Arothron is an R package [1] containing brand new tools for geometric morphometric analysis. The package comes with examples
pertaining to the field of virtual anthropology, yet it is addressed to the entire audience of geometric morphometricians. The functions
embedded in the package allow aligning disarticulated parts belonging to a single specimen (i.e. broken skull fragments), to
build internal cavities such as endocasts, and to reproduce and analyse the shapes of three-dimensional objects. Arothron functions
import and export landmark coordinates and 3D paths into ’landmarkAscii’ and ’am’ format files. The Digital Tool for Alignment
(DTA) is a landmark-based methodology which allows aligning two or more portions of a 3D mesh (i.e. a disarticulated model,
DM) by using a reference sample or model (RM) for comparison. To run DTA, a set of anatomical landmarks is defined on two
separated portions of the DM. Each point of the landmark sets is moved to the nearest vertex of the triangles. This way, each landmark
is identified by a number corresponding to a row of the vertex matrix of the mesh and its position is tracked on the 3D models
moved in the Cartesian coordinate system.The second step is the alignment via Generalized Procrustes Analysis (GPA) of each part
of the DM on each RM of the comparative sample, where the same landmark configuration as with the DM has been previously
defined. The items of the reference sample are previously scaled to the mean of the single scale factors calculated for each half of
the DM, separately, and symmetrized via reflection and relabelling, thereby producing a perfectly symmetrical, bilateral, and scaled
landmark configurations (to avoid alignment error as introduced by asymmetry). The last step consists in the quantification of the
morphological (Euclidean) distances between each part of the DM and the corresponding landmark configurations on each item in
the RM set. Computer-Aided Laser Scanner Emulator (CA-LSE) and Automatic Segmentation Tool for 3D objects (AST-3D) are
two new tools designed for the reconstruction of virtual cavities and external shapes [2]. CA-LSE provides the reconstruction of the
external portions of a 3D mesh by simulating the action of a laser scanner. AST-3D performs the digital reconstruction of anatomical
cavities as endocasts. Both tools use the definition of points of views that can be placed externally to the object (CA-LSE) or
inside the object (AST-3D). By applying these tools is possible in few minutes to build virtual cavities as endocast, maxillary sinuses
and trabecular bone. In the Arothron R package, we supplied three examples of reconstructing: the dental pulp cavity within a deciduous
Neanderthal tooth, the network of blood vessels within a human malleus bone, and an endocast of a human skull.The tools
could be used in virtual anthropology application.The digital alignment tool is efficient in find ideal alignments of broken pieces. It
could be applied as the first step in virtual reconstruction on human fossil specimens that often consist of a disarticulated fragments
such as BOU-VP12/130 (Australopithecus garhi), AL-442 (Australopithecus afarensis), OH5 (Paranthropus boisei), ATD6-15 and
ATD6-69 (Homo antecessor), Amud 1 (Homo neanderthalensis), Le Moustier 1 (Homo neanderthalensis). The easily and quickly
use of the Arothron R package to build virtual cavities may provide a new means largely applicable in virtual Anthropology.
References:[1] Profico A., Veneziano A., Melchionna M., Piras P. & Raia P., 2018. Arothron: Geometric Morphometrics Analyses. R package version 1.0.1, developer version available at
https://github/Arothron DOI:10.5281/zenodo.1218712.[2] Profico A., Schlager S., Valoriani V., Buzi C., Melchionna M., Veneziano A., Raia P., MoggifiCecchi J. & Manzi G., 2018. Reproducing the
internal and external anatomy of fossil bones: Two new automatic digital tools. American Journal of Physical Anthropology
