Package: tabula 3.1.1

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:Nicolas Frerebeau [aut, cre], Brice Lebrun [ctb], Matthew Peeples [ctb], Ben Marwick [ctb], Anne Philippe [ctb], Jean-Baptiste Fourvel [ctb], Université Bordeaux Montaigne [fnd], CNRS [fnd]

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NEWS

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

Peer review:

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

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

Datasets:
  • aves - Birds Species and Abundances
  • cantabria - Early Magdalenian Engraved Bones
  • pueblo - Pueblo IV Period Ceramics
  • woodland - Trees Incidences

On CRAN:

archaeological-sciencearchaeologydata-visualization

8.29 score 35 stars 2 packages 51 scripts 396 downloads 1 mentions 70 exports 2 dependencies

Last updated 4 months agofrom:fd8d044791 (on v3.1.1). Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 05 2024
R-4.5-winOKDec 05 2024
R-4.5-linuxOKDec 05 2024
R-4.4-winOKDec 05 2024
R-4.4-macOKDec 05 2024
R-4.3-winOKDec 05 2024
R-4.3-macOKDec 05 2024

Exports:as.data.framebootstrapcolorcompositiondoubletoneppmevennessget_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_wilsonjackknifematrigraphobservedoccurrencepalette_color_continuouspalette_color_discretepalette_color_pickerplotplot_bertinplot_diceleraasplot_fordplot_heatmapplot_rankplot_spotprofilespvirarefactionremove_constantremove_NAremove_zeroreplace_NAreplace_zeroresamplerichnessseriographshesimilaritysimulatesingletonsparsitytest_diversitytest_shannontest_simpsonturnover

Dependencies:arkhekhroma

alpha Diversity

N. Frerebeau

Rendered fromalpha.Rmdusingknitr::knitron Dec 05 2024.

Last update: 2024-05-16
Started: 2024-02-23

beta Diversity

N. Frerebeau

Rendered frombeta.Rmdusingknitr::knitron Dec 05 2024.

Last update: 2024-05-16
Started: 2024-02-23

Readme and manuals

Help Manual

Help pageTopics
Birds Species and Abundancesaves
Bootstrap Estimationbootstrap bootstrap,DiversityIndex-method
Early Magdalenian Engraved Bonescantabria
Coerce to a Data Frameas.data.frame,DiversityIndex-method data.frame
Heterogeneity and Evennessevenness evenness,data.frame-method evenness,matrix-method evenness-method heterogeneity heterogeneity,data.frame-method heterogeneity,matrix-method heterogeneity-method
Abundance-based Coverage Estimatorindex_ace index_ace,numeric-method index_ace-method
Baxter's Rarefactionindex_baxter index_baxter,numeric-method index_baxter-method
Berger-Parker Dominance Indexindex_berger index_berger,numeric-method index_berger-method
Binomial Co-Occurrence Assessmentindex_binomial index_binomial,numeric,numeric-method index_binomial-method
Boone Heterogeneity Measureindex_boone index_boone,matrix-method index_boone-method
Brainerd-Robinson Quantitative Indexindex_brainerd index_brainerd,numeric,numeric-method index_brainerd-method
Sorenson Quantitative Indexindex_bray index_bray,numeric,numeric-method index_bray-method
Brillouin Diversity Index.index_brillouin index_brillouin,numeric-method index_brillouin-method
Chao1 Estimatorindex_chao1 index_chao1,numeric-method index_chao1-method
Chao2 Estimatorindex_chao2 index_chao2,matrix-method index_chao2-method
Cody Measureindex_cody index_cody,matrix-method index_cody-method
Hurlbert's Rarefactionindex_hurlbert index_hurlbert,numeric-method index_hurlbert-method
Incidence-based Coverage Estimatorindex_ice index_ice,matrix-method index_ice-method
Jaccard Indexindex_jaccard index_jaccard,character,character-method index_jaccard,logical,logical-method index_jaccard,numeric,numeric-method index_jaccard-method
Margalef Richness Indexindex_margalef index_margalef,numeric-method index_margalef-method
McIntosh Dominance Index.index_mcintosh index_mcintosh,numeric-method index_mcintosh-method
Menhinick Richness Indexindex_menhinick index_menhinick,numeric-method index_menhinick-method
Morisita-Horn Quantitative Indexindex_morisita index_morisita,numeric,numeric-method index_morisita-method
Routledge Measuresindex_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 Indexindex_shannon index_shannon,numeric-method index_shannon-method
Simpson Dominance Indexindex_simpson index_simpson,numeric-method index_simpson-method
Sorenson Qualitative Indexindex_sorenson index_sorenson,logical,logical-method index_sorenson,numeric,numeric-method index_sorenson-method
Squares Estimatorindex_squares index_squares,numeric-method index_squares-method
Whittaker Measureindex_whittaker index_whittaker,matrix-method index_whittaker-method
Wilson Measureindex_wilson index_wilson,matrix-method index_wilson-method
Jackknife Estimationjackknife jackknife,DiversityIndex-method
Matrigraphmatrigraph 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 Objectget get_method get_method,DiversityIndex-method get_method-method labels,DiversityIndex-method labels,RarefactionIndex-method mutators set
Number of Observed Speciesdoubleton doubleton,numeric-method doubleton-method observed observed,numeric-method observed-method singleton singleton,numeric-method singleton-method
Co-Occurrenceoccurrence occurrence,data.frame-method occurrence,matrix-method occurrence-method
Bertin DiagramBertin plot_bertin plot_bertin,data.frame-method plot_bertin,matrix-method plot_bertin-method
Dice-Leraas Diagramplot_diceleraas plot_diceleraas,data.frame-method plot_diceleraas,matrix-method plot_diceleraas-method
Diversity Plotplot,DiversityIndex,missing-method plot_diversity
Ford DiagramFord plot_ford plot_ford,data.frame-method plot_ford,matrix-method plot_ford-method
Heatmapplot_heatmap plot_heatmap,data.frame-method plot_heatmap,dist-method plot_heatmap,matrix-method plot_heatmap-method
Rank Plotplot_rank plot_rank,data.frame-method plot_rank,matrix-method plot_rank-method
Rarefaction Plotplot,RarefactionIndex,missing-method plot_rarefaction
Spot Plotplot_spot plot_spot,data.frame-method plot_spot,dist-method plot_spot,matrix-method plot_spot-method
Diversity Profilesprofiles profiles,data.frame-method profiles,matrix-method profiles-method
Pueblo IV Period Ceramicspueblo
Rarefactionrarefaction rarefaction,data.frame-method rarefaction,matrix-method rarefaction-method
Resampleresample resample,numeric-method resample-method
Richnesscomposition composition,data.frame-method composition,matrix-method composition-method richness richness,data.frame-method richness,matrix-method richness-method
Seriographeppm eppm,data.frame-method eppm,matrix-method eppm-method seriograph seriograph,data.frame-method seriograph,matrix-method seriograph-method
SHE Analysisshe she,data.frame-method she,matrix-method she-method
Similaritysimilarity similarity,data.frame-method similarity,matrix-method similarity-method
Measure Diversity by Comparing to Simulated Assemblagessimulate simulate,DiversityIndex-method
Diversity Testtest 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
Turnoverturnover turnover,data.frame-method turnover,matrix-method turnover-method
Trees Incidenceswoodland