tabula

Overview

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. tabula provides methods for:

• Diversity measurement: heterogeneity(), evenness(), richness(), rarefaction(), turnover().
• Similarity measurement and co-occurrence: similarity(), occurrence().
• Assessing sample size and significance: bootstrap(), jackknife(), simulate().
• Bertin (1977) or Ford (1962) (battleship curve) diagrams: plot_bertin(), plot_ford().
• Seriograph (Desachy 2004): seriograph(), matrigraph().
• Heatmaps: plot_heatmap(), plot_spot().

kairos is a companion package to tabula that provides functions for chronological modeling and dating of archaeological assemblages from count data.

To cite tabula in publications use:

Frerebeau N (2019). “tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data.” Journal of Open Source Software, 4(44). doi:10.21105/joss.01821 https://doi.org/10.21105/joss.01821.

Frerebeau N (2024). tabula: Analysis and Visualization of Archaeological Count Data. Université Bordeaux Montaigne, Pessac, France. doi:10.5281/zenodo.1489944 https://doi.org/10.5281/zenodo.1489944, R package version 3.1.0, https://packages.tesselle.org/tabula/.

This package is a part of the tesselle project https://www.tesselle.org.

Installation

You can install the released version of tabula from CRAN with:

install.packages("tabula")

And the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("tesselle/tabula")

Usage

## Install extra packages (if needed)
# install.packages("folio")

## Load packages
library(tabula)

It assumes that you keep your data tidy: each variable (type/taxa) must be saved in its own column and each observation (sample/case) must be saved in its own row.

## Data from Lipo et al. 2015
data("mississippi", package = "folio")

## Ford diagram
plot_ford(mississippi)

## Co-occurrence of ceramic types
mississippi |> 
  occurrence() |> 
  plot_spot()

## Data from Conkey 1980, Kintigh 1989, p. 28
data("chevelon", package = "folio")

## Measure diversity by comparing to simulated assemblages
set.seed(12345)

chevelon |>
  heterogeneity(method = "shannon") |>
  simulate() |>
  plot()

chevelon |>
  richness(method = "count") |>
  simulate() |>
  plot()

Contributing

Please note that the tabula project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Alroy, John. 2018. “Limits to Species Richness in Terrestrial Communities.” Edited by Eric Seabloom. Ecology Letters 21 (12): 1781–89. https://doi.org/10.1111/ele.13152.

Baxter, M. J. 2001. “Methodological Issues in the Study of Assemblage Diversity.” American Antiquity 66 (4): 715–25. https://doi.org/10.2307/2694184.

Berger, W. H., and F. L. Parker. 1970. “Diversity of Planktonic Foraminifera in Deep Sea Sediments.” Science 168 (3937): 1345–47. https://doi.org/10.1126/science.168.3937.1345.

Bertin, Jacques. 1977. La graphique et le traitement graphique de l’information. Nouvelle bibliothèque scientifique. Paris: Flammarion.

Bobrowsky, P. T., and B. F. Ball. 1989. “The Theory and Mechanics of Ecological Diversity in Archaeology.” In Quantifying Diversity in Archaeology, edited by R. D. Leonard and G. T. Jones, 4–12. New Directions in Archaeology. Cambridge: Cambridge University Press.

Boone, James L. 1987. “Defining and Measuring Midden Catchment.” American Antiquity 52 (2): 336–45. https://doi.org/10.2307/281785.

Bowman, K. O., K. Hutcheson, E. P. Odum, and L. R. Shenton. 1971. “Comments on the Distribution of Indices of Diversity.” In Statistical Ecology, edited by E. C. Patil, E. C. Pielou, and W. E. Waters, 3:315–66. University Park, PA: Pennsylvania State University Press.

Brainerd, G. W. 1951. “The Place of Chronological Ordering in Archaeological Analysis.” American Antiquity 16 (4): 301–13. https://doi.org/10.2307/276979.

Bray, J. R., and J. T. Curtis. 1957. “An Ordination of the Upland Forest Communities of Southern Wisconsin.” Ecological Monographs 27 (4): 325–49. https://doi.org/10.2307/1942268.

Brillouin, L. 1956. Science and Information Theory. New York: Academic Press.

Buzas, M. A., and L.-A. C. Hayek. 1998. “SHE Analysis for Biofacies Identification.” Journal of Foraminiferal Research 28 (3): 233–39.

Caprariis, P. de, R. H. Lindemann, and C. M. Collins. 1976. “A Method for Determining Optimum Sample Size in Species Diversity Studies.” Journal of the International Association for Mathematical Geology 8 (5): 575–81. https://doi.org/10.1007/BF01042995.

Chao, A. 1984. “Nonparametric Estimation of the Number of Classes in a Population.” Scandinavian Journal of Statistics 11 (4): 265–70.

———. 1987. “Estimating the Population Size for Capture Recapture Data with Unequal Catchability.” Biometrics 43 (4): 783–91. https://doi.org/10.2307/2531532.

Chao, A., and C.-H. Chiu. 2016. “Species Richness: Estimation and Comparison.” In Wiley StatsRef: Statistics Reference Online, edited by N. Balakrishnan, T. Colton, B. Everitt, W. Piegorsch, F. Ruggeri, and J. L. Teugels, 1–26. Chichester, UK: John Wiley & Sons, Ltd. https://doi.org/10.1002/9781118445112.stat03432.pub2.

Chao, A., and S.-M. Lee. 1992. “Estimating the Number of Classes Via Sample Coverage.” Journal of the American Statistical Association 87 (417): 210–17. https://doi.org/10.1080/01621459.1992.10475194.

Chiu, C.-H., Y.-T. Wang, B. A. Walther, and A. Chao. 2014. “An Improved Nonparametric Lower Bound of Species Richness Via a Modified Good-Turing Frequency Formula.” Biometrics 70 (3): 671–82. https://doi.org/10.1111/biom.12200.

Cody, M. L. 1975. “Towards a Theory of Continental Species Diversity: Bird Distributions Over Mediterranean Habitat Gradients.” In Ecology and Evolution of Communities, edited by M. L. Cody and J. M. Diamond, 214–57. Cambridge, MA: Harvard University Press.

Conkey, Margaret W. 1980. “The Identification of Prehistoric Hunter-Gatherer Aggregation Sites: The Case of Altamira.” Current Anthropology 21 (5): 609–30. https://escholarship.org/uc/item/0q29504g.

Desachy, B. 2004. “Le sériographe EPPM: un outil informatisé de sériation graphique pour tableaux de comptages.” Revue archéologique de Picardie 3 (1): 39–56. https://doi.org/10.3406/pica.2004.2396.

Dice, L. R., and H. J. Leraas. 1936. “A Graphic Method for Comparing Several Sets of Measurements.” Contributions from the Laboratory of Vertebrate Genetics 3: 1–3.

Eren, Metin I., Anne Chao, Wen-Han Hwang, and Robert K. Colwell. 2012. “Estimating the Richness of a Population When the Maximum Number of Classes Is Fixed: A Nonparametric Solution to an Archaeological Problem.” Edited by Alex Mesoudi. PLoS ONE 7 (5): e34179. https://doi.org/10.1371/journal.pone.0034179.

Fisher, R. A., A. S. Corbet, and C. B. Williams. 1943. “The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population.” The Journal of Animal Ecology 12 (1): 42. https://doi.org/10.2307/1411.

Ford, J. A. 1962. A Quantitative Method for Deriving Cultural Chronology. Technical Manual 1. Washington, DC: Pan American Union.

Frerebeau, Nicolas. 2019. “Tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data.” Journal of Open Source Software 4 (44): 1821. https://doi.org/10.21105/joss.01821.

Gleason, H. A. 1922. “On the Relation Between Species and Area.” Ecology 3 (2): 158–62. https://doi.org/10.2307/1929150.

Gotelli, Nicholas J., and Robert K. Colwell. 2011. “Estimating Species Richness.” In Biological Diversity: Frontiers in Measurement and Assessment, edited by Anne E. Magurran and Brian J. McGill, 39–54. Oxford: Oxford University Press.

Hayek, L.-A. C., and M. A. Buzas. 2010. Surveying Natural Populations: Quantitative Tools for Assessing Biodiversity. Second edition. New York: Columbia University Press.

Hubbs, C. L., and C. Hubbs. 1953. “An Improved Graphical Analysis and Comparison of Series of Samples.” Systematic Biology 2 (2): 49–56. https://doi.org/10.2307/sysbio/2.2.49.

Huntley, Deborah L. 2004. “Interaction, Boundaries, and Identities: A Multiscalar Approach to the Organizational Scale of Pueblo IV Zuni Society.” PhD thesis, Arizona State University.

———. 2008. Ancestral Zuni Glaze-Decorated Pottery: Viewing Pueblo IV Regional Organization Through Ceramic Production and Exchange. Anthropological Papers of the University of Arizona 72. Tucson: University of Arizona Press. https://doi.org/10.2307/j.ctv2ngx5n8.

Hurlbert, S. H. 1971. “The Nonconcept of Species Diversity: A Critique and Alternative Parameters.” Ecology 52 (4): 577–86. https://doi.org/10.2307/1934145.

Hutcheson, K. 1970. “A Test for Comparing Diversity Based on the Shannon Formula.” Journal of Theoretical Biology 29 (1): 151–54. https://doi.org/10.1016/0022-5193(70)90124-4.

Kilburn, P. D. 1966. “Analysis of the Species-Area Relation.” Ecology 47 (5): 831–43. https://doi.org/10.2307/1934269.

Kintigh, K. 2006. “Ceramic Dating and Type Associations.” In Managing Archaeological Data: Essays in Honor of Sylvia W. Gaines, edited by J. Hantman and R. Most, 17–26. Anthropological Research Paper 57. Tempe, AZ: Arizona State University. https://doi.org/10.6067/XCV8J38QSS.

Kintigh, K. W. 1984. “Measuring Archaeological Diversity by Comparison with Simulated Assemblages.” American Antiquity 49 (1): 44–54. https://doi.org/10.2307/280511.

———. 1989. “Sample Size, Significance, and Measures of Diversity.” In Quantifying Diversity in Archaeology, edited by R. D. Leonard and G. T. Jones, 25–36. New Directions in Archaeology. Cambridge: Cambridge University Press.

Laxton, R. R. 1978. “The Measure of Diversity.” Journal of Theoretical Biology 70 (1): 51–67. https://doi.org/10.1016/0022-5193(78)90302-8.

Leonard, Robert D., and George T. Jones, eds. 1989. Quantifying Diversity in Archaeology. New Directions in Archaeology. Cambridge: Cambridge University Press.

Macarthur, R. H. 1965. “Patterns of Species Diversity.” Biological Reviews 40 (4): 510–33. https://doi.org/10.1111/j.1469-185X.1965.tb00815.x.

Magurran, A. E. 1988. Ecological Diversity and Its Measurement. Princeton, NJ: Princeton University Press.

Magurran, A. E., and B. J. McGill, eds. 2011. Biological Diversity: Frontiers in Measurement and Assessment. Oxford: Oxford University Press.

Margalef, R. 1958. “Information Theory in Ecology.” General Systems 3: 36–71.

McIntosh, R. P. 1967. “An Index of Diversity and the Relation of Certain Concepts to Diversity.” Ecology 48 (3): 392–404. https://doi.org/10.2307/1932674.

Menhinick, E. F. 1964. “A Comparison of Some Species-Individuals Diversity Indices Applied to Samples of Field Insects.” Ecology 45 (4): 859–61. https://doi.org/10.2307/1934933.

Moreno, C. E., and P. Rodríguez. 2010. “A Consistent Terminology for Quantifying Species Diversity?” Oecologia 163 (2): 279–82. https://doi.org/10.1007/s00442-010-1591-7.

Odum, H. T., J. E. Cantlon, and L. S. Kornicker. 1960. “An Organizational Hierarchy Postulate for the Interpretation of Species-Individual Distributions, Species Entropy, Ecosystem Evolution, and the Meaning of a Species-Variety Index.” Ecology 41 (2): 395–95. https://doi.org/10.2307/1930248.

Peet, R. K. 1974. “The Measurement of Species Diversity.” Annual Review of Ecology and Systematics 5 (1): 285–307. https://doi.org/10.1146/annurev.es.05.110174.001441.

Pielou, E. C. 1975. Ecological Diversity. New York: Wiley.

Preston, F. W. 1948. “The Commonness, and Rarity, of Species.” Ecology 29 (3): 254–83. https://doi.org/10.2307/1930989.

———. 1962a. “The Canonical Distribution of Commonness and Rarity: Part I.” Ecology 43 (2): 185. https://doi.org/10.2307/1931976.

———. 1962b. “The Canonical Distribution of Commonness and Rarity: Part II.” Ecology 43 (3): 410–32. https://doi.org/10.2307/1933371.

Robinson, W. S. 1951. “A Method for Chronologically Ordering Archaeological Deposits.” American Antiquity 16 (4): 293–301. https://doi.org/10.2307/276978.

Routledge, R. D. 1977. “On Whittaker’s Components of Diversity.” Ecology 58 (5): 1120–27. https://doi.org/10.2307/1936932.

Sander, H. L. 1968. “Marine Benthic Diversity: A Comparative Study.” The American Naturalist 102 (925): 243–82. https://www.jstor.org/stable/2459027.

Shannon, C. E. 1948. “A Mathematical Theory of Communication.” The Bell System Technical Journal 27: 379–423. https://doi.org/10.1002/j.1538-7305.1948.tb01338.x.

Simpson, E. H. 1949. “Measurement of Diversity.” Nature 163 (4148): 688–88. https://doi.org/10.1038/163688a0.

Simpson, Georges Gaylord, Anne Roe, and Richard C. Lewontin. 1960. Quantitative Zoology. Édition revue. New York: Harcourt, Brace and Company.

Tóthmérész, B. 1995. “Comparison of Different Methods for Diversity Ordering.” Journal of Vegetation Science 6 (2): 283–90. https://doi.org/10.2307/3236223.

Whittaker, R. H. 1960. “Vegetation of the Siskiyou Mountains, Oregon and California.” Ecological Monographs 30 (3): 279–338. https://doi.org/10.2307/1943563.

Wilson, M. V., and A. Shmida. 1984. “Measuring Beta Diversity with Presence-Absence Data.” The Journal of Ecology 72 (3): 1055–64. https://doi.org/10.2307/2259551.