Package: nexus 0.3.0.9000

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 [ctb], Arthur Leck [ctb], Université Bordeaux Montaigne [fnd], CNRS [fnd]

nexus_0.3.0.9000.tar.gz
nexus_0.3.0.9000.zip(r-4.5)nexus_0.3.0.9000.zip(r-4.4)nexus_0.3.0.9000.zip(r-4.3)
nexus_0.3.0.9000.tgz(r-4.4-any)nexus_0.3.0.9000.tgz(r-4.3-any)
nexus_0.3.0.9000.tar.gz(r-4.5-noble)nexus_0.3.0.9000.tar.gz(r-4.4-noble)
nexus_0.3.0.9000.tgz(r-4.4-emscripten)nexus_0.3.0.9000.tgz(r-4.3-emscripten)
nexus.pdf |nexus.html
nexus/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/tesselle/nexus/issues

Datasets:

On CRAN:

archaeological-sciencearchaeologyarchaeometrycompositional-dataprovenance-studies

65 exports 5 stars 6.92 score 5 dependencies 2 dependents 24 scripts 344 downloads

Last updated 1 months agofrom:92a6d2a03a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 03 2024
R-4.5-winOKOct 03 2024
R-4.5-linuxOKOct 03 2024
R-4.4-winOKOct 03 2024
R-4.4-macOKOct 03 2024
R-4.3-winOKOct 03 2024
R-4.3-macOKOct 03 2024

Exports:%perturbe%%power%aggregateany_assignedas_amountsas_compositionas_graphbarplotclosurecolorcondensecovariancedescribedetect_outlierdistextractgroupsgroups<-histis_assignedis_element_majoris_element_minoris_element_traceis_outlieris_oxidelabelsmahalanobismarginmeanmixpalette_color_continuouspalette_color_discretepalette_color_pickerpalette_linepalette_shapepalette_size_rangepcaperturbationpippoweringquantilerbind2remove_constantremove_NAremove_zeroreplace_NAreplace_zeroscalarscalesparsitysplitttotalstotals<-transform_alrtransform_clrtransform_ilrtransform_inversetransform_lrtransform_plrunivariate_ilrvariancevariance_totalvariationweights

Dependencies:arkhedimensioisopleuroskhromaMASS

Introduction to nexus

Rendered fromnexus.Rmdusingknitr::knitron Oct 03 2024.

Last update: 2024-09-03
Started: 2022-11-11

Readme and manuals

Help Manual

Help pageTopics
Compute Summary Statistics of Data Subsetsaggregate aggregate,CompositionMatrix-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
Barplot of Compositional Databarplot barplot,CompositionMatrix-method
Combine Two Composition Matricesbind rbind2,CompositionMatrix,CompositionMatrix-method
Boxite Mineralogyboxite
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-method
Covariance Matrixcovariance covariance,ALR-method covariance,CLR-method covariance,CompositionMatrix-method covariance-method
Coxite Mineralogycoxite
Data Descriptiondescribe describe,CompositionMatrix-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-based Subsetextract extract,CompositionMatrix-method extract-method
Working With Groupsany_assigned any_assigned,CompositionMatrix-method any_assigned,LogRatio-method any_assigned-method groups groups,CompositionMatrix,ANY-method groups,CompositionMatrix,list-method groups,CompositionMatrix-method groups,LogRatio-method groups,OutlierIndex-method groups-method groups<- groups<-,CompositionMatrix,ANY-method groups<-,CompositionMatrix,list-method is_assigned is_assigned,CompositionMatrix-method is_assigned,LogRatio-method is_assigned-method
Histogram of Compositional Datahist hist,CompositionMatrix-method
Hongite Mineralogyhongite
Kongite Mineralogykongite
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
Get or Set Parts of an Objectget labels,CompositionMatrix-method labels,LogRatio-method mutators set weights,ALR-method weights,LogRatio-method weights,LR-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 Compositional Dataplot plot,CompositionMatrix,missing-method
Plot Log-Ratiosplot,LogRatio,missing-method plot_logratio
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
Divide into Groupssplit split,CompositionMatrix-method split,LogRatio-method
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-method
Centered Log-Ratios (CLR)transform_clr transform_clr,ALR-method transform_clr,CompositionMatrix-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-method
Inverse Log-Ratio Transformationtransform_inverse transform_inverse,ALR,missing-method transform_inverse,CLR,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-method
Pivot Log-Ratios (PLR)transform_plr transform_plr,CompositionMatrix-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