https://doi.org/10.5061/dryad.000000094

Description of the data and file structure

The data made available for this study consist of the following:

• The database containing information on each individual (reference number, collection, age group (AG), sex, and analyses performed (microscopic analysis (BM) and/or geometric morphometric (GM) analysis)

  • Database_Schuhetal.xlsx
    • Species: name of the species
    • REF: reference number
    • Collection: place where the material is stored
    • AG: age group (1 = newborns; 2 = deciduous dentition developing; 3 = M1 in occlusion; 4 = M2 in occlusion; 5 = M3 in occlusion)
    • Sex: M = male, F = female, Unk = unknown
    • CT or Surface scan used for an individual
    • Taken for microscopic analysis (BM): whether the individual was taken for the BM analysis or not depending on surface preservation
    • Taken for GM analysis (GM): whether the individual was included in the GM analysis or not (sometimes scans could not be used)

• The matrices necessary ton run both the PC analysis on shape and bone modeling data and size (txt.files):

  • Labels.txt** and Labels_BM.txt**
    • Name: ref number of the individual
    • Species
    • Group: age group
  • Mat_GPA.txt
    • Matrix of Procrustes distances
  • Mat_BM.txt
  • Mean.txt
    • Grand Mean of the sample (needed to compute the warps, see R code)
  • Size.txt
    • Matrix of centroid sizes
  • MinText_PCX.txt
    • Example of how to organize the file for the texture at each PC's extreme

• The mean shapes of age groups 1,3 and 5 (or 2 if 1 is missing) and species (.ply) to compute the heatmaps

  • **File "Mean shapes"* *
    • Example for age group 1 chimpanzee: Warp_AG1_Ch.ply

• The txt files to compute the mean maps (see R code for when and how to use them)

  • Data_All_BM.txt, Ex_Mean_AG1_Pongo.txt

• The txt files to compute the mean BM maps

  • Labels_BM.txt
    • Name: ref number of the individual
    • Species
    • Group: age group
  • Data_All_BM.txt
    • The txt file containing all individual maps (with percentages of bone resorption for each map
  • Ex_Mean_AG1_Pongo.txt
    • Example of how the txt file should be structured for the mean

• The txt file to compute the boxplot

  • DF_BR.txt
    • Name: ref number of the individual
    • Species
    • Value: percentage of bone resorption
    • AG: age group

• The R code to perform all these above steps (PCA analyses, heatmaps, and statistics)

Code/Software

The R (version 4.2.3.) script given available consists of codes on how to run a PCA on the shape and bone modeling data (figures 1 and 3), how to compute the extreme shapes/textures on each axis (figures 1 and 3), how to create the heatmaps (figure 2), how to create the mean bone modeling maps (figure 4), how to create the boxplot for figure 5, and how to run some statistics on the data.