2018
DOI: 10.1002/ece3.4018
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ShapeRotator: An R tool for standardized rigid rotations of articulated three‐dimensional structures with application for geometric morphometrics

Abstract: The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures.… Show more

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Cited by 23 publications
(17 citation statements)
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“…Adams’ (1999) “Fixed Angle Method” and Vidal‐Garcia and colleagues’ shapeRotator R package (Vidal‐García et al. 2018) for 3D structures are approaches that minimize variation due to mobility by fixing the angle between articulating structures at their joint, for all specimens, and then performing a common superimposition as if the newly rotated articulating structure was rigid. These approaches have been used to answer a wide range of questions (e.g., Adams and Rohlf 2000; Adams 2004; Davis et al.…”
Section: Methodsmentioning
confidence: 99%
“…Adams’ (1999) “Fixed Angle Method” and Vidal‐Garcia and colleagues’ shapeRotator R package (Vidal‐García et al. 2018) for 3D structures are approaches that minimize variation due to mobility by fixing the angle between articulating structures at their joint, for all specimens, and then performing a common superimposition as if the newly rotated articulating structure was rigid. These approaches have been used to answer a wide range of questions (e.g., Adams and Rohlf 2000; Adams 2004; Davis et al.…”
Section: Methodsmentioning
confidence: 99%
“…Because the 3D coordinates had been gathered from different trials, the position of the xz -coordinate plane differed across specimens. In order to make 3D jumping trajectories comparable across all specimens, we standardized the position of all xz -coordinate planes by rigidly rotating each 3D coordinate to the ( x , 0, z ) plane, following the methodology from Vidal-García et al [ 37 ] and using internal functions from the R package ShapeRotator [ 38 ]. With these aligned 3D coordinates (in cm) of the snout and cloaca for each individual, and in each frame, we extracted the following kinematic variables: mean velocity (cm s −1 ), maximum velocity (cm s −1 ), distance (cm), height (cm) and jumping angles (calculated between the xz -plane and the vector from the cloaca to the snout) at take-off and at landing.…”
Section: Methodsmentioning
confidence: 99%
“…43 Here we present a virtual retrodeformation workflow for dorso-ventrally taphonomic deformations based on 3D landmark data, using the open-source software R. 25 Landmark data and 3D surface meshes were imported into R using the file2mesh function in Morpho. 29 We used the R package ShapeRotator 44,45 to place both skulls on the x,z plane, thereby facilitating all subsequent retrodeformation operations. Since each Oculudentavis specimen exhibited deformations in different regions of the cranium, identified by asymmetries, distortions, and bone displacements, we performed different retrodeformation operations on each specimen.…”
Section: Retrodeformation Analysismentioning
confidence: 99%