# Sourcing Archaeological Materials by Chemical Composition

## Documentation for package ‘nexus’ version 0.6.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D G H I K L M P Q R S T U V W misc

## -- A --

aggregate | Compute Summary Statistics of Data Subsets
aggregate-method | Compute Summary Statistics of Data Subsets
all_assigned | Grouped Data
all_assigned-method | Grouped Data
any_assigned | Grouped Data
any_assigned-method | Grouped Data
arctic | Arctic Lake
arithmetic | Operations in the Simplex
as.data.frame | Coerce to a Data Frame
as.data.frame-method | Coerce to a Data Frame
as_amounts | Coerce to Amounts
as_amounts-method | Coerce to Amounts
as_composition | Coerce to a Closed Compositional Matrix
as_composition-method | Coerce to a Closed Compositional Matrix
as_graph | Graph of Log-ratios
as_graph-method | Graph of Log-ratios

## -- B --

barplot | Barplot of Compositional Data
barplot-method | Barplot of Compositional Data
bind | Combine Two Composition Matrices
boxite | Boxite Mineralogy
boxplot | Boxplot of Log-Ratios
boxplot-method | Boxplot of Log-Ratios

## -- C --

chemistry | Chemical Elements and Oxides
closure | Closure Operation
closure-method | Closure Operation
condense | Compositional Mean of Data Subsets
condense-method | Compositional Mean of Data Subsets
covariance | Covariance Matrix
covariance-method | Covariance Matrix
coxite | Coxite Mineralogy

## -- D --

describe | Data Description
describe-method | Data Description
detect_outlier | Outlier Detection
detect_outlier-method | Outlier Detection
dist | Distances
dist-method | Distances

## -- G --

get | Weights
group | Group by One or More Variables
group-method | Group by One or More Variables
group_factor | Grouping Metadata
group_factor-method | Grouping Metadata
group_indices | Grouping Metadata
group_indices-method | Grouping Metadata
group_levels | Grouping Metadata
group_levels-method | Grouping Metadata
group_n | Grouping Metadata
group_n-method | Grouping Metadata
group_names | Grouping Metadata
group_names-method | Grouping Metadata
group_rows | Grouping Metadata
group_rows-method | Grouping Metadata
group_size | Grouping Metadata
group_size-method | Grouping Metadata
group_split | Divide into Groups
group_split-method | Divide into Groups
group_subset | Group-based Subset
group_subset-method | Group-based Subset

## -- H --

hist | Histogram of Compositional Data
hist-method | Histogram of Compositional Data
hongite | Hongite Mineralogy

## -- I --

is_assigned | Grouped Data
is_assigned-method | Grouped Data
is_element_major | Chemical Elements and Oxides
is_element_major-method | Chemical Elements and Oxides
is_element_minor | Chemical Elements and Oxides
is_element_minor-method | Chemical Elements and Oxides
is_element_trace | Chemical Elements and Oxides
is_element_trace-method | Chemical Elements and Oxides
is_outlier | Outlier Detection
is_outlier-method | Outlier Detection
is_oxide | Chemical Elements and Oxides
is_oxide-method | Chemical Elements and Oxides

## -- K --

kongite | Kongite Mineralogy

## -- L --

labels | Labels
labels-method | Labels
lava | Skye Lavas Compositions
lra | Principal Components Analysis

## -- M --

mahalanobis | Mahalanobis Distance
mahalanobis-method | Mahalanobis Distance
margin | Marginal Compositions
margin-method | Marginal Compositions
mean | Compositional Mean
mean-method | Compositional Mean
missing | Missing Values Policy
mix | Mixed-Mode Analysis
mix-method | Mixed-Mode Analysis

## -- P --

pairs | Plot Compositional Data
pairs-method | Plot Compositional Data
pca | Principal Components Analysis
pca-method | Principal Components Analysis
perturbation | Perturbation Operation
perturbation-method | Perturbation Operation
pip | Proportionality Index of Parts (PIP)
pip-method | Proportionality Index of Parts (PIP)
plot | Plot Log-Ratios
plot-method | Plot Log-Ratios
plot-method | Plot Outliers
plot_outlier | Plot Outliers
powering | Powering Operation
powering-method | Powering Operation
predator | Predator-Prey Compositions

## -- Q --

quantile | Sample Quantiles
quantile-method | Sample Quantiles

## -- R --

rbind2-method | Combine Two Composition Matrices
replace_NA | Missing Values Replacement
replace_NA-method | Missing Values Replacement
replace_zero | Zero-Replacement
replace_zero-method | Zero-Replacement

## -- S --

scalar | Scalar Product
scalar-method | Scalar Product
scale | Scaling and Centering of Compositional Data
scale-method | Scaling and Centering of Compositional Data
set | Weights
slides | Thin Sections Compositions
split-method | Divide into Groups
subset | Extract or Replace Parts of an Object

## -- T --

totals | Row Sums
totals-method | Row Sums
totals<- | Row Sums
totals<--method | Row Sums
transform_alr | Additive Log-Ratios (ALR)
transform_alr-method | Additive Log-Ratios (ALR)
transform_clr | Centered Log-Ratios (CLR)
transform_clr-method | Centered Log-Ratios (CLR)
transform_ilr | Isometric Log-Ratios (ILR)
transform_ilr-method | Isometric Log-Ratios (ILR)
transform_inverse | Inverse Log-Ratio Transformation
transform_inverse-method | Inverse Log-Ratio Transformation
transform_lr | Pairwise Log-Ratios (LR)
transform_lr-method | Pairwise Log-Ratios (LR)
transform_plr | Pivot Log-Ratios (PLR)
transform_plr-method | Pivot Log-Ratios (PLR)

## -- U --

ungroup | Group by One or More Variables
ungroup-method | Group by One or More Variables

## -- V --

variance | Log-Ratios Variances
variance-method | Log-Ratios Variances
variance_total | Total Variance
variance_total-method | Total Variance
variation | Variation Matrix
variation-method | Variation Matrix

## -- W --

weights | Weights
weights-method | Weights

## -- misc --

%perturbe% | Operations in the Simplex
%perturbe%-method | Operations in the Simplex
%power% | Operations in the Simplex
%power%-method | Operations in the Simplex
[-method | Extract or Replace Parts of an Object
[<--method | Extract or Replace Parts of an Object
[[<--method | Extract or Replace Parts of an Object
`%perturbe%`-method | Operations in the Simplex
`%power%`-method | Operations in the Simplex