Package: nexus 0.6.0.9000

Nicolas Frerebeau

nexus: Sourcing Archaeological Materials by Chemical Composition

Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.

Authors:Nicolas Frerebeau [aut, cre], Anne Philippe [aut], Brice Lebrun [art], Université Bordeaux Montaigne [fnd], CNRS [fnd]

nexus_0.6.0.9000.tar.gz
nexus_0.6.0.9000.zip(r-4.7)nexus_0.6.0.9000.zip(r-4.6)nexus_0.6.0.9000.zip(r-4.5)
nexus_0.6.0.9000.tgz(r-4.6-any)nexus_0.6.0.9000.tgz(r-4.5-any)
nexus_0.6.0.9000.tar.gz(r-4.7-any)nexus_0.6.0.9000.tar.gz(r-4.6-any)
nexus_0.6.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
nexus/json (API)
NEWS

# Install 'nexus' in R:
install.packages('nexus', repos = c('https://tesselle.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://codeberg.org/tesselle/nexus

Pkgdown/docs site:https://packages.tesselle.org

Datasets:

On CRAN:

Conda:

archaeologyarchaeological-sciencearchaeometrycompositional-dataprovenance-studies

5.70 score 2 packages 28 scripts 172 downloads 78 exports 5 dependencies

Last updated from:cc331cbe7d. Checks:8 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK159
source / vignettesOK196
linux-release-x86_64OK137
macos-release-arm64OK140
macos-oldrel-arm64OK118
windows-develERROR113
windows-releaseOK90
windows-oldrelOK133
wasm-releaseOK107

Exports:%perturbe%%power%aggregateall_assignedany_assignedas_amountsas_compositionas_graphbarplotboxplotclosurecolorcondensecovariancedescribedetect_outlierdistgroupgroup_factorgroup_indicesgroup_levelsgroup_ngroup_namesgroup_rowsgroup_sizegroup_splitgroup_subsethistis_assignedis_compositionis_element_majoris_element_minoris_element_traceis_groupedis_logratiois_outlieris_oxidelabelsmahalanobismarginmeanmixpairspalette_color_continuouspalette_color_discretepalette_color_pickerpalette_linepalette_shapepalette_size_divergingpalette_size_sequentialpcaperturbationpippoweringquantilerbind2remove_NAremove_zeroreplace_NAreplace_zeroscalarscalesplitttotalstotals<-transform_alrtransform_clrtransform_ilrtransform_inversetransform_lrtransform_plrungroupunivariate_ilrvariancevariance_totalvariationweights

Dependencies:arkhedimensioisopleuroskhromaMASS

Grouped Compositional Data

N. Frerebeau

Rendered fromgroups.Rmdusingknitr::knitron Jun 03 2026.

Last update: 2025-06-02
Started: 2024-12-18

Introduction to nexus

N. Frerebeau

Rendered fromnexus.Rmdusingknitr::knitron Jun 03 2026.

Last update: 2025-06-02
Started: 2022-11-11

Readme and manuals

Help Manual

Help pageTopics
Compute Summary Statistics of Data Subsetsaggregate aggregate,CompositionMatrix-method aggregate,GroupedComposition-method
Arctic Lakearctic
Operations in the Simplex%perturbe% %perturbe%,CompositionMatrix,CompositionMatrix-method %power% %power%,CompositionMatrix,numeric-method %power%,numeric,CompositionMatrix-method arithmetic `%perturbe%`,CompositionMatrix,CompositionMatrix-method `%perturbe%`-method `%power%`,CompositionMatrix,numeric-method `%power%`,numeric,CompositionMatrix-method `%power%`-method
Coerce to Amountsas_amounts as_amounts,CompositionMatrix-method as_amounts-method
Coerce to a Closed Compositional Matrixas_composition as_composition,data.frame-method as_composition,matrix-method as_composition,numeric-method as_composition-method
Graph of Log-ratiosas_graph as_graph,ALR-method as_graph,ILR-method as_graph,LR-method as_graph-method
Coerce to a Data Frameas.data.frame as.data.frame,CompositionMatrix-method as.data.frame,LogRatio-method as.data.frame,OutlierIndex-method
Barplot of Compositional Databarplot barplot,CompositionMatrix-method
Combine Two Composition Matricesbind rbind2,CompositionMatrix,CompositionMatrix-method rbind2,GroupedComposition,GroupedComposition-method
Boxite Mineralogyboxite
Boxplot of Log-Ratiosboxplot boxplot,GroupedLogRatio-method boxplot,LogRatio-method
Chemical Elements and Oxideschemistry is_element_major is_element_major,CompositionMatrix-method is_element_major-method is_element_minor is_element_minor,CompositionMatrix-method is_element_minor-method is_element_trace is_element_trace,CompositionMatrix-method is_element_trace-method is_oxide is_oxide,character-method is_oxide,CompositionMatrix-method is_oxide-method
Closure Operationclosure closure,matrix-method closure,numeric-method closure-method
Compositional Mean of Data Subsetscondense condense,CompositionMatrix-method condense,GroupedComposition-method condense-method
Covariance Matrixcovariance covariance,ALR-method covariance,CLR-method covariance,CompositionMatrix-method covariance-method
Coxite Mineralogycoxite
Data Descriptiondescribe describe,CompositionMatrix-method describe,GroupedComposition-method
Outlier Detectiondetect_outlier detect_outlier,CompositionMatrix,CompositionMatrix-method detect_outlier,CompositionMatrix,missing-method detect_outlier-method is_outlier is_outlier,OutlierIndex-method is_outlier-method
Distancesdist dist,CompositionMatrix-method
Group by One or More Variablesgroup group,CompositionMatrix-method group,GroupedComposition-method group-method ungroup ungroup,GroupedALR-method ungroup,GroupedCLR-method ungroup,GroupedComposition-method ungroup,GroupedILR-method ungroup,GroupedLR-method ungroup,GroupedPLR-method
Grouping Metadatagroup_factor group_factor,ReferenceGroups-method group_factor-method group_indices group_indices,ReferenceGroups-method group_indices-method group_levels group_levels,ReferenceGroups-method group_levels-method group_n group_n,ReferenceGroups-method group_n-method group_names group_names,ReferenceGroups-method group_names-method group_rows group_rows,ReferenceGroups-method group_rows-method group_size group_size,ReferenceGroups-method group_size-method
Divide into Groupsgroup_split group_split,GroupedComposition-method group_split,GroupedLogRatio-method group_split-method split,CompositionMatrix-method split,LogRatio-method
Group-based Subsetgroup_subset group_subset,GroupedComposition-method group_subset,GroupedLogRatio-method group_subset-method
Histogram of Compositional Datahist hist,CompositionMatrix-method
Hongite Mineralogyhongite
Grouped Dataall_assigned all_assigned,ReferenceGroups-method any_assigned any_assigned,ReferenceGroups-method any_assigned-method is_assigned is_assigned,ReferenceGroups-method is_assigned-method
Kongite Mineralogykongite
Labelslabels labels,CompositionMatrix-method labels,LogRatio-method
Skye Lavas Compositionslava
Mahalanobis Distancemahalanobis mahalanobis,CompositionMatrix-method mahalanobis,ILR-method
Marginal Compositionsmargin margin,CompositionMatrix-method margin-method
Compositional Meanmean mean,CompositionMatrix-method
Missing Values Policymissing
Mixed-Mode Analysismix mix,dist,dist-method mix,matrix,matrix-method mix-method
Plot Compositional Datapairs pairs,CompositionMatrix-method pairs,GroupedComposition-method
Principal Components Analysislra pca pca,CompositionMatrix-method pca,LogRatio-method
Perturbation Operationperturbation perturbation,CompositionMatrix,CompositionMatrix-method perturbation,CompositionMatrix,matrix-method perturbation,CompositionMatrix,numeric-method perturbation,numeric,numeric-method perturbation-method
Proportionality Index of Parts (PIP)pip pip,CompositionMatrix-method pip-method
Plot Log-Ratiosplot plot,GroupedLogRatio,missing-method plot,LogRatio,missing-method
Plot Outliersplot,OutlierIndex,missing-method plot_outlier
Powering Operationpowering powering,CompositionMatrix,numeric-method powering,numeric,numeric-method powering-method
Predator-Prey Compositionspredator
Sample Quantilesquantile quantile,CompositionMatrix-method
Missing Values Replacementreplace_NA replace_NA,CompositionMatrix-method
Zero-Replacementreplace_zero replace_zero,CompositionMatrix-method
Scalar Productscalar scalar,CompositionMatrix,CompositionMatrix-method scalar,numeric,numeric-method scalar-method
Scaling and Centering of Compositional Datascale scale,CompositionMatrix-method
Thin Sections Compositionsslides
Extract or Replace Parts of an Objectsubset [,CompositionMatrix,index,index,logical-method [,CompositionMatrix,index,index,missing-method [,CompositionMatrix,index,missing,logical-method [,CompositionMatrix,index,missing,missing-method [,CompositionMatrix,missing,index,logical-method [,CompositionMatrix,missing,index,missing-method [,CompositionMatrix,missing,missing,logical-method [,CompositionMatrix,missing,missing,missing-method [<-,CompositionMatrix-method [[<-,CompositionMatrix-method
Row Sumstotals totals,CompositionMatrix-method totals,LogRatio-method totals-method totals<- totals<-,CompositionMatrix-method
Additive Log-Ratios (ALR)transform_alr transform_alr,CLR-method transform_alr,CompositionMatrix-method transform_alr,GroupedCLR-method transform_alr,GroupedComposition-method transform_alr-method
Centered Log-Ratios (CLR)transform_clr transform_clr,ALR-method transform_clr,CompositionMatrix-method transform_clr,GroupedALR-method transform_clr,GroupedComposition-method transform_clr-method
Isometric Log-Ratios (ILR)transform_ilr transform_ilr,ALR,missing-method transform_ilr,ALR-method transform_ilr,CLR,missing-method transform_ilr,CLR-method transform_ilr,CompositionMatrix,missing-method transform_ilr,CompositionMatrix-method transform_ilr,GroupedALR,missing-method transform_ilr,GroupedALR-method transform_ilr,GroupedCLR,missing-method transform_ilr,GroupedCLR-method transform_ilr,GroupedComposition,missing-method transform_ilr,GroupedComposition-method transform_ilr-method
Inverse Log-Ratio Transformationtransform_inverse transform_inverse,ALR,missing-method transform_inverse,CLR,missing-method transform_inverse,GroupedALR,missing-method transform_inverse,GroupedCLR,missing-method transform_inverse,GroupedILR,missing-method transform_inverse,ILR,missing-method transform_inverse,matrix,ILR-method transform_inverse-method
Pairwise Log-Ratios (LR)transform_lr transform_lr,CompositionMatrix-method transform_lr,GroupedComposition-method transform_lr-method
Pivot Log-Ratios (PLR)transform_plr transform_plr,CompositionMatrix-method transform_plr,GroupedComposition-method transform_plr-method
Log-Ratios Variancesvariance variance,LogRatio-method variance-method
Total Variancevariance_total variance_total,CompositionMatrix-method variance_total,LogRatio-method variance_total-method
Variation Matrixvariation variation,CompositionMatrix-method variation-method
Weightsget set weights weights,ALR-method weights,LogRatio-method weights,LR-method