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:
nexus_0.3.0.9000.tar.gz
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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')) |
Bug tracker:https://github.com/tesselle/nexus/issues
Pkgdown:https://packages.tesselle.org
Datasets:
archaeological-sciencearchaeologyarchaeometrycompositional-dataprovenance-studies
Last updated 11 hours agofrom:69a66f4d8a. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | OK | Dec 18 2024 |
| R-4.5-linux | OK | Dec 18 2024 |
| R-4.4-win | OK | Dec 18 2024 |
| R-4.4-mac | OK | Dec 18 2024 |
| R-4.3-win | OK | Dec 18 2024 |
| R-4.3-mac | OK | Dec 18 2024 |
Exports:%perturbe%%power%aggregateall_assignedany_assignedas_amountsas_compositionas_graphas.data.framebarplotclosurecolorcondensecovariancedescribedetect_outlierdistgroupgroup_extractgroup_indicesgroup_lengthgroup_levelsgroup_namesgroup_rowsgroup_sizegroup_splithistis_assignedis_element_majoris_element_minoris_element_traceis_groupedis_outlieris_oxidelabelsmahalanobismarginmeanmixpalette_color_continuouspalette_color_discretepalette_color_pickerpalette_linepalette_shapepalette_size_rangepcaperturbationpippoweringquantilerbind2remove_constantremove_NAremove_zeroreplace_NAreplace_zeroscalarscalesparsitysplitttotalstotals<-transform_alrtransform_clrtransform_ilrtransform_inversetransform_lrtransform_plrungroupunivariate_ilrvariancevariance_totalvariationweights
Dependencies:arkhedimensioisopleuroskhromaMASS
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute Summary Statistics of Data Subsets | aggregate aggregate,CompositionMatrix-method aggregate,GroupedComposition-method |
| Arctic Lake | arctic |
| 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 Amounts | as_amounts as_amounts,CompositionMatrix-method as_amounts-method |
| Coerce to a Closed Compositional Matrix | as_composition as_composition,data.frame-method as_composition,matrix-method as_composition,numeric-method as_composition-method |
| Graph of Log-ratios | as_graph as_graph,ALR-method as_graph,ILR-method as_graph,LR-method as_graph-method |
| Coerce to a Data Frame | as.data.frame as.data.frame,CompositionMatrix-method as.data.frame,GroupedComposition-method as.data.frame,GroupedLogRatio-method as.data.frame,LogRatio-method as.data.frame,OutlierIndex-method |
| Barplot of Compositional Data | barplot barplot,CompositionMatrix-method |
| Combine Two Composition Matrices | bind rbind2,CompositionMatrix,CompositionMatrix-method |
| Boxite Mineralogy | boxite |
| Chemical Elements and Oxides | chemistry 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 Operation | closure closure,matrix-method closure,numeric-method closure-method |
| Compositional Mean of Data Subsets | condense condense,CompositionMatrix-method condense,GroupedComposition-method condense-method |
| Covariance Matrix | covariance covariance,ALR-method covariance,CLR-method covariance,CompositionMatrix-method covariance-method |
| Coxite Mineralogy | coxite |
| Data Description | describe describe,CompositionMatrix-method describe,GroupedComposition-method |
| Outlier Detection | detect_outlier detect_outlier,CompositionMatrix,CompositionMatrix-method detect_outlier,CompositionMatrix,missing-method detect_outlier-method is_outlier is_outlier,OutlierIndex-method is_outlier-method |
| Distances | dist dist,CompositionMatrix-method |
| Working With Groups | group 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 |
| Group-based Subset | group_extract group_extract,GroupedComposition-method group_extract-method |
| Grouping Metadata | all_assigned all_assigned,ReferenceGroups-method any_assigned any_assigned,ReferenceGroups-method any_assigned-method group_indices group_indices,ReferenceGroups-method group_indices-method group_length group_length,ReferenceGroups-method group_length-method group_levels group_levels,ReferenceGroups-method group_levels-method group_metadata 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 is_assigned is_assigned,ReferenceGroups-method is_assigned-method |
| Divide into Groups | group_split group_split,CompositionMatrix-method group_split,GroupedComposition-method group_split,GroupedLogRatio-method group_split-method split,CompositionMatrix-method split,LogRatio-method |
| Histogram of Compositional Data | hist hist,CompositionMatrix-method |
| Hongite Mineralogy | hongite |
| Check if an Object is Grouped | is_grouped |
| Kongite Mineralogy | kongite |
| Skye Lavas Compositions | lava |
| Mahalanobis Distance | mahalanobis mahalanobis,CompositionMatrix-method mahalanobis,ILR-method |
| Marginal Compositions | margin margin,CompositionMatrix-method margin-method |
| Compositional Mean | mean mean,CompositionMatrix-method |
| Missing Values Policy | missing |
| Mixed-Mode Analysis | mix mix,dist,dist-method mix,matrix,matrix-method mix-method |
| Get or Set Parts of an Object | get labels,CompositionMatrix-method labels,LogRatio-method mutators set weights,ALR-method weights,LogRatio-method weights,LR-method |
| Plot Compositional Data | pairs plot,CompositionMatrix,missing-method plot,GroupedComposition,missing-method |
| Principal Components Analysis | lra pca pca,CompositionMatrix-method pca,LogRatio-method |
| Perturbation Operation | perturbation 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-Ratios | plot plot,LogRatio,missing-method |
| Plot Outliers | plot,OutlierIndex,missing-method plot_outlier |
| Powering Operation | powering powering,CompositionMatrix,numeric-method powering,numeric,numeric-method powering-method |
| Predator-Prey Compositions | predator |
| Sample Quantiles | quantile quantile,CompositionMatrix-method |
| Missing Values Replacement | replace_NA replace_NA,CompositionMatrix-method |
| Zero-Replacement | replace_zero replace_zero,CompositionMatrix-method |
| Scalar Product | scalar scalar,CompositionMatrix,CompositionMatrix-method scalar,numeric,numeric-method scalar-method |
| Scaling and Centering of Compositional Data | scale scale,CompositionMatrix-method |
| Thin Sections Compositions | slides |
| Extract or Replace Parts of an Object | subset [,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 Sums | totals 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 Transformation | transform_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 Variances | variance variance,LogRatio-method variance-method |
| Total Variance | variance_total variance_total,CompositionMatrix-method variance_total,LogRatio-method variance_total-method |
| Variation Matrix | variation variation,CompositionMatrix-method variation-method |
