Package index • nexus

Compositional Data

as_amounts(): Coerce to Amounts

as_composition(): Coerce to a Closed Compositional Matrix

Reference Groups

group() ungroup(): Working With Groups

group_extract(): Group-based Subset

group_levels() group_names() group_rows() group_length() group_size() group_indices() is_assigned() any_assigned() all_assigned(): Grouping Metadata

group_split() split(<CompositionMatrix>) split(<LogRatio>): Divide into Groups

Operations in the Simplex

`%perturbe%` `%power%`: Operations in the Simplex

closure(): Closure Operation

perturbation(): Perturbation Operation

powering(): Powering Operation

scalar(): Scalar Product

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

condense(): Compositional Mean of Data Subsets

covariance(): Covariance Matrix

dist(<CompositionMatrix>): Distances

mahalanobis(<CompositionMatrix>) mahalanobis(<ILR>): Mahalanobis Distance

margin(): Marginal Compositions

mean(<CompositionMatrix>): Compositional Mean

pip(): Proportionality Index of Parts (PIP)

quantile(<CompositionMatrix>): Sample Quantiles

scale(<CompositionMatrix>): Scaling and Centering of Compositional Data

variance(): Log-Ratios Variances

variance_total(): Total Variance

variation(): Variation Matrix

Data Summary

describe(<CompositionMatrix>) describe(<GroupedComposition>): Data Description

Visualization

as_graph(): Graph of Log-ratios

barplot(<CompositionMatrix>): Barplot of Compositional Data

hist(<CompositionMatrix>): Histogram of Compositional Data

pairs(<CompositionMatrix>) pairs(<GroupedComposition>): Plot Compositional Data

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

Missing Values

missing: Missing Values Policy

replace_NA(<CompositionMatrix>): Missing Values Replacement

replace_zero(<CompositionMatrix>): Zero-Replacement

Outlier Detection

detect_outlier() is_outlier(): Outlier Detection

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

Multivariate Analysis

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

Provenance Tools

mix(): Mixed-Mode Analysis

Tools

is_element_major() is_element_minor() is_element_trace() is_oxide(): Chemical Elements and Oxides

Subsets

rbind2(<CompositionMatrix>,<CompositionMatrix>): Combine Two Composition Matrices

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

Getters and Setters

as.data.frame(<CompositionMatrix>) as.data.frame(<GroupedComposition>) as.data.frame(<LogRatio>) as.data.frame(<GroupedLogRatio>) as.data.frame(<OutlierIndex>): Coerce to a Data Frame

labels(<CompositionMatrix>) labels(<LogRatio>) weights(<ALR>) weights(<LR>) weights(<LogRatio>): Get or Set Parts of an Object

totals() `totals<-`(): Row Sums

Datasets

arctic: Arctic Lake

boxite: Boxite Mineralogy

coxite: Coxite Mineralogy

hongite: Hongite Mineralogy

kongite: Kongite Mineralogy

lava: Skye Lavas Compositions

predator: Predator-Prey Compositions

slides: Thin Sections Compositions