Skip to content

Commit

Permalink
Update README
Browse files Browse the repository at this point in the history
  • Loading branch information
@nfrerebeau
nfrerebeau committed Aug 26, 2024
1 parent 3350bcd commit 7f54ed2
Show file tree
Hide file tree
Showing 2 changed files with 207 additions and 13 deletions.
9 changes: 5 additions & 4 deletions README.Rmd
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
---
output: github_document
bibliography: vignettes/bibliography.bib
nocite: '@*'
---

<!-- README.md is generated from README.Rmd. Please edit that file -->
Expand All @@ -24,9 +25,9 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
[![Dependencies](https://tinyverse.netlify.app/badge/nexus)](https://cran.r-project.org/package=nexus)

[![r-universe](https://tesselle.r-universe.dev/badges/nexus)](https://tesselle.r-universe.dev/nexus){.pkgdown-devel}
[![CRAN Version](http://www.r-pkg.org/badges/version/nexus)](https://cran.r-project.org/package=nexus){.pkgdown-release}
[![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](http://cranlogs.r-pkg.org/badges/nexus)](https://cran.r-project.org/package=nexus){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/nexus)](https://cran.r-project.org/package=nexus){.pkgdown-release}

[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

Expand All @@ -35,6 +36,8 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale

## Overview

This package is currently *experimental*. This means that it is functional, but interfaces and functionalities may change over time, testing and documentation may be lacking.

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:

* Logratio transformations: `transform_lr()`, `transform_clr()`, `transform_alr()`, `transform_ilr()`, `transform_plr()`.
Expand All @@ -49,8 +52,6 @@ This package also includes methods for provenance studies:

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

This package is currently *experimental*. This means that it is functional, but interfaces and functionalities may change over time, testing and documentation may be lacking.

---

```{r citation, echo=FALSE, comment='', results='asis'}
Expand Down
211 changes: 202 additions & 9 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,16 @@ src="https://tesselle.r-universe.dev/badges/nexus"
alt="r-universe" /></a>
<a href="https://cran.r-project.org/package=nexus"
class="pkgdown-release"><img
src="http://www.r-pkg.org/badges/version/nexus"
src="https://www.r-pkg.org/badges/version/nexus"
alt="CRAN Version" /></a>
<a href="https://cran.r-project.org/web/checks/check_results_nexus.html"
class="pkgdown-release"><img
src="https://badges.cranchecks.info/worst/nexus.svg"
alt="CRAN checks" /></a>
<a href="https://cran.r-project.org/package=nexus"
class="pkgdown-release"><img
src="http://cranlogs.r-pkg.org/badges/nexus" alt="CRAN Downloads" /></a>
src="https://cranlogs.r-pkg.org/badges/nexus"
alt="CRAN Downloads" /></a>

[![Project Status: WIP – Initial development is in progress, but there
has not yet been a stable, usable release suitable for the
Expand All @@ -35,7 +36,11 @@ public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostat

## Overview

Exploration and analysis of compositional data in the framework of
This package is currently *experimental*. This means that it is
functional, but interfaces and functionalities may change over time,
testing and documentation may be lacking.

Exploration and analysis of compositional data in the framework of J.
Aitchison (1986). **nexus** provides tools for chemical fingerprinting
and source tracking of ancient materials. This package provides methods
for compositional data analysis:
Expand All @@ -55,10 +60,6 @@ This package also includes methods for provenance studies:
[**isopleuros**](https://packages.tesselle.org/isopleuros/) is a
companion package to **nexus** that allows to create ternary plots.

This package is currently *experimental*. This means that it is
functional, but interfaces and functionalities may change over time,
testing and documentation may be lacking.

------------------------------------------------------------------------

To cite nexus in publications use:
Expand Down Expand Up @@ -99,8 +100,8 @@ library(nexus)
**nexus** provides a set of S4 classes that represent different special
types of matrix. 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
(Aitchison 1986).
some whole, carrying relative, rather than absolute, information (J.
Aitchison 1986).

*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
Expand Down Expand Up @@ -159,6 +160,14 @@ York, USA: Chapman and Hall.

</div>

<div id="ref-aitchison2002" class="csl-entry">

Aitchison, John, and Michael Greenacre. 2002. “Biplots of Compositional
Data.” *Journal of the Royal Statistical Society: Series C (Applied
Statistics)* 51 (4): 375–92. <https://doi.org/10.1111/1467-9876.00275>.

</div>

<div id="ref-baxter2008" class="csl-entry">

Baxter, M. J., C. C. Beardah, I. Papageorgiou, M. A. Cau, P. M. Day, and
Expand All @@ -168,4 +177,188 @@ Artefacts Using Geochemical and Petrographic Data.” *Archaeometry* 50

</div>

<div id="ref-beardah2003" class="csl-entry">

Beardah, C. C., M. J. Baxter, I. Papageorgiou, and M. A. Cau. 2003.
“"<span class="nocase">Mixed-mode</span>" Approaches to the Grouping of
Ceramic Artefacts Using S-Plus.” In *The Digital Heritage of
Archaeology.*, edited by M. Doerr and A. Sarris, 261–66. Athens: Archive
of Monuments and Publications, Hellenic Ministry of Culture.

</div>

<div id="ref-vandenboogaart2013" class="csl-entry">

Boogaart, K. Gerald van den, and Raimon Tolosana-Delgado. 2013.
*Analyzing Compositional Data with R*. Use R! Berlin Heidelberg:
Springer-Verlag. <https://doi.org/10.1007/978-3-642-36809-7>.

</div>

<div id="ref-cau2004" class="csl-entry">

Cau, Miguel-Angel, Peter M Day, Michael J Baxter, Ioulia Papageorgiou,
Ioannis Iliopoulos, and Giuseppe Montana. 2004. “Exploring Automatic
Grouping Procedures in Ceramic Petrology.” *Journal of Archaeological
Science* 31 (9): 1325–38. <https://doi.org/10.1016/j.jas.2004.03.006>.

</div>

<div id="ref-egozcue2003" class="csl-entry">

Egozcue, J. J., V. Pawlowsky-Glahn, G. Mateu-Figueras, and C.
Barceló-Vidal. 2003. “Isometric Logratio Transformations for
Compositional Data Analysis.” *Mathematical Geology* 35 (3): 279–300.
<https://doi.org/10.1023/A:1023818214614>.

</div>

<div id="ref-filzmoser2005" class="csl-entry">

Filzmoser, Peter, Robert G. Garrett, and Clemens Reimann. 2005.
“Multivariate Outlier Detection in Exploration Geochemistry.” *Computers
& Geosciences* 31 (5): 579–87.
<https://doi.org/10.1016/j.cageo.2004.11.013>.

</div>

<div id="ref-filzmoser2008" class="csl-entry">

Filzmoser, Peter, and Karel Hron. 2008. “Outlier Detection for
Compositional Data Using Robust Methods.” *Mathematical Geosciences* 40
(3): 233–48. <https://doi.org/10.1007/s11004-007-9141-5>.

</div>

<div id="ref-filzmoser2009" class="csl-entry">

Filzmoser, Peter, Karel Hron, and Clemens Reimann. 2009a. “Principal
Component Analysis for Compositional Data with Outliers.”
*Environmetrics* 20 (6): 621–32. <https://doi.org/10.1002/env.966>.

</div>

<div id="ref-filzmoser2009a" class="csl-entry">

———. 2009b. “Univariate Statistical Analysis of Environmental
(Compositional) Data: Problems and Possibilities.” *Science of The Total
Environment* 407 (23): 6100–6108.
<https://doi.org/10.1016/j.scitotenv.2009.08.008>.

</div>

<div id="ref-filzmoser2012" class="csl-entry">

———. 2012. “Interpretation of Multivariate Outliers for Compositional
Data.” *Computers & Geosciences* 39: 77–85.
<https://doi.org/10.1016/j.cageo.2011.06.014>.

</div>

<div id="ref-filzmoser2018" class="csl-entry">

Filzmoser, Peter, Karel Hron, and Matthias Templ. 2018. *Applied
Compositional Data Analysis: With Worked Examples in R*. Use R! Berlin
Heidelberg: Springer-Verlag.
<https://doi.org/10.1007/978-3-319-96422-5>.

</div>

<div id="ref-fiserova2011" class="csl-entry">

Fišerová, Eva, and Karel Hron. 2011. “On the Interpretation of
Orthonormal Coordinates for Compositional Data.” *Mathematical
Geosciences* 43 (4): 455–68.
<https://doi.org/10.1007/s11004-011-9333-x>.

</div>

<div id="ref-greenacre2021" class="csl-entry">

Greenacre, Michael. 2021. “Compositional Data Analysis.” *Annual Review
of Statistics and Its Application* 8 (1): 271–99.
<https://doi.org/10.1146/annurev-statistics-042720-124436>.

</div>

<div id="ref-greenacre2019" class="csl-entry">

Greenacre, Michael J. 2019. *Compositional Data Analysis in Practice*.
Chapman & Hall/CRC Interdisciplinary Statistics. Boca Raton: CRC Press,
Taylor & Francis Group.

</div>

<div id="ref-hron2017" class="csl-entry">

Hron, Karel, Peter Filzmoser, Patrice de Caritat, Eva Fišerová, and
Alžběta Gardlo. 2017. “Weighted Pivot Coordinates for Compositional Data
and Their Application to Geochemical Mapping.” *Mathematical
Geosciences* 49 (6): 797–814.
<https://doi.org/10.1007/s11004-017-9684-z>.

</div>

<div id="ref-hron2011" class="csl-entry">

Hron, Karel, and Lubomír Kubáček. 2011. “Statistical Properties of the
Total Variation Estimator for Compositional Data.” *Metrika* 74 (2):
221–30. <https://doi.org/10.1007/s00184-010-0299-3>.

</div>

<div id="ref-hron2010" class="csl-entry">

Hron, K., M. Templ, and P. Filzmoser. 2010. “Imputation of Missing
Values for Compositional Data Using Classical and Robust Methods.”
*Computational Statistics & Data Analysis* 54 (12): 3095–3107.
<https://doi.org/10.1016/j.csda.2009.11.023>.

</div>

<div id="ref-martin-fernandez2003" class="csl-entry">

Martín-Fernández, J. A., C. Barceló-Vidal, and V. Pawlowsky-Glahn. 2003.
“Dealing with Zeros and Missing Values in Compositional Data Sets Using
Nonparametric Imputation.” *Mathematical Geology* 35 (3): 253–78.
<https://doi.org/10.1023/A:1023866030544>.

</div>

<div id="ref-pawlowsky-glahn2001" class="csl-entry">

Pawlowsky-Glahn, V., and J. J. Egozcue. 2001. “Geometric Approach to
Statistical Analysis on the Simplex.” *Stochastic Environmental Research
and Risk Assessment* 15 (5): 384–98.
<https://doi.org/10.1007/s004770100077>.

</div>

<div id="ref-rousseeuw1990" class="csl-entry">

Rousseeuw, Peter J., and Bert C. van Zomeren. 1990. “Unmasking
Multivariate Outliers and Leverage Points.” *Journal of the American
Statistical Association* 85 (411): 633–39.
<https://doi.org/10.1080/01621459.1990.10474920>.

</div>

<div id="ref-santos2020" class="csl-entry">

Santos, Frédéric. 2020. “Modern Methods for Old Data: An Overview of
Some Robust Methods for Outliers Detection with Applications in
Osteology.” *Journal of Archaeological Science: Reports* 32: 102423.
<https://doi.org/10.1016/j.jasrep.2020.102423>.

</div>

<div id="ref-weigand1977" class="csl-entry">

Weigand, P. C., G. Harbottle, and E. Sayre. 1977. “Turquoise Sources and
Source Analysisis: Mesoamerica and the Southwestern U.S.A.” In *Exchange
Systems in Prehistory*, edited by J. Ericson and T. K. Earle, 15–34. New
York, NY: Academic Press.

</div>

</div>

0 comments on commit 7f54ed2

Please sign in to comment.