Package: tabula 3.1.0
Nicolas Frerebeau
tabula: Analysis and Visualization of Archaeological Count Data
An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Authors:
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tabula/json (API)
NEWS
| # Install 'tabula' in R: |
| install.packages('tabula', repos = c('https://tesselle.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tesselle/tabula/issues
archaeological-sciencearchaeologydata-visualization
Last updated 2 months agofrom:b37eb0aa0c (on v3.1.0)
Exports:bootstrapcompositioneppmevennessget_methodheterogeneityindex_aceindex_baxterindex_bergerindex_binomialindex_booneindex_brainerdindex_brayindex_brillouinindex_chao1index_chao2index_codyindex_hurlbertindex_iceindex_jaccardindex_margalefindex_mcintoshindex_menhinickindex_morisitaindex_routledge1index_routledge2index_routledge3index_shannonindex_simpsonindex_sorensonindex_squaresindex_whittakerindex_wilsonjackknifematrigraphoccurrenceplotplot_bertinplot_diceleraasplot_fordplot_heatmapplot_rankplot_spotprofilespvirarefactionremove_constantremove_NAremove_zeroreplace_NAreplace_zeroresamplerichnessseriographshesimilaritysimulatesparsitytest_diversitytest_shannontest_simpsonturnover
Dependencies:arkhe
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Birds Species and Abundances | aves |
| Bootstrap Estimation | bootstrap bootstrap,DiversityIndex-method |
| Early Magdalenian Engraved Bones | cantabria |
| Heterogeneity and Evenness | evenness evenness,data.frame-method evenness,matrix-method evenness-method heterogeneity heterogeneity,data.frame-method heterogeneity,matrix-method heterogeneity-method |
| Abundance-based Coverage Estimator | index_ace index_ace,numeric-method index_ace-method |
| Baxter's Rarefaction | index_baxter index_baxter,numeric-method index_baxter-method |
| Berger-Parker Dominance Index | index_berger index_berger,numeric-method index_berger-method |
| Binomial Co-Occurrence Assessment | index_binomial index_binomial,numeric,numeric-method index_binomial-method |
| Boone Heterogeneity Measure | index_boone index_boone,matrix-method index_boone-method |
| Brainerd-Robinson Quantitative Index | index_brainerd index_brainerd,numeric,numeric-method index_brainerd-method |
| Sorenson Quantitative Index | index_bray index_bray,numeric,numeric-method index_bray-method |
| Brillouin Diversity Index. | index_brillouin index_brillouin,numeric-method index_brillouin-method |
| Chao1 Estimator | index_chao1 index_chao1,numeric-method index_chao1-method |
| Chao2 Estimator | index_chao2 index_chao2,matrix-method index_chao2-method |
| Cody Measure | index_cody index_cody,matrix-method index_cody-method |
| Hurlbert's Rarefaction | index_hurlbert index_hurlbert,numeric-method index_hurlbert-method |
| Incidence-based Coverage Estimator | index_ice index_ice,matrix-method index_ice-method |
| Jaccard Index | index_jaccard index_jaccard,character,character-method index_jaccard,logical,logical-method index_jaccard,numeric,numeric-method index_jaccard-method |
| Margalef Richness Index | index_margalef index_margalef,numeric-method index_margalef-method |
| McIntosh Dominance Index. | index_mcintosh index_mcintosh,numeric-method index_mcintosh-method |
| Menhinick Richness Index | index_menhinick index_menhinick,numeric-method index_menhinick-method |
| Morisita-Horn Quantitative Index | index_morisita index_morisita,numeric,numeric-method index_morisita-method |
| Routledge Measures | index_routledge index_routledge1 index_routledge1,matrix-method index_routledge1-method index_routledge2 index_routledge2,matrix-method index_routledge2-method index_routledge3 index_routledge3,matrix-method index_routledge3-method |
| Shannon-Wiener Diversity Index | index_shannon index_shannon,numeric-method index_shannon-method |
| Simpson Dominance Index | index_simpson index_simpson,numeric-method index_simpson-method |
| Sorenson Qualitative Index | index_sorenson index_sorenson,logical,logical-method index_sorenson,numeric,numeric-method index_sorenson-method |
| Squares Estimator | index_squares index_squares,numeric-method index_squares-method |
| Whittaker Measure | index_whittaker index_whittaker,matrix-method index_whittaker-method |
| Wilson Measure | index_wilson index_wilson,matrix-method index_wilson-method |
| Jackknife Estimation | jackknife jackknife,DiversityIndex-method |
| Matrigraph | matrigraph matrigraph,data.frame-method matrigraph,matrix-method matrigraph-method pvi pvi,data.frame-method pvi,matrix-method pvi-method |
| Get or Set Parts of an Object | get get_method get_method,DiversityIndex-method get_method-method labels,DiversityIndex-method labels,RarefactionIndex-method mutators set |
| Co-Occurrence | occurrence occurrence,data.frame-method occurrence,matrix-method occurrence-method |
| Bertin Diagram | Bertin plot_bertin plot_bertin,data.frame-method plot_bertin,matrix-method plot_bertin-method |
| Dice-Leraas Diagram | plot_diceleraas plot_diceleraas,data.frame-method plot_diceleraas,matrix-method plot_diceleraas-method |
| Diversity Plot | plot,DiversityIndex,missing-method plot_diversity |
| Ford Diagram | Ford plot_ford plot_ford,data.frame-method plot_ford,matrix-method plot_ford-method |
| Heatmap | plot_heatmap plot_heatmap,data.frame-method plot_heatmap,dist-method plot_heatmap,matrix-method plot_heatmap-method |
| Rank Plot | plot_rank plot_rank,data.frame-method plot_rank,matrix-method plot_rank-method |
| Rarefaction Plot | plot,RarefactionIndex,missing-method plot_rarefaction |
| Spot Plot | plot_spot plot_spot,data.frame-method plot_spot,dist-method plot_spot,matrix-method plot_spot-method |
| Diversity Profiles | profiles profiles,data.frame-method profiles,matrix-method profiles-method |
| Pueblo IV Period Ceramics | pueblo |
| Rarefaction | rarefaction rarefaction,data.frame-method rarefaction,matrix-method rarefaction-method |
| Resample | resample resample,numeric-method resample-method |
| Richness | composition composition,data.frame-method composition,matrix-method composition-method richness richness,data.frame-method richness,matrix-method richness-method |
| Seriograph | eppm eppm,data.frame-method eppm,matrix-method eppm-method seriograph seriograph,data.frame-method seriograph,matrix-method seriograph-method |
| SHE Analysis | she she,data.frame-method she,matrix-method she-method |
| Similarity | similarity similarity,data.frame-method similarity,matrix-method similarity-method |
| Measure Diversity by Comparing to Simulated Assemblages | simulate simulate,DiversityIndex-method |
| Diversity Test | test test_shannon test_shannon,data.frame,missing-method test_shannon,matrix,missing-method test_shannon,numeric,numeric-method test_shannon-method test_simpson test_simpson,data.frame,missing-method test_simpson,matrix,missing-method test_simpson,numeric,numeric-method test_simpson-method |
| Turnover | turnover turnover,data.frame-method turnover,matrix-method turnover-method |
| Trees Incidences | woodland |
