Morphometrics with R: Practical session

University of Bordeaux, Summer school 2024

Authors
Affiliation

Floriane Rémy

CNRS, Univ. Bordeaux, MCC – UMR 5199 PACEA

Frédéric Santos

CNRS, Univ. Bordeaux, MCC – UMR 5199 PACEA

Published

05 Jul 2024

1 Course overview

This website is a companion for a pratical session “Morphometrics with R” which is part of the Summer school “Digital Archaeology” (University of Bordeaux). This short practical session requires no previous knowledge of R, so that it will cover the most elementary notions both for R as a language, and for applied morphometrics.

2 Why use R?

There are other (very good) software out there for geometric morphometrics and statistics, such as PAST (Hammer & Harper, 2006) or MorphoJ. But R has several key advantages:

  • quantity and quality of documentation;
  • access to a wider range of advanced methods;
  • ease of automating repetitive tasks;
  • large community of users;
  • ability to work following literate programming principles (Knuth, 1984) ;
  • reproducible and transparent analyses (when done right!).

3 External resources

  • A general introduction to R, by Alex Douglas et al.
  • Claude (2008) is a very complete reference, although a bit old, so that it does not document the most recent and efficient R packages for doing morphometrics.
  • Zelditch et al. (2012) is another good reference, with many concrete use cases and R scripts provided in appendices.
  • Elewa (2010) and Webster & Sheets (2010) are other excellent resources to begin with morphometrics – although not specifically in R.

4 My R installation does not work!

You can still follow the course with a server session by following this link: Binder

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References

Claude, J. (2008). Morphometrics with R. Springer.
Elewa, A. M. T. (Ed.). (2010). Morphometrics for Nonmorphometricians (Vol. 124). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-540-95853-6
Hammer, Ø., & Harper, D. A. T. (2006). Paleontological data analysis. Blackwell Pub.
Knuth, D. E. (1984). Literate Programming. The Computer Journal, 27(2), 97–111. https://doi.org/10.1093/comjnl/27.2.97
Webster, M., & Sheets, H. D. (2010). A Practical Introduction to Landmark-Based Geometric Morphometrics. The Paleontological Society Papers, 16, 163–188. https://doi.org/10.1017/S1089332600001868
Zelditch, M., Swiderski, D. L., & Sheets, H. D. (2012). Geometric morphometrics for biologists: A primer (Second edition). Elsevier/Academic Press.