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Compositional Data

as_amounts()
Coerce to Amounts
as_composition()
Coerce to a Closed Compositional Matrix
as_features()
Coerce to Features

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>)
Compute Summary Statistics of Data Subsets
covariance()
Covariance Matrix
dist(<CompositionMatrix>)
Distances
mahalanobis(<CompositionMatrix>) mahalanobis(<ILR>)
Mahalanobis Distance
margin()
Marginal Compositions
mean(<CompositionMatrix>)
Compositional Mean
metric_var() metric_sd()
Metric Variance and Standard Deviation
quantile(<CompositionMatrix>)
Sample Quantiles
scale(<CompositionMatrix>)
Scaling and Centering of Compositional Data
variation()
Variation Matrix

Visualization

as_graph()
Graph of Log-ratios
barplot(<CompositionMatrix>)
Barplot of Compositional Data
hist(<CompositionMatrix>)
Histogram of Compositional Data
plot(<CompositionMatrix>,<missing>)
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

outliers()
Outlier Detection
plot(<OutlierIndex>,<missing>)
Plot Outliers

Multivariate Analysis

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

Provenance Tools

mix()
Mixed-Mode Analysis

Getters and Setters

Datasets

arctic
Arctic Lake
chemistry
Can Sora Chemical Data
hongite
Hongite Mineralogy
petrography
Can Sora Petrographic Data
slides
Thin Sections