kairos

R-CMD-check codecov CodeFactor Dependencies

r-universe CRAN Version CRAN checks CRAN Downloads

Project Status: Active – The project has reached a stable, usable state and is being actively developed.

DOI

Overview

A toolkit for relative and absolute dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site. kairos provides methods for:

tabula is a companion package to kairos that provides functions for visualization and analysis of archaeological count data.

To cite kairos in publications use:

Frerebeau N (2024). kairos: Analysis of Chronological Patterns from Archaeological Count Data. Université Bordeaux Montaigne, Pessac, France. doi:10.5281/zenodo.5653896 https://doi.org/10.5281/zenodo.5653896, R package version 2.2.0, https://packages.tesselle.org/kairos/.

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

Installation

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

install.packages("kairos")

And the development version from GitHub with:

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

Usage

## Load packages
library(kairos)
#> Loading required package: dimensio

kairos uses aion for internal date representation. Look at vignette("aion", package = "aion") before you start.

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 Husi 2022
data("loire", package = "folio")
keep <- c("Anjou", "Blésois", "Orléanais", "Haut-Poitou", "Touraine")
loire <- subset(loire, area %in% keep)

## Get time range
loire_range <- loire[, c("lower", "upper")]

## Calculate aoristic sum (weights) by group
ao <- aoristic(loire_range, step = 50, weight = TRUE, groups = loire$area)

## Plot
plot(ao, col = "grey")


## Rate of change by group
set.seed(12345) # Set seed for reproductibility
ro <- roc(ao, n = 30)
plot(ro)

Translation

This package provides translations of user-facing communications, like messages, warnings and errors, and graphical elements (axis labels). The preferred language is by default taken from the locale. This can be overridden by setting of the environment variable LANGUAGE (you only need to do this once per session):

Sys.setenv(LANGUAGE = "<language code>")

Languages currently available are English (en) and French (fr).

Contributing

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

References

Baxter, M. J., and H. E. M. Cool. 2016. “Reinventing the Wheel? Modelling Temporal Uncertainty with Applications to Brooch Distributions in Roman Britain.” Journal of Archaeological Science 66: 120–27. https://doi.org/10.1016/j.jas.2015.12.007.
Bellanger, L., and P. Husi. 2012. “Statistical Tool for Dating and Interpreting Archaeological Contexts Using Pottery.” Journal of Archaeological Science 39 (4): 777–90. https://doi.org/10.1016/j.jas.2011.06.031.
———. 2013. “Mesurer et modéliser le temps inscrit dans la matière à partir d’une source matérielle : la céramique médiévale.” In Mesure et histoire médiévale, 119–34. Histoire ancienne et médiévale. Paris: Publication de la Sorbonne.
Bellanger, L., P. Husi, and R. Tomassone. 2006a. “Statistical Aspects of Pottery Quantification for the Dating of Some Archaeological Contexts.” Archaeometry 48 (1): 169–83. https://doi.org/10.1111/j.1475-4754.2006.00249.x.
———. 2006b. “Une approche statistique pour la datation de contextes archéologiques.” Revue de statistique appliquée 54 (2): 65–81. http://www.numdam.org/item/RSA_2006__54_2_65_0/.
Bellanger, L., R. Tomassone, and P. Husi. 2008. “A Statistical Approach for Dating Archaeological Contexts.” Journal of Data Science 6: 135–54.
Brainerd, G. W. 1951. “The Place of Chronological Ordering in Archaeological Analysis.” American Antiquity 16 (4): 301–13. https://doi.org/10.2307/276979.
Colman, S. M., K. Pierce, and P. W. Birkeland. 1987. “Suggested Terminology for Quaternary Dating Methods.” Quaternary Research 28 (2): 314–19. https://doi.org/10.1016/0033-5894(87)90070-6.
Crema, E. R. 2012. “Modelling Temporal Uncertainty in Archaeological Analysis.” Journal of Archaeological Method and Theory 19 (3): 440–61. https://doi.org/10.1007/s10816-011-9122-3.
Crema, E. R., A. Kandler, and S. Shennan. 2016. “Revealing Patterns of Cultural Transmission from Frequency Data: Equilibrium and Non-Equilibrium Assumptions.” Scientific Reports 6 (1). https://doi.org/10.1038/srep39122.
Dean, J. S. 1978. “Independent Dating in Archaeological Analysis.” In Advances in Archaeological Method and Theory, 223–55. Elsevier. https://doi.org/10.1016/B978-0-12-003101-6.50013-5.
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.
Dunnell, R. C. 1970. “Seriation Method and Its Evaluation.” American Antiquity 35 (3): 305–19. https://doi.org/10.2307/278341.
Dye, T. S. 2016. “Long-Term Rhythms in the Development of Hawaiian Social Stratification.” Journal of Archaeological Science 71: 1–9. https://doi.org/10.1016/j.jas.2016.05.006.
Feder, A. F., S. Kryazhimskiy, and J. B. Plotkin. 2014. “Identifying Signatures of Selection in Genetic Time Series.” Genetics 196 (2): 509–22. https://doi.org/10.1534/genetics.113.158220.
Ihm, P. 2005. “A Contribution to the History of Seriation in Archaeology.” In Classification – the Ubiquitous Challenge, edited by C. Weihs and W. Gaul, 307–16. Berlin Heidelberg: Springer. https://doi.org/10.1007/3-540-28084-7_34.
Johnson, I. 2004. “Aoristic Analysis: Seeds of a New Approach to Mapping Archaeological Distributions Through Time.” In Enter the Past - The E-way into the Four Dimensions of Cultural Heritage, edited by K. F. Ausserer, W. Börner, M. Goriany, and L. Karlhuber-Vöckl, 448–52. BAR International Series 1227. Oxford: Archaeopress.
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.
Lipo, C. P., M. E. Madsen, and R. C. Dunnell. 2015. “A Theoretically-Sufficient and Computationally-Practical Technique for Deterministic Frequency Seriation.” PLOS ONE 10 (4): e0124942. https://doi.org/10.1371/journal.pone.0124942.
Müller-Scheeßel, N., and M. Hinz. 2018. “Aoristic Research in R: Correcting Temporal Categorizations in Archaeology.” Presented at the Human History and Digital Future (CAA 2018), Tubingen, March 21. https://www.youtube.com/watch?v=bUBukex30QI.
O’Brien, M. J., and R. L. Lyman. 2002. Seriation, Stratigraphy, and Index Fossils: The Backbone of Archaeological Dating. Dordrecht: Springer.
Orton, D., J. Morris, and A. Pipe. 2017. “Catch Per Unit Research Effort: Sampling Intensity, Chronological Uncertainty, and the Onset of Marine Fish Consumption in Historic London.” Open Quaternary 3: 1. https://doi.org/10.5334/oq.29.
Palmisano, A., A. Bevan, and S. Shennan. 2017. “Comparing Archaeological Proxies for Long-Term Population Patterns: An Example from Central Italy.” Journal of Archaeological Science 87: 59–72. https://doi.org/10.1016/j.jas.2017.10.001.
Peeples, M. A., and G. Schachner. 2012. “Refining Correspondence Analysis-Based Ceramic Seriation of Regional Data Sets.” Journal of Archaeological Science 39 (8): 2818–27. https://doi.org/10.1016/j.jas.2012.04.040.
Petrie, W. M. F. 1899. “Sequences in Prehistoric Remains.” Journal of the Anthropological Institute of Great Britain and Ireland 29 (3/4): 295–301. https://doi.org/10.2307/2843012.
Philippe, A., and M.-A. Vibet. 2020. “Analysis of Archaeological Phases Using the R Package ArchaeoPhases.” Journal of Statistical Software 93. https://doi.org/10.18637/jss.v093.c01.
Poblome, J., and P. J. F. Groenen. 2003. “Constrained Correspondence Analysis for Seriation of Sagalassos Tablewares.” In The Digital Heritage of Archaeology, edited by M. Doerr and A. Sarris. Athens: Hellenic Ministry of Culture.
Porčić, M. 2013. “The Goodness of Fit and Statistical Significance of Seriation Solutions.” Journal of Archaeological Science 40 (12): 4552–59. https://doi.org/10.1016/j.jas.2013.07.013.
Ratcliffe, J. H. 2000. “Aoristic Analysis: The Spatial Interpretation of Unspecific Temporal Events.” International Journal of Geographical Information Science 14 (7): 669–79. https://doi.org/10.1080/136588100424963.
———. 2002. “Aoristic Signatures and the Spatio-Temporal Analysis of High Volume Crime Patterns.” Journal of Quantitative Criminology 18 (1): 23–43. https://doi.org/10.1023/A:1013240828824.
Roberts, J. M., B. J. Mills, J. J. Clark, W. R. Haas, D. L. Huntley, and M. A. Trowbridge. 2012. “A Method for Chronological Apportioning of Ceramic Assemblages.” Journal of Archaeological Science 39 (5): 1513–20. https://doi.org/10.1016/j.jas.2011.12.022.
Robinson, W. S. 1951. “A Method for Chronologically Ordering Archaeological Deposits.” American Antiquity 16 (4): 293–301. https://doi.org/10.2307/276978.
South, S. A. 1977. Method and Theory in Historical Archaeology. Studies in Archeology. New York: Academic Press.
Velden, M. vande, P. J. F. Groenen, and J. Poblome. 2009. “Seriation by Constrained Correspondence Analysis: A Simulation Study.” Computational Statistics & Data Analysis 53 (8): 3129–38. https://doi.org/10.1016/j.csda.2008.08.020.