.13375140"),
    list(description = "The versioned DOI for version 0.10.0",
         type = "doi",
         value = "10.5281/zenodo.14054667"),
    list(description = "The versioned DOI for version 0.10.1",
         type = "doi",
         value = "10.5281/zenodo.14356468"),
    list(description = "The versioned DOI for version 0.11.0",
         type = "doi",
         value = "10.5281/zenodo.14623616"),
    list(description = "The versioned DOI for version 0.12.0",
         type = "doi",
         value = "10.5281/zenodo.14927451"),
    list(description = "The versioned DOI for version 0.13.0",
         type = "doi",
         value = "10.5281/zenodo.15126551"),
    list(description = "The versioned DOI for version 0.14.0",
         type = "doi",
         value = "10.5281/zenodo.15470800"),
    list(description = "The CRAN DOI",
         type = "doi",
         value = "10.32614/cran.package.dimensio")
  )
)
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 "dimensio" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'dimensio: Multivariate Data Analysis'
version: 0.14.0
doi: 10.5281/zenodo.4478530
identifiers:
- description: The concept DOI.
  type: doi
  value: 10.5281/zenodo.4478530
- description: The versioned DOI for version 0.1.0.
  type: doi
  value: 10.5281/zenodo.4478531
- description: The versioned DOI for version 0.2.0.
  type: doi
  value: 10.5281/zenodo.4709122
- description: The versioned DOI for version 0.2.1.
  type: doi
  value: 10.5281/zenodo.4769401
- description: The versioned DOI for version 0.2.2.
  type: doi
  value: 10.5281/zenodo.5515458
- description: The versioned DOI for version 0.3.0.
  type: doi
  value: 10.5281/zenodo.6993004
- description: The versioned DOI for version 0.3.1.
  type: doi
  value: 10.5281/zenodo.7798592
- description: The versioned DOI for version 0.4.0.
  type: doi
  value: 10.5281/zenodo.8277200
- description: The versioned DOI for version 0.4.1.
  type: doi
  value: 10.5281/zenodo.10022325
- description: The versioned DOI for version 0.5.0.
  type: doi
  value: 10.5281/zenodo.10207582
- description: The versioned DOI for version 0.6.0.
  type: doi
  value: 10.5281/zenodo.10696035
- description: The versioned DOI for version 0.7.0.
  type: doi
  value: 10.5281/zenodo.10948604
- description: The versioned DOI for version 0.8.0.
  type: doi
  value: 10.5281/zenodo.11518715
- description: The versioned DOI for version 0.8.1.
  type: doi
  value: 10.5281/zenodo.13135650
- description: The versioned DOI for version 0.9.0
  type: doi
  value: 10.5281/zenodo.13375140
- description: The versioned DOI for version 0.10.0
  type: doi
  value: 10.5281/zenodo.14054667
- description: The versioned DOI for version 0.10.1
  type: doi
  value: 10.5281/zenodo.14356468
- description: The versioned DOI for version 0.11.0
  type: doi
  value: 10.5281/zenodo.14623616
- description: The versioned DOI for version 0.12.0
  type: doi
  value: 10.5281/zenodo.14927451
- description: The versioned DOI for version 0.13.0
  type: doi
  value: 10.5281/zenodo.15126551
- description: The versioned DOI for version 0.14.0
  type: doi
  value: 10.5281/zenodo.15470800
- description: The CRAN DOI
  type: doi
  value: 10.32614/cran.package.dimensio
abstract: 'Simple Principal Components Analysis (PCA) and (Multiple) Correspondence
  Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides
  S4 classes and methods to compute, extract, summarize and visualize results of multivariate
  data analysis. It also includes methods for partial bootstrap validation described
  in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN: 978-2-10-049616-7).'
authors:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
preferred-citation:
  type: manual
  title: 'dimensio: Multivariate Data Analysis'
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    email: nicolas.frerebeau@u-bordeaux-montaigne.fr
    orcid: https://orcid.org/0000-0001-5759-4944
  year: '2025'
  institution:
    name: Université Bordeaux Montaigne
    address: Pessac, France
  notes: R package version 0.14.0
  doi: 10.5281/zenodo.4478530
  url: https://packages.tesselle.org/dimensio/
repository: https://CRAN.R-project.org/package=dimensio
repository-code: https://codeberg.org/tesselle/dimensio
url: https://packages.tesselle.org/dimensio/
contact:
- family-names: Frerebeau
  given-names: Nicolas
  email: nicolas.frerebeau@u-bordeaux-montaigne.fr
  orcid: https://orcid.org/0000-0001-5759-4944
keywords:
- data-analysis
- multivariate-analysis
- 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: 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: '>= 1.10.0'
- 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: 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: 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: 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: 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: 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": "dimensio",
  "description": "Simple Principal Components Analysis (PCA) and (Multiple) Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN: 978-2-10-049616-7).",
  "name": "dimensio: Multivariate Data Analysis",
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  ],
  "codeRepository": "https://codeberg.org/tesselle/dimensio",
  "issueTracker": "https://codeberg.org/tesselle/dimensio/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "0.14.1",
  "programmingLanguage": {
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  "funder": [
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      "@type": "Organization",
      "name": "CNRS"
    }
  ],
  "maintainer": [
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      "@type": "Person",
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}

GitHub Events

Total
  • Release event: 2
  • Push event: 35
  • Create event: 5
Last Year
  • Release event: 2
  • Push event: 35
  • Create event: 5

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 113
  • Total Committers: 1
  • Avg Commits per committer: 113.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 33
  • Committers: 1
  • Avg Commits per committer: 33.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
nfrerebeau n****u@u****r 113
Committer Domains (Top 20 + Academic)
u-bordeaux-montaigne.fr: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • arkhe >= 1.4.0 imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • ggplot2 * suggests
  • khroma * suggests
  • knitr * suggests
  • markdown * suggests
  • rsvg * suggests
  • svglite * suggests
  • tinysnapshot * suggests
  • tinytest * suggests