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lem-usp

evolqg:Evolutionary Quantitative Genetics

Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) <doi:10.12688/f1000research.7082.3>.

Maintained by Diogo Melo. Last updated 11 months ago.

openblascpp

10 stars 6.26 score 114 scripts

stla

gyro:Hyperbolic Geometry

Hyperbolic geometry in the Minkowski model and the Poincaré model. The methods are based on the gyrovector space theory developed by A. A. Ungar that can be found in the book 'Analytic Hyperbolic Geometry: Mathematical Foundations And Applications' <doi:10.1142/5914>. The package provides functions to plot three-dimensional hyperbolic polyhedra and to plot hyperbolic tilings of the Poincaré disk.

Maintained by Stéphane Laurent. Last updated 1 years ago.

geometryhyperbolic-geometryrglcpp

4 stars 5.69 score 81 scripts 1 dependents

stevenvb12

patternize:Quantification of Color Pattern Variation

Quantification of variation in organismal color patterns as obtained from image data. Patternize defines homology between pattern positions across images either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using RGB thresholds or image segmentation.

Maintained by Steven Van Belleghem. Last updated 9 months ago.

31 stars 4.97 score 30 scripts

telfer

pressuRe:Imports, Processes, and Visualizes Biomechanical Pressure Data

Allows biomechanical pressure data from a range of systems to be imported and processed in a reproducible manner. Automatic and manual tools are included to let the user define regions (masks) to be analyzed. Also includes functions for visualizing and animating pressure data. Example methods are described in Shi et al., (2022) <doi:10.1038/s41598-022-19814-0>, Lee et al., (2014) <doi:10.1186/1757-1146-7-18>, van der Zward et al., (2014) <doi:10.1186/1757-1146-7-20>, Najafi et al., (2010) <doi:10.1016/j.gaitpost.2009.09.003>, Cavanagh and Rodgers (1987) <doi:10.1016/0021-9290(87)90255-7>.

Maintained by Scott Telfer. Last updated 6 days ago.

2 stars 4.62 score

mohsentaherishalmani

ETRep:Analysis of Elliptical Tubes Under the Relative Curvature Condition

Analysis of elliptical tubes with applications in biological modeling. The package is based on the references: Taheri, M., Pizer, S. M., & Schulz, J. (2024) "The Mean Shape under the Relative Curvature Condition." arXiv <doi:10.48550/arXiv.2404.01043>. Mohsen Taheri Shalmani (2024) "Shape Statistics via Skeletal Structures", PhD Thesis, University of Stavanger, Norway <doi:10.13140/RG.2.2.34500.23685>. Key features include constructing discrete elliptical tubes, calculating transformations, validating structures under the Relative Curvature Condition (RCC), computing means, and generating simulations. Supports intrinsic and non-intrinsic mean calculations and transformations, size estimation, plotting, and random sample generation based on a reference tube. The intrinsic approach relies on the interior path of the original non-convex space, incorporating the RCC, while the non-intrinsic approach uses a basic robotic arm transformation that disregards the RCC.

Maintained by Mohsen Taheri Shalmani. Last updated 3 months ago.

3.54 score 3 scripts

stla

Apollonius:2D Apollonius Graphs

Computation of the Apollonius diagram of given 2D points and its dual the Apollonius graph, also known as the additively weighted Voronoï diagram, and which is a generalization of the classical Voronoï diagram. For references, see the bibliography in the CGAL documentation at <https://doc.cgal.org/latest/Apollonius_graph_2/citelist.html>.

Maintained by Stéphane Laurent. Last updated 1 years ago.

cgalcomputational-geometryrcppvoronoi-diagramgmpcpp

3 stars 3.18 score 5 scripts

nialsig

doolkit:Exploration of Dental Surface Topography

Tools for exploring the topography of 3d triangle meshes. The functions were developed with dental surfaces in mind, but could be applied to any triangle mesh of class 'mesh3d'. More specifically, 'doolkit' allows to isolate the border of a mesh, or a subpart of the mesh using the polygon networks method; crop a mesh; compute basic descriptors (elevation, orientation, footprint area); compute slope, angularity and relief index (Ungar and Williamson (2000) <https://palaeo-electronica.org/2000_1/gorilla/issue1_00.htm>; Boyer (2008) <doi:10.1016/j.jhevol.2008.08.002>), inclination and occlusal relief index or gamma (Guy et al. (2013) <doi:10.1371/journal.pone.0066142>), OPC (Evans et al. (2007) <doi:10.1038/nature05433>), OPCR (Wilson et al. (2012) <doi:10.1038/nature10880>), DNE (Bunn et al. (2011) <doi:10.1002/ajpa.21489>; Pampush et al. (2016) <doi:10.1007/s10914-016-9326-0>), form factor (Horton (1932) <doi:10.1029/TR013i001p00350>), basin elongation (Schum (1956) <doi:10.1130/0016-7606(1956)67[597:EODSAS]2.0.CO;2>), lemniscate ratio (Chorley et al; (1957) <doi:10.2475/ajs.255.2.138>), enamel-dentine distance (Guy et al. (2015) <doi:10.1371/journal.pone.0138802>; Thiery et al. (2017) <doi:10.3389/fphys.2017.00524>), absolute crown strength (Schwartz et al. (2020) <doi:10.1098/rsbl.2019.0671>), relief rate (Thiery et al. (2019) <doi:10.1002/ajpa.23916>) and area-relative curvature; draw cumulative profiles of a topographic variable; and map a variable over a 3d triangle mesh.

Maintained by Ghislain Thiery. Last updated 1 years ago.

1 stars 2.70 score 1 scripts

cran

TestDimorph:Analysis of the Interpopulation Difference in Degree of Sexual Dimorphism Using Summary Statistics

Offers a solution for the unavailability of raw data in most anthropological studies by facilitating the calculations of several sexual dimorphism related analyses using the published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Relethford, J. H., & Hodges, D. C. (1985) <doi:10.1002/ajpa.1330660105>, Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.

Maintained by Bassam A. Abulnoor. Last updated 1 years ago.

1 stars 2.70 score

aprofico

Arothron:Geometric Morphometric Methods and Virtual Anthropology Tools

Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen, to build virtual cavities as endocast (Profico et al, 2021 <doi:10.1002/ajpa.24340>).

Maintained by Antonio Profico. Last updated 2 years ago.

2.59 score 13 scripts 2 dependents

aprofico

morphomap:Morphometric Maps, Bone Landmarking and Cross Sectional Geometry

Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.

Maintained by Antonio Profico. Last updated 1 years ago.

2 stars 2.48 score 7 scripts 1 dependents

cran

prWarp:Warping Landmark Configurations

Compute bending energies, principal warps, partial warp scores, and the non-affine component of shape variation for 2D landmark configurations, as well as Mardia-Dryden distributions and self-similar distributions of landmarks, as described in Mitteroecker et al. (2020) <doi:10.1093/sysbio/syaa007>. Working examples to decompose shape variation into small-scale and large-scale components, and to decompose the total shape variation into outline and residual shape components are provided. Two landmark datasets are provided, that quantify skull morphology in humans and papionin primates, respectively from Mitteroecker et al. (2020) <doi:10.5061/dryad.j6q573n8s> and Grunstra et al. (2020) <doi:10.5061/dryad.zkh189373>.

Maintained by Anne Le Maitre. Last updated 1 years ago.

2.30 score

cran

SRTsim:Simulator for Spatially Resolved Transcriptomics

An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.

Maintained by Jiaqiang Zhu. Last updated 7 months ago.

2.00 score

aprofico

Toothnroll:Dental Tissues Landmarking Measuring and Mapping

Two- and three-dimensional morphometric maps of enamel and dentine thickness and multivariate analysis. Volume calculation of dental materials. Principal component analysis of thickness maps with associated morphometric map variations.

Maintained by Antonio Profico. Last updated 12 months ago.

1.00 score

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