Function reference • nexus

Compositional Data

as_amounts(): Coerce to Amounts

as_composition(): Coerce to a Closed Compositional Matrix

closure(): Closure Operation

Log-ratio

transform_alr(): Additive Log-Ratios (ALR)

transform_clr(): Centered Log-Ratios (CLR)

transform_ilr(): Isometric Log-Ratios (ILR)

transform_inverse(): Inverse Log-Ratio Transformation

transform_lr(): Pairwise Log-Ratios (LR)

transform_plr(): Pivot Log-Ratios (PLR)

Statistics

aggregate(<CompositionMatrix>): Compute Summary Statistics of Data Subsets

var(<CompositionMatrix>) cov(<CompositionMatrix>): Variance and Covariance

dist(<CompositionMatrix>): Distances

mahalanobis(<CompositionMatrix>): Mahalanobis Distance

mean(<CompositionMatrix>): Compositional Mean

variation(): Variation Matrix

Visualization

as_graph(): Graph of Log-ratios

autoplot(<CompositionMatrix>) plot(<CompositionMatrix>,<missing>): Plot Compositional Data

autoplot(<LogRatio>) plot(<LogRatio>,<missing>): Plot Log-Ratios

Multivariate Analysis

pca(<CompositionMatrix>) pca(<LogRatio>): Principal Components Analysis

Outlier Detection

outliers(): Outlier Detection

autoplot(<OutlierIndex>) plot(<OutlierIndex>,<missing>): Plot Outliers

Isotope Analysis

lia_age(): Geological Model Age from Lead Isotope Analysis

Getters and Setters

has_groups() get_groups() `set_groups<-`(): Deal With Groups

has_replicates() get_samples() `set_samples<-`(): Deal With Samples

`[`(<CompositionMatrix>) `[<-`(<CompositionMatrix>) `[[<-`(<CompositionMatrix>): Extract or Replace Parts of an Object

get_totals() `set_totals<-`(): Row Sums

Classes

CompositionMatrix-class .CompositionMatrix: Compositional Matrix

LogRatio-class .LogRatio LR-class .LR CLR-class .CLR ALR-class .ALR ILR-class .ILR PLR-class .PLR: Log-Ratio Matrix

OutlierIndex-class .OutlierIndex: Outliers

Datasets

hongite: Hongite Mineralogy