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nexus

r-universe

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

Exploration and analysis of compositional data in the framework of Aitchison (1986). This package provides tools for chemical fingerprinting and source tracking of ancient materials.

Initial development is in progress.

Installation

You can install the released version of nexus from CRAN with:

And the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("tesselle/nexus")

Usage 

## Load the package
library(nexus)
#> 
#> Attachement du package : 'nexus'
#> L'objet suivant est masqué depuis 'package:stats':
#> 
#>     biplot

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).

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.

These new classes are of simple use as they inherit from base matrix:

## Mineral compositions of rock specimens
data("hongite")
head(hongite)
#>       A    B    C    D    E
#> H1 48.8 31.7  3.8  6.4  9.3
#> H2 48.2 23.8  9.0  9.2  9.8
#> H3 37.0  9.1 34.2  9.5 10.2
#> H4 50.9 23.8  7.2 10.1  8.0
#> H5 44.2 38.3  2.9  7.7  6.9
#> H6 52.3 26.2  4.2 12.5  4.8

## Coerce to compositional data
coda <- as_composition(hongite)
head(coda)
#> <CompositionMatrix: 6 x 5>
#>        A     B     C     D     E
#> H1 0.488 0.317 0.038 0.064 0.093
#> H2 0.482 0.238 0.090 0.092 0.098
#> H3 0.370 0.091 0.342 0.095 0.102
#> H4 0.509 0.238 0.072 0.101 0.080
#> H5 0.442 0.383 0.029 0.077 0.069
#> H6 0.523 0.262 0.042 0.125 0.048

The CompositionMatrix class has special slots (see vignette("manual")):

  • samples for repeated measurements/observation,
  • groups to group data by site/area.

When coercing a data.frame to a CompositionMatrix object, an attempt is made to automatically assign values to these slots by mapping column names. This behavior can be disabled by setting options(nexus.autodetect = FALSE).

## Create a data.frame
X <- data.frame(
  samples = c("A", "A", "A", "B", "B", "B", "C", "C", "C"),
  groups = c("X", "X", "X", "X", "X", "X", "Y", "Y", "Y"),
  Ca = c(7.72, 7.32, 3.11, 7.19, 7.41, 5, 4.18, 1, 4.51),
  Fe = c(6.12, 5.88, 5.12, 6.18, 6.02, 7.14, 5.25, 5.28, 5.72),
  Na = c(0.97, 1.59, 1.25, 0.86, 0.76, 0.51, 0.75, 0.52, 0.56)
)

## Coerce to a compositional matrix
Y <- as_composition(X)

## Get samples
get_samples(Y)
#> [1] "A" "A" "A" "B" "B" "B" "C" "C" "C"

## Get groups
get_groups(Y)
#> [1] "X" "X" "X" "X" "X" "X" "Y" "Y" "Y"

Contributing

Please note that the nexus project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Aitchison, J. 1986. The Statistical Analysis of Compositional Data. Monographs on Statistics and Applied Probability. Londres, UK ; New York, USA: Chapman and Hall. http://dx.doi.org/10.1007/978-94-009-4109-0.