close

Showing 29 of total 29 results (show query)

zarquon42b

Morpho:Calculations and Visualisations Related to Geometric Morphometrics

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

Maintained by Stefan Schlager. Last updated 5 months ago.

openblascppopenmp

51 stars 10.01 score 218 scripts 13 dependents

sebastien-plutniak

archeoViz:Visualisation, Exploration, and Web Communication of Archaeological Spatial Data

An R 'Shiny' application for visual and statistical exploration and web communication of archaeological spatial data, either remains or sites. It offers interactive 3D and 2D visualisations (cross sections and maps of remains, timeline of the work made in a site) which can be exported in SVG and HTML formats. It performs simple spatial statistics (convex hull, regression surfaces, 2D kernel density estimation) and allows exporting data to other online applications for more complex methods. 'archeoViz' can be used offline locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.

Maintained by Sebastien Plutniak. Last updated 2 months ago.

archaeologyarcheologydata-visualization

19 stars 7.23 score 6 scripts

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

jmadinlab

habtools:Tools and Metrics for 3D Surfaces and Objects

A collection of functions for sampling and simulating 3D surfaces and objects and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity, second moments of area and volume, and more.

Maintained by Nina Schiettekatte. Last updated 24 days ago.

12 stars 6.10 score 9 scripts

stla

cxhull:Convex Hull

Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.

Maintained by Stéphane Laurent. Last updated 1 years ago.

computational-geometryconvex-hull

14 stars 5.93 score 81 scripts 5 dependents

stla

RCDT:Fast 2D Constrained Delaunay Triangulation

Performs 2D Delaunay triangulation, constrained or unconstrained, with the help of the C++ library 'CDT'. A function to plot the triangulation is provided. The constrained Delaunay triangulation has applications in geographic information systems.

Maintained by Stéphane Laurent. Last updated 1 years ago.

constrained-delaunay-triangulationcppdelaunay-triangulationcpp

6 stars 5.85 score 39 scripts 2 dependents

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

stla

tessellation:Delaunay and Voronoï Tessellations

Delaunay and Voronoï tessellations, with emphasis on the two-dimensional and the three-dimensional cases (the package provides functions to plot the tessellations for these cases). Delaunay tessellations are computed in C with the help of the 'Qhull' library <http://www.qhull.org/>.

Maintained by Stéphane Laurent. Last updated 1 years ago.

cdelaunay-triangulationvoronoi-tessellation

17 stars 5.23 score 67 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

stla

jacobi:Jacobi Theta Functions and Related Functions

Evaluation of the Jacobi theta functions and related functions: Weierstrass elliptic function, Weierstrass sigma function, Weierstrass zeta function, Klein j-function, Dedekind eta function, lambda modular function, Jacobi elliptic functions, Neville theta functions, Eisenstein series, lemniscate elliptic functions, elliptic alpha function, Rogers-Ramanujan continued fractions, and Dixon elliptic functions. Complex values of the variable are supported.

Maintained by Stéphane Laurent. Last updated 1 years ago.

elliptic-functionstheta-functionscpp

2 stars 4.01 score 103 scripts

stla

polyhedralCubature:Multiple Integration over Convex Polyhedra

Evaluation of multiple integrals over convex polyhedra. This is useful when the bounds of the integrals are some linear combinations of the variables.

Maintained by Stéphane Laurent. Last updated 1 years ago.

integrationmultidimensional-integration

3.70 score 4 scripts

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

cran

ashapesampler:Generating Alpha Shapes

Understanding morphological variation is an important task in many applications. Recent studies in computational biology have focused on developing computational tools for the task of sub-image selection which aims at identifying structural features that best describe the variation between classes of shapes. A major part in assessing the utility of these approaches is to demonstrate their performance on both simulated and real datasets. However, when creating a model for shape statistics, real data can be difficult to access and the sample sizes for these data are often small due to them being expensive to collect. Meanwhile, the landscape of current shape simulation methods has been mostly limited to approaches that use black-box inference---making it difficult to systematically assess the power and calibration of sub-image models. In this R package, we introduce the alpha-shape sampler: a probabilistic framework for simulating realistic 2D and 3D shapes based on probability distributions which can be learned from real data or explicitly stated by the user. The 'ashapesampler' package supports two mechanisms for sampling shapes in two and three dimensions. The first, empirically sampling based on an existing data set, was highlighted in the original main text of the paper. The second, probabilistic sampling from a known distribution, is the computational implementation of the theory derived in that paper. Work based on Winn-Nunez et al. (2024) <doi:10.1101/2024.01.09.574919>.

Maintained by Emily Winn-Nunez. Last updated 1 years ago.

3.30 score

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

cran

espadon:Easy Study of Patient DICOM Data in Oncology

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

Maintained by Cathy Fontbonne. Last updated 2 months ago.

cpp

2.85 score

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

stla

concom:Connected Components of an Undirected Graph

Provides a function for fast computation of the connected components of an undirected graph (though not faster than the components() function of the 'igraph' package) from the edges or the adjacency matrix of the graph. Based on this one, a function to compute the connected components of a triangle 'rgl' mesh is also provided.

Maintained by Stéphane Laurent. Last updated 3 years ago.

cpp

1 stars 2.70 score 7 scripts

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

jisunjang19

JSDNE:Estimating the Age using Auricular Surface by DNE

The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), principal component regression analysis (PCR), and principal component logistic regression analysis (PCLR) methods. The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan.

Maintained by Jisun Jang. Last updated 7 months ago.

2.48 score 3 scripts

cran

molaR:Dental Surface Complexity Measurement Tools

Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.

Maintained by James D. Pampush. Last updated 2 years ago.

1 stars 2.48 score 1 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

rdinnager

rbff:R Interface to Boundary First Flattening Software (BFF)

Flatten 3D meshes into arbitrary 2D shapes using boundary first flattening (<https://github.com/GeometryCollective/boundary-first-flattening>).

Maintained by Russell Dinnage. Last updated 3 years ago.

suitesparsecpp

5 stars 2.40 score 6 scripts

dfsp-spirit

haze:Smoothing of per-Vertex Data on Triangular Meshes

Smoothing of per-vertex data on triangular meshes, sub mesh creation based on vertex indices, per-vertex data interpolation based on k-d trees.

Maintained by Tim Schäfer. Last updated 2 years ago.

per-vertexsmoothingtriangular-meshcpp

5 stars 2.40 score

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

riccarl

JFM:Rock Mass Structural Analysis from 3D Mesh of Point Cloud

Provides functions to extract joint planes from 3D triangular mesh derived from point cloud and makes data available for structural analysis.

Maintained by Riccardo Campana. Last updated 3 years ago.

openblascpp

1.00 score 1 scripts

: