30 mars 2020
Some useful R ressources for archaeologists and anthropologists
“R packages, like friends, should be few and well chosen.” — Approximately by Charles Caleb Colton.
As far as I know (and as of march 2020), there is no CRAN task view for past sciences. Ben Marwick seems to maintain a beta version of such a task view, but this very long list of packages may be more intimidating than useful for beginners or casual R users1. Here is a much shorter, opinionated and clearly non-exhaustive list.
Age and sex estimation
- AnthropMMD  allows to compute the mean measure of divergence with a graphical user interface.
- smacof is a package implementing modern algorithms for computing multidimensional scaling (MDS), even when some distances are missing .
- vegan implements various useful methods for working with biodistances (Mantel test, …) and performing NPMANOVAs.
- Diaphysator, along with its companion software Extractor, generates maps and graphs based on cortical thickness and cross-sectional geometry for the cartography of long bones diaphysis .
- morphomap allow to extract cross sections from long bone meshes at specified intervals along the diaphysis, and many other things.
Inter- or intra-observer error assessment
- irr implements numerous measures of interrater reliability and agreement for quantitative, ordinal and nominal data.
- FactoMineR is probably the best R packages to perform principal component analyses  and related methods (MCA, FAMD, …). It also has a great documentation, with a very complete website and video tutorials. It has also a good graphical user interface with the package Factoshiny.
- missMDA allows to handle and impute missing data upstream of multivariate analyses .
|||Jaroslav Bruzek. A method for visual determination of sex, using the human hip bone. American Journal of Physical Anthropology, 117(2):157--168, 2002. [ DOI ]|
|||Jan de Leeuw and Patrick Mair. Multidimensional Scaling Using Majorization: SMACOF in R. Journal of Statistical Software, 31(1):1--30, 2009. [ DOI ]|
|||Julie Josse and François Husson. missMDA : A Package for Handling Missing Values in Multivariate Data Analysis. Journal of Statistical Software, 70(1), 2016. [ DOI ]|
|||Sébastien Lê, Julie Josse, and François Husson. FactoMineR: An R Package for Multivariate Analysis. Journal of Statistical Software, 25(1), 2008. [ DOI ]|
|||Frédéric Santos. AnthropMMD: An R package with a graphical user interface for the mean measure of divergence. American Journal of Physical Anthropology, 165(1):200--205, 2018. [ DOI ]|
|||Frédéric Santos, Pierre Guyomarc'h, Rebeka Rmoutilova, and Jaroslav Bruzek. A method of sexing the human os coxae based on logistic regressions and Bruzek's nonmetric traits. American Journal of Physical Anthropology, 169(3):435--447, 2019. [ DOI ]|
|||Frédéric Santos and Alizé Lacoste Jeanson. Diaphysator: An online application for the exhaustive cartography and user-friendly statistical analysis of long bone diaphyses. American Journal of Physical Anthropology, 0(0). [ DOI ]|
|||Stef van Buuren and Karin Groothuis-Oudshoorn. Mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(1):1--67, 2011. [ DOI ]|
Furthermore, many of them have a very general scope, and are perfectly dispensable for any R user.