Showing 126 of total 126 results (show query)
davidcsterratt
retistruct:Retinal Reconstruction Program
Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. For more details see Sterratt, D. C., Lyngholm, D., Willshaw, D. J. and Thompson, I. D. (2013) <doi:10.1371/journal.pcbi.1002921>.
Maintained by David C. Sterratt. Last updated 10 days ago.
56.5 match 8 stars 4.60 score
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 3 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
7.6 match 582 stars 21.11 score 31k scripts 1.9k dependents
joeguinness
GpGp:Fast Gaussian Process Computation Using Vecchia's Approximation
Functions for fitting and doing predictions with Gaussian process models using Vecchia's (1988) approximation. Package also includes functions for reordering input locations, finding ordered nearest neighbors (with help from 'FNN' package), grouping operations, and conditional simulations. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. The original approximation is due to Vecchia (1988) <http://www.jstor.org/stable/2345768>, and the reordering and grouping methods are from Guinness (2018) <doi:10.1080/00401706.2018.1437476>. Model fitting employs a Fisher scoring algorithm described in Guinness (2019) <doi:10.48550/arXiv.1905.08374>.
Maintained by Joseph Guinness. Last updated 5 months ago.
14.8 match 10 stars 6.16 score 160 scripts 6 dependents
iandryden
shapes:Statistical Shape Analysis
Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.
Maintained by Ian Dryden. Last updated 4 months ago.
10.6 match 7 stars 8.50 score 225 scripts 24 dependents
tylermorganwall
rayrender:Build and Raytrace 3D Scenes
Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Maintained by Tyler Morgan-Wall. Last updated 17 days ago.
8.3 match 630 stars 10.78 score 188 scripts 8 dependents
dmurdoch
rgl:3D Visualization Using OpenGL
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Maintained by Duncan Murdoch. Last updated 2 months ago.
graphicsopenglrglwebgllibglulibglvndlibpnglibx11freetypecpp
4.5 match 91 stars 17.49 score 7.3k scripts 300 dependents
ropensci
QuadratiK:Collection of Methods Constructed using Kernel-Based Quadratic Distances
It includes test for multivariate normality, test for uniformity on the d-dimensional Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson kernel-based density and clustering algorithm for spherical data. For more information see Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024) <doi:10.48550/arXiv.2402.02290> Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>, Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>, and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.
Maintained by Giovanni Saraceno. Last updated 1 months ago.
11.6 match 1 stars 6.36 score 27 scripts
egarpor
sphunif:Uniformity Tests on the Circle, Sphere, and Hypersphere
Implementation of uniformity tests on the circle and (hyper)sphere. The main function of the package is unif_test(), which conveniently collects more than 35 tests for assessing uniformity on S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are implemented in the unif_stat() function, which allows computing several statistics for different samples within a single call, thus facilitating Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows parallelizing them in a simple way. The asymptotic null distributions of the statistics are available through the function unif_stat_distr(). The core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package. The package also provides several novel datasets and gives the replicability for the data applications/simulations in García-Portugués et al. (2021) <doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023) <doi:10.3150/21-BEJ1454>, García-Portugués et al. (2024) <doi:10.48550/arXiv.2108.09874>, and Fernández-de-Marcos and García-Portugués (2024) <doi:10.48550/arXiv.2405.13531>.
Maintained by Eduardo García-Portugués. Last updated 10 months ago.
circular-statisticsdirectional-statisticsuniformityuniformity-testsopenblascpp
11.7 match 8 stars 6.11 score 18 scripts 2 dependents
schloerke
geozoo:Zoo of Geometric Objects
Geometric objects defined in 'geozoo' can be simulated or displayed in the R package 'tourr'.
Maintained by Barret Schloerke. Last updated 9 years ago.
13.3 match 5 stars 5.21 score 100 scripts 2 dependents
kisungyou
Riemann:Learning with Data on Riemannian Manifolds
We provide a variety of algorithms for manifold-valued data, including Fréchet summaries, hypothesis testing, clustering, visualization, and other learning tasks. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> for general exposition to statistics on manifolds.
Maintained by Kisung You. Last updated 2 years ago.
17.1 match 10 stars 3.70 score 8 scripts
dfsp-spirit
fsbrain:Managing and Visualizing Brain Surface Data
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Maintained by Tim Schäfer. Last updated 4 months ago.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
9.2 match 66 stars 6.47 score 15 scripts
baddstats
globe:Plot 2D and 3D Views of the Earth, Including Major Coastline
Basic functions for plotting 2D and 3D views of a sphere, by default the Earth with its major coastline, and additional lines and points.
Maintained by Adrian Baddeley. Last updated 8 years ago.
earth-continentsglobegraphicsspatial-datasphere
15.3 match 5 stars 3.90 score 32 scripts
stla
uniformly:Uniform Sampling
Uniform sampling on various geometric shapes, such as spheres, ellipsoids, simplices.
Maintained by Stéphane Laurent. Last updated 2 years ago.
9.1 match 10 stars 6.21 score 109 scripts 1 dependents
rspatial
geosphere:Spherical Trigonometry
Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Maintained by Robert J. Hijmans. Last updated 6 months ago.
3.6 match 36 stars 13.79 score 5.7k scripts 116 dependentstylermorganwall
rayvertex:3D Software Rasterizer
Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
Maintained by Tyler Morgan-Wall. Last updated 1 months ago.
5.8 match 68 stars 8.23 score 25 scripts 11 dependents
dipterix
threeBrain:Your Advanced 3D Brain Visualization
A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. Please check the publication by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode localization. This viewer has been fully adopted by 'RAVE' <https://rave.wiki>, an interactive toolbox to analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>). Please check citation("threeBrain") for details.
Maintained by Zhengjia Wang. Last updated 2 hours ago.
brainecogelectroencephalographyieeglocalizationmri-brainneuroimagingtemplate-brains
5.6 match 44 stars 8.26 score 38 scripts 1 dependents
bioc
TrajectoryGeometry:This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.
Maintained by Michael Shapiro. Last updated 5 months ago.
biologicalquestionstatisticalmethodgeneexpressionsinglecell
9.9 match 4.60 score 7 scripts
jayanilakshika
cardinalR:Collection of Data Structures
A collection of simple simulation datasets designed for generating Nonlinear Dimension Reduction representations techniques such as t-distributed Stochastic Neighbor Embedding, and Uniform Manifold Approximation and Projection. These datasets serve as a valuable resource for understanding the reliability of Nonlinear Dimension Reduction representations in various contexts.
Maintained by Jayani P.G. Lakshika. Last updated 12 days ago.
9.5 match 4.54 score
tarnduong
ks:Kernel Smoothing
Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Maintained by Tarn Duong. Last updated 6 months ago.
4.1 match 6 stars 10.14 score 920 scripts 262 dependents
coolbutuseless
isocubes:Voxel Rendering with Isometric Cubes
Visualising three-dimensional voxel data.
Maintained by Mike Cheng. Last updated 4 months ago.
8.0 match 67 stars 5.13 score 8 scripts
mfasiolo
mgcViz:Visualisations for Generalized Additive Models
Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Maintained by Matteo Fasiolo. Last updated 7 months ago.
3.8 match 77 stars 9.38 score 1000 scripts
romanflury
mrbsizeR:Scale Space Multiresolution Analysis of Random Signals
A method for the multiresolution analysis of spatial fields and images to capture scale-dependent features. mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales. To infer which of the captured features are credible, Bayesian analysis is used. The scale space multiresolution analysis has three steps: (1) Bayesian signal reconstruction. (2) Using differences of smooths, scale-dependent features of the reconstructed signal can be found. (3) Posterior credibility analysis of the differences of smooths created. The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <DOI:10.1016/j.csda.2011.04.011>. Matlab code is available under <http://cc.oulu.fi/~lpasanen/MRBSiZer/>.
Maintained by Roman Flury. Last updated 5 years ago.
8.4 match 1 stars 4.22 score 33 scripts
jakobbossek
smoof:Single and Multi-Objective Optimization Test Functions
Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.
Maintained by Jakob Bossek. Last updated 1 years ago.
benchmark-functionsmulti-objective-optimizationsingle-objective-optimizationcpp
4.1 match 36 stars 8.54 score 261 scripts 9 dependents
seungwoo-stat
rvMF:Fast Generation of von Mises-Fisher Distributed Pseudo-Random Vectors
Generates pseudo-random vectors that follow an arbitrary von Mises-Fisher distribution on a sphere. This method is fast and efficient when generating a large number of pseudo-random vectors. Functions to generate random variates and compute density for the distribution of an inner product between von Mises-Fisher random vector and its mean direction are also provided. Details are in Kang and Oh (2024) <doi:10.1007/s11222-024-10419-3>.
Maintained by Seungwoo Kang. Last updated 12 months ago.
random-samplingspherevon-mises-fishercpp
11.5 match 1 stars 3.00 score 3 scripts
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 12 months ago.
6.6 match 143 stars 5.01 score 143 scripts
rrrlw
TDAstats:Pipeline for Topological Data Analysis
A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. The published form of TDAstats can be found in Wadhwa et al. (2018) <doi:10.21105/joss.00860>. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>. This package has been published as Wadhwa et al. (2018) <doi:10.21105/joss.00860>.
Maintained by Raoul Wadhwa. Last updated 3 years ago.
data-scienceggplot2homologyhomology-calculationshomology-computationjosspersistent-homologypipelineripsertdatopological-data-analysistopologytopology-visualizationvisualizationcpp
3.5 match 40 stars 8.30 score 46 scripts 4 dependents
cran
mgcv:Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
Maintained by Simon Wood. Last updated 1 years ago.
2.3 match 32 stars 12.71 score 17k scripts 7.8k dependents
jdtuck
fdasrvf:Elastic Functional Data Analysis
Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.
Maintained by J. Derek Tucker. Last updated 28 days ago.
3.5 match 11 stars 7.74 score 83 scripts 3 dependents
rpruim
fastR2:Foundations and Applications of Statistics Using R (2nd Edition)
Data sets and utilities to accompany the second edition of "Foundations and Applications of Statistics: an Introduction using R" (R Pruim, published by AMS, 2017), a text covering topics from probability and mathematical statistics at an advanced undergraduate level. R is integrated throughout, and access to all the R code in the book is provided via the snippet() function.
Maintained by Randall Pruim. Last updated 1 years ago.
4.5 match 13 stars 5.85 score 108 scriptsdavidcsterratt
geometry:Mesh Generation and Surface Tessellation
Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Maintained by David C. Sterratt. Last updated 1 months ago.
2.0 match 16 stars 12.98 score 776 scripts 139 dependents
novacta
nprotreg:Nonparametric Rotations for Sphere-Sphere Regression
Fits sphere-sphere regression models by estimating locally weighted rotations. Simulation of sphere-sphere data according to non-rigid rotation models. Provides methods for bias reduction applying iterative procedures within a Newton-Raphson learning scheme. Cross-validation is exploited to select smoothing parameters. See Marco Di Marzio, Agnese Panzera & Charles C. Taylor (2018) <doi:10.1080/01621459.2017.1421542>.
Maintained by Giovanni Lafratta. Last updated 1 years ago.
11.0 match 1 stars 2.34 score 44 scripts
r-spatial
sf:Simple Features for R
Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.
Maintained by Edzer Pebesma. Last updated 17 days ago.
1.1 match 1.4k stars 22.42 score 117k scripts 1.2k dependents
swsoyee
r3dmol:Create Interactive 3D Visualizations of Molecular Data
Create rich and fully interactive 3D visualizations of molecular data. Visualizations can be included in Shiny apps and R markdown documents, or viewed from the R console and 'RStudio' Viewer. 'r3dmol' includes an extensive API to manipulate the visualization after creation, and supports getting data out of the visualization into R. Based on the '3dmol.js' and the 'htmlwidgets' R package.
Maintained by Wei Su. Last updated 1 years ago.
3dcomputational-biologycomputational-chemistryhacktoberfesthtmlwidgetsmolecular-graphicsmolecular-modelingproteinprotein-structurevisualization
4.0 match 90 stars 6.35 score 166 scripts 1 dependents
projectmosaic
mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities
Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Maintained by Randall Pruim. Last updated 1 years ago.
1.9 match 93 stars 13.32 score 7.2k scripts 7 dependents
spatstat
spatstat.explore:Exploratory Data Analysis for the 'spatstat' Family
Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Maintained by Adrian Baddeley. Last updated 4 hours ago.
cluster-detectionconfidence-intervalshypothesis-testingk-functionroc-curvesscan-statisticssignificance-testingsimulation-envelopesspatial-analysisspatial-data-analysisspatial-sharpeningspatial-smoothingspatial-statistics
2.3 match 1 stars 10.18 score 67 scripts 149 dependents
jpnolan
SphericalCubature:Numerical Integration over Spheres and Balls in n-Dimensions; Multivariate Polar Coordinates
Provides several methods to integrate functions over the unit sphere and ball in n-dimensional Euclidean space. Routines for converting to/from multivariate polar/spherical coordinates are also provided.
Maintained by John P. Nolan. Last updated 4 years ago.
12.1 match 1.78 score 5 scripts 2 dependentsstla
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
3.5 match 14 stars 5.93 score 81 scripts 5 dependents
robinhankin
clifford:Arbitrary Dimensional Clifford Algebras
A suite of routines for Clifford algebras, using the 'Map' class of the Standard Template Library. Canonical reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra to geometric calculus"). Special cases including Lorentz transforms, quaternion multiplication, and Grassmann algebra, are discussed. Vignettes presenting conformal geometric algebra, quaternions and split quaternions, dual numbers, and Lorentz transforms are included. The package follows 'disordR' discipline.
Maintained by Robin K. S. Hankin. Last updated 1 months ago.
3.0 match 5 stars 6.71 score 4 scriptscran
SphereOptimize:Optimization on a Unit Sphere
A simple tool for numerical optimization on the unit sphere. This is achieved by combining the spherical coordinating system with L-BFGS-B optimization. This algorithm is implemented in Kolkiewicz, A., Rice, G., & Xie, Y. (2020) <doi:10.1016/j.jspi.2020.07.001>.
Maintained by Yijun Xie. Last updated 5 years ago.
11.7 match 1.70 score
indrag49
QGameTheory:Quantum Game Theory Simulator
General purpose toolbox for simulating quantum versions of game theoretic models (Flitney and Abbott 2002) <arXiv:quant-ph/0208069>. Quantum (Nielsen and Chuang 2010, ISBN:978-1-107-00217-3) versions of models that have been handled are: Penny Flip Game (David A. Meyer 1998) <arXiv:quant-ph/9804010>, Prisoner's Dilemma (J. Orlin Grabbe 2005) <arXiv:quant-ph/0506219>, Two Person Duel (Flitney and Abbott 2004) <arXiv:quant-ph/0305058>, Battle of the Sexes (Nawaz and Toor 2004) <arXiv:quant-ph/0110096>, Hawk and Dove Game (Nawaz and Toor 2010) <arXiv:quant-ph/0108075>, Newcomb's Paradox (Piotrowski and Sladkowski 2002) <arXiv:quant-ph/0202074> and Monty Hall Problem (Flitney and Abbott 2002) <arXiv:quant-ph/0109035>.
Maintained by Indranil Ghosh. Last updated 5 months ago.
game-theorygame-theory-modelquantum-computationquantum-computingquantum-computing-algorithms
5.3 match 11 stars 3.74 score 1 scripts
ggobi
tourr:Tour Methods for Multivariate Data Visualisation
Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Maintained by Dianne Cook. Last updated 17 days ago.
1.7 match 65 stars 11.17 score 426 scripts 9 dependents
laresbernardo
lares:Analytics & Machine Learning Sidekick
Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Maintained by Bernardo Lares. Last updated 24 days ago.
analyticsapiautomationautomldata-sciencedescriptive-statisticsh2omachine-learningmarketingmmmpredictive-modelingpuzzlerlanguagerobynvisualization
1.9 match 233 stars 9.84 score 185 scripts 1 dependents
juanv66x
qvirus:Quantum Computing for Analyzing CD4 Lymphocytes and Antiretroviral Therapy
Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.
Maintained by Juan Pablo Acuña González. Last updated 12 days ago.
3.3 match 5.43 score 15 scripts
kybak90
spheresmooth:Piecewise Geodesic Smoothing for Spherical Data
Fitting a smooth path to a given set of noisy spherical data observed at known time points. It implements a piecewise geodesic curve fitting method on the unit sphere based on a velocity-based penalization scheme. The proposed approach is implemented using the Riemannian block coordinate descent algorithm. To understand the method and algorithm, one can refer to Bak, K. Y., Shin, J. K., & Koo, J. Y. (2023) <doi:10.1080/02664763.2022.2054962> for the case of order 1. Additionally, this package includes various functions necessary for handling spherical data.
Maintained by Kwan-Young Bak. Last updated 3 months ago.
5.5 match 3.18 score 2 scripts
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.
1.8 match 51 stars 10.00 score 218 scripts 13 dependents
gmcmacran
tidydann:Add the 'dann' Model and the 'sub_dann' Model to the Tidymodels Ecosystem
Provides model specifications, tuning parameters for models in 'dann' package. Models based on Hastie (1996) <https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Maintained by Greg McMahan. Last updated 9 months ago.
5.3 match 3.30 score 20 scripts
numbats
woylier:Alternative Tour Frame Interpolation Method
This method generates a tour path by interpolating between d-D frames in p-D using Givens rotations. The algorithm arises from the problem of zeroing elements of a matrix. This interpolation method is useful for showing specific d-D frames in the tour, as opposed to d-D planes, as done by the geodesic interpolation. It is useful for projection pursuit indexes which are not s invariant. See more details in Buj, Cook, Asimov and Hurley (2005) <doi:10.1016/S0169-7161(04)24014-7> and Batsaikhan, Cook and Laa (2023) <doi:10.48550/arXiv.2311.08181>.
Maintained by Dianne Cook. Last updated 6 months ago.
3.8 match 4.60 score 10 scriptsbioc
SpacePAC:Identification of Mutational Clusters in 3D Protein Space via Simulation.
Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein's tertiary structure.
Maintained by Gregory Ryslik. Last updated 3 days ago.
3.7 match 4.65 score 2 scripts 1 dependentsegarpor
DirStats:Nonparametric Methods for Directional Data
Nonparametric kernel density estimation, bandwidth selection, and other utilities for analyzing directional data. Implements the estimator in Bai, Rao and Zhao (1987) <doi:10.1016/0047-259X(88)90113-3>, the cross-validation bandwidth selectors in Hall, Watson and Cabrera (1987) <doi:10.1093/biomet/74.4.751> and the plug-in bandwidth selectors in García-Portugués (2013) <doi:10.1214/13-ejs821>.
Maintained by Eduardo García-Portugués. Last updated 2 years ago.
directional-statisticsnonparametric-statisticsstatisticsfortran
4.0 match 12 stars 4.26 score 7 scripts 1 dependentscran
HDiR:Directional Highest Density Regions
We provide an R tool for computation and nonparametric plug-in estimation of Highest Density Regions (HDRs) and general level sets in the directional setting. Concretely, circular and spherical HDRs can be reconstructed from a data sample following Saavedra-Nieves and Crujeiras (2021) <doi:10.1007/s11634-021-00457-4>. This library also contains two real datasets in the circular and spherical settings. The first one concerns a problem from animal orientation studies and the second one is related to earthquakes occurrences.
Maintained by Paula Saavedra-Nieves. Last updated 2 years ago.
16.7 match 1.00 score
adrian-bowman
sm:Smoothing Methods for Nonparametric Regression and Density Estimation
This is software linked to the book 'Applied Smoothing Techniques for Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University Press.
Maintained by Adrian Bowman. Last updated 1 years ago.
2.3 match 1 stars 6.99 score 732 scripts 36 dependents
thomasp85
ambient:A Generator of Multidimensional Noise
Generation of natural looking noise has many application within simulation, procedural generation, and art, to name a few. The 'ambient' package provides an interface to the 'FastNoise' C++ library and allows for efficient generation of perlin, simplex, worley, cubic, value, and white noise with optional perturbation in either 2, 3, or 4 (in case of simplex and white noise) dimensions.
Maintained by Thomas Lin Pedersen. Last updated 3 years ago.
1.9 match 97 stars 8.09 score 956 scripts 2 dependents
peterbiber
viscomplexr:Phase Portraits of Functions in the Complex Number Plane
Functionality for creating phase portraits of functions in the complex number plane. Works with R base graphics, whose full functionality is available. Parallel processing is used for optimum performance.
Maintained by Peter Biber. Last updated 4 months ago.
3.1 match 4 stars 4.75 score 14 scripts
stathin
ggm:Graphical Markov Models with Mixed Graphs
Provides functions for defining mixed graphs containing three types of edges, directed, undirected and bi-directed, with possibly multiple edges. These graphs are useful because they capture fundamental independence structures in multivariate distributions and in the induced distributions after marginalization and conditioning. The package is especially concerned with Gaussian graphical models for (i) ML estimation for directed acyclic graphs, undirected and bi-directed graphs and ancestral graph models (ii) testing several conditional independencies (iii) checking global identification of DAG Gaussian models with one latent variable (iv) testing Markov equivalences and generating Markov equivalent graphs of specific types.
Maintained by Giovanni M. Marchetti. Last updated 1 years ago.
2.0 match 7.07 score 295 scripts 29 dependents
neurodata
mgc:Multiscale Graph Correlation
Multiscale Graph Correlation (MGC) is a framework developed by Vogelstein et al. (2019) <DOI:10.7554/eLife.41690> that extends global correlation procedures to be multiscale; consequently, MGC tests typically require far fewer samples than existing methods for a wide variety of dependence structures and dimensionalities, while maintaining computational efficiency. Moreover, MGC provides a simple and elegant multiscale characterization of the potentially complex latent geometry underlying the relationship.
Maintained by Eric Bridgeford. Last updated 4 years ago.
1.9 match 9 stars 7.50 score 59 scripts 2 dependents
jkim82133
TDA:Statistical Tools for Topological Data Analysis
Tools for Topological Data Analysis. The package focuses on statistical analysis of persistent homology and density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries 'GUDHI' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements methods from Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2015) <doi:10.20382/jocg.v6i2a8> for analyzing the statistical significance of persistent homology features.
Maintained by Jisu Kim. Last updated 1 months ago.
1.8 match 9 stars 7.18 score 204 scripts 5 dependents
ericarcher
swfscMisc:Miscellaneous Functions for Southwest Fisheries Science Center
Collection of conversion, analytical, geodesic, mapping, and plotting functions. Used to support packages and code written by researchers at the Southwest Fisheries Science Center of the National Oceanic and Atmospheric Administration.
Maintained by Eric Archer. Last updated 11 months ago.
2.0 match 2 stars 6.18 score 101 scripts 20 dependents
marshalllab
MGDrivE:Mosquito Gene Drive Explorer
Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.
Maintained by Héctor Manuel Sánchez Castellanos. Last updated 4 years ago.
1.8 match 6 stars 7.06 score 61 scripts
mharinga
spatialrisk:Calculating Spatial Risk
Methods for spatial risk calculations. It offers an efficient approach to determine the sum of all observations within a circle of a certain radius. This might be beneficial for insurers who are required (by a recent European Commission regulation) to determine the maximum value of insured fire risk policies of all buildings that are partly or fully located within a circle of a radius of 200m. See Church (1974) <doi:10.1007/BF01942293> for a description of the problem.
Maintained by Martin Haringa. Last updated 7 months ago.
actuarial-scienceinsurancesolvency-iispatialcpp
2.3 match 19 stars 5.06 score 30 scripts
roliveros-ramos
calibrar:Automated Parameter Estimation for Complex Models
General optimisation and specific tools for the parameter estimation (i.e. calibration) of complex models, including stochastic ones. It implements generic functions that can be used for fitting any type of models, especially those with non-differentiable objective functions, with the same syntax as 'stats::optim()'. It supports multiple phases estimation (sequential parameter masking), constrained optimization (bounding box restrictions) and automatic parallel computation of numerical gradients. Some common maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs is provided. See <https://roliveros-ramos.github.io/calibrar/> for more details.
Maintained by Ricardo Oliveros-Ramos. Last updated 19 days ago.
modelingoptimizationoptimization-methods
1.9 match 7 stars 6.05 score 27 scriptscran
MDSMap:High Density Genetic Linkage Mapping using Multidimensional Scaling
Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.
Maintained by Bram Boskamp. Last updated 7 years ago.
3.7 match 3.08 score 1 dependents
hiskp-lqcd
qsimulatR:A Quantum Computer Simulator
A quantum computer simulator framework with up to 24 qubits. It allows to define general single qubit gates and general controlled single qubit gates. For convenience, it currently provides the most common gates (X, Y, Z, H, Z, S, T, Rx, Ry, Rz, CNOT, SWAP, Toffoli or CCNOT, Fredkin or CSWAP). 'qsimulatR' also implements noise models. 'qsimulatR' supports plotting of circuits and is able to export circuits to 'Qiskit' <https://qiskit.org/>, a python package which can be used to run on IBM's hardware <https://quantum-computing.ibm.com/>.
Maintained by Carsten Urbach. Last updated 1 years ago.
2.3 match 11 stars 4.98 score 58 scripts 1 dependents
e-tau
MultiStatM:Multivariate Statistical Methods
Algorithms to build set partitions and commutator matrices and their use in the construction of multivariate d-Hermite polynomials; estimation and derivation of theoretical vector moments and vector cumulants of multivariate distributions; conversion formulae for multivariate moments and cumulants. Applications to estimation and derivation of multivariate measures of skewness and kurtosis; estimation and derivation of asymptotic covariances for d-variate Hermite polynomials, multivariate moments and cumulants and measures of skewness and kurtosis. The formulae implemented are discussed in Terdik (2021, ISBN:9783030813925), "Multivariate Statistical Methods".
Maintained by Emanuele Taufer. Last updated 8 months ago.
5.6 match 2.00 score 2 scripts
gtatters
Thermimage:Thermal Image Analysis
A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous functions for converting thermal image, videos, rewriting and exporting. v3.1. Added new functions to convert files. v3.2. Fixed the various functions related to finding frame times. v4.0. fixed an error in atmospheric attenuation constants, affecting raw2temp and temp2raw functions. Recommend update for use with long distance calculations. v.4.1.3. changed to frameLocates to reflect change to as.character() to format().
Maintained by Glenn J. Tattersall. Last updated 3 years ago.
animal-physiologyheat-exchangeheat-fluximage-framestemperaturethermal-biologythermal-images
1.9 match 169 stars 5.85 score 83 scripts
byzheng
weaana:Analysis the Weather Data
Functions are collected to analyse weather data for agriculture purposes including to read weather records in multiple formats, calculate extreme climate index.
Maintained by Bangyou Zheng. Last updated 1 months ago.
2.0 match 3 stars 5.32 score 23 scripts 1 dependents
cliffordlai
bestglm:Best Subset GLM and Regression Utilities
Best subset glm using information criteria or cross-validation, carried by using 'leaps' algorithm (Furnival and Wilson, 1974) <doi:10.2307/1267601> or complete enumeration (Morgan and Tatar, 1972) <doi:10.1080/00401706.1972.10488918>. Implements PCR and PLS using AIC/BIC. Implements one-standard deviation rule for use with the 'caret' package.
Maintained by Yuanhao Lai. Last updated 5 years ago.
2.0 match 5.29 score 418 scripts 5 dependents
kjohnsson
intrinsicDimension:Intrinsic Dimension Estimation
A variety of methods for estimating intrinsic dimension of data sets (i.e the manifold or Hausdorff dimension of the support of the distribution that generated the data) as reviewed in Johnsson, K. (2016, ISBN:978-91-7623-921-6) and Johnsson, K., Soneson, C. and Fontes, M. (2015) <doi:10.1109/TPAMI.2014.2343220>. Furthermore, to evaluate the performance of these estimators, functions for generating data sets with given intrinsic dimensions are provided.
Maintained by Kerstin Johnsson. Last updated 6 years ago.
1.8 match 12 stars 6.03 score 59 scripts 1 dependents
shwilks
r3js:'WebGL'-Based 3D Plotting using the 'three.js' Library
Provides R and 'JavaScript' functions to allow 'WebGL'-based 3D plotting using the 'three.js' 'JavaScript' library. Interactivity through roll-over highlighting and toggle buttons is also supported.
Maintained by Sam Wilks. Last updated 4 months ago.
1.8 match 14 stars 5.99 score 47 scripts
jongminlee-stat
spherepc:Spherical Principal Curves
Fitting dimension reduction methods to data lying on two-dimensional sphere. This package provides principal geodesic analysis, principal circle, principal curves proposed by Hauberg, and spherical principal curves. Moreover, it offers the method of locally defined principal geodesics which is underway. The detailed procedures are described in Lee, J., Kim, J.-H. and Oh, H.-S. (2021) <doi:10.1109/TPAMI.2020.3025327>. Also see Kim, J.-H., Lee, J. and Oh, H.-S. (2020) <arXiv:2003.02578>.
Maintained by Jongmin Lee. Last updated 3 years ago.
10.4 match 1 stars 1.00 score 4 scripts
karlines
ReacTran:Reactive Transport Modelling in 1d, 2d and 3d
Routines for developing models that describe reaction and advective-diffusive transport in one, two or three dimensions. Includes transport routines in porous media, in estuaries, and in bodies with variable shape.
Maintained by Karline Soetaert. Last updated 8 years ago.
2.3 match 6 stars 4.57 score 52 scripts
kisungyou
maotai:Tools for Matrix Algebra, Optimization and Inference
Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Maintained by Kisung You. Last updated 1 days ago.
1.8 match 8 stars 5.51 score 15 scripts 9 dependents
tdaverse
tdaunif:Uniform Manifold Samplers for Topological Data Analysis
Uniform random samples from simple manifolds, sometimes with noise, are commonly used to test topological data analytic (TDA) tools. This package includes samplers powered by two techniques: analytic volume-preserving parameterizations, as employed by Arvo (1995) <doi:10.1145/218380.218500>, and rejection sampling, as employed by Diaconis, Holmes, and Shahshahani (2013) <doi:10.1214/12-IMSCOLL1006>.
Maintained by Jason Cory Brunson. Last updated 9 months ago.
manifoldssamplertdatopological-data-analysistopological-statistics
2.0 match 3 stars 4.95 score 8 scripts
icosa-grid
icosa:Global Triangular and Penta-Hexagonal Grids Based on Tessellated Icosahedra
Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.
Maintained by Adam T. Kocsis. Last updated 7 months ago.
1.8 match 4 stars 5.41 score 65 scripts
functionaldata
frechet:Statistical Analysis for Random Objects and Non-Euclidean Data
Provides implementation of statistical methods for random objects lying in various metric spaces, which are not necessarily linear spaces. The core of this package is Fréchet regression for random objects with Euclidean predictors, which allows one to perform regression analysis for non-Euclidean responses under some mild conditions. Examples include distributions in L^2-Wasserstein space, covariance matrices endowed with power metric (with Frobenius metric as a special case), Cholesky and log-Cholesky metrics. References: Petersen, A., & Müller, H.-G. (2019) <doi:10.1214/17-AOS1624>.
Maintained by Yaqing Chen. Last updated 6 months ago.
2.0 match 11 stars 4.82 score 20 scripts
codymarquart
rENA:Epistemic Network Analysis
ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
Maintained by Cody L Marquart. Last updated 1 years ago.
4.3 match 1 stars 2.26 score 36 scripts
aaronolsen
svgViewR:3D Animated Interactive Visualizations Using SVG and WebGL
Creates 3D animated, interactive visualizations that can be viewed in a web browser.
Maintained by Aaron M Olsen. Last updated 2 years ago.
4.5 match 2.12 score 22 scripts 2 dependents
nano-optics
cubs:Cubature on the 2-sphere
Cubature methods for numerical integration over the sphere, such as angular averaging over the full solid angle
Maintained by Baptiste Auguie. Last updated 3 years ago.
3.9 match 1 stars 2.45 score 19 scripts 1 dependents
jonathanlees
RFOC:Graphics for Spherical Distributions and Earthquake Focal Mechanisms
Graphics for statistics on a sphere, as applied to geological fault data, crystallography, earthquake focal mechanisms, radiation patterns, ternary plots and geographical/geological maps. Non-double couple plotting of focal spheres and source type maps are included for statistical analysis of moment tensors.
Maintained by Jonathan M. Lees. Last updated 2 years ago.
4.5 match 2.12 score 133 scripts
zzawadz
DepthProc:Statistical Depth Functions for Multivariate Analysis
Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Maintained by Zygmunt Zawadzki. Last updated 3 years ago.
depth-functionsexploratory-data-analysisstatisticsopenblascppopenmp
1.8 match 6 stars 5.27 score 104 scripts 2 dependents
dipterix
ravetools:Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data
Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for details.
Maintained by Zhengjia Wang. Last updated 4 days ago.
1.8 match 3 stars 5.13 score 20 scripts 1 dependents
klausherrmann
multIntTestFunc:Provides Test Functions for Multivariate Integration
Provides implementations of functions that can be used to test multivariate integration routines. The package covers six different integration domains (unit hypercube, unit ball, unit sphere, standard simplex, non-negative real numbers and R^n). For each domain several functions with different properties (smooth, non-differentiable, ...) are available. The functions are available in all dimensions n >= 1. For each function the exact value of the integral is known and implemented to allow testing the accuracy of multivariate integration routines. Details on the available test functions can be found at on the development website.
Maintained by Klaus Herrmann. Last updated 6 months ago.
2.1 match 4.30 score 1 scripts
bernice0321
MultiRNG:Multivariate Pseudo-Random Number Generation
Pseudo-random number generation for 11 multivariate distributions: Normal, t, Uniform, Bernoulli, Hypergeometric, Beta (Dirichlet), Multinomial, Dirichlet-Multinomial, Laplace, Wishart, and Inverted Wishart. The details of the method are explained in Demirtas (2004) <DOI:10.22237/jmasm/1099268340>.
Maintained by Ran Gao. Last updated 4 years ago.
4.0 match 2.15 score 47 scripts 1 dependents
neerajdhanraj
Jaya:Gradient-Free Optimization Algorithm for Single and Multi-Objective Problems
An implementation of the Jaya optimization algorithm for both single-objective and multi-objective problems. Jaya is a population-based, gradient-free optimization algorithm capable of solving constrained and unconstrained optimization problems without hyperparameters. This package includes features such as multi-objective Pareto optimization, adaptive population adjustment, and early stopping. For further details, see R.V. Rao (2016) <doi:10.5267/j.ijiec.2015.8.004>.
Maintained by Neeraj Bokde. Last updated 4 months ago.
2.5 match 1 stars 3.48 score 5 scripts
merliseclyde
bark:Bayesian Additive Regression Kernels
Bayesian Additive Regression Kernels (BARK) provides an implementation for non-parametric function estimation using Levy Random Field priors for functions that may be represented as a sum of additive multivariate kernels. Kernels are located at every data point as in Support Vector Machines, however, coefficients may be heavily shrunk to zero under the Cauchy process prior, or even, set to zero. The number of active features is controlled by priors on precision parameters within the kernels, permitting feature selection. For more details see Ouyang, Z (2008) "Bayesian Additive Regression Kernels", Duke University. PhD dissertation, Chapter 3 and Wolpert, R. L, Clyde, M.A, and Tu, C. (2011) "Stochastic Expansions with Continuous Dictionaries Levy Adaptive Regression Kernels, Annals of Statistics Vol (39) pages 1916-1962 <doi:10.1214/11-AOS889>.
Maintained by Merlise Clyde. Last updated 5 months ago.
bayesianclassificationlevy-processesnonparametric-regressionpredictionregressionopenblascpp
1.8 match 1 stars 4.18 score 15 scripts
sungkyujung
ClusTorus:Prediction and Clustering on the Torus by Conformal Prediction
Provides various tools of for clustering multivariate angular data on the torus. The package provides angular adaptations of usual clustering methods such as the k-means clustering, pairwise angular distances, which can be used as an input for distance-based clustering algorithms, and implements clustering based on the conformal prediction framework. Options for the conformal scores include scores based on a kernel density estimate, multivariate von Mises mixtures, and naive k-means clusters. Moreover, the package provides some basic data handling tools for angular data.
Maintained by Seungki Hong. Last updated 3 years ago.
1.7 match 3 stars 4.18 score 8 scriptsr-spatial
s2:Spherical Geometry Operators Using the S2 Geometry Library
Provides R bindings for Google's s2 library for geometric calculations on the sphere. High-performance constructors and exporters provide high compatibility with existing spatial packages, transformers construct new geometries from existing geometries, predicates provide a means to select geometries based on spatial relationships, and accessors extract information about geometries.
Maintained by Edzer Pebesma. Last updated 2 hours ago.
0.5 match 74 stars 13.76 score 207 scripts 1.2k dependents
asgr
sphereplot:Spherical Plotting
Various functions for creating spherical coordinate system plots via extensions to rgl.
Maintained by Aaron Robotham. Last updated 2 years ago.
2.0 match 3 stars 3.52 score 37 scripts 1 dependentscran
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 1 months ago.
2.3 match 2.85 score
marcvidalbadia
pfica:Independent Components Analysis Techniques for Functional Data
This package includes a set of tools to perform smoothed (and non-smoothed) principal/independent components analysis of functional data. Various functional pre-whitening approaches are implemented as discussed in Vidal and Aguilera (2022) “Novel whitening approaches in functional settings", <doi:10.1002/sta4.516>. Further whitening representations of functional data can be derived in terms of a few principal components, providing a powerful avenue to explore hidden structures in low dimensional settings: see Vidal, Rosso and Aguilera (2021) “Bi-smoothed functional independent component analysis for EEG artifact removal”, <doi:10.3390/math9111243>.
Maintained by Marc Vidal. Last updated 2 years ago.
b-splinesfobiicakurtosispenalization
1.9 match 2 stars 3.00 score 3 scriptscran
gek:Gradient-Enhanced Kriging
Gradient-Enhanced Kriging as an emulator for computer experiments based on Maximum-Likelihood estimation.
Maintained by Carmen van Meegen. Last updated 3 days ago.
5.6 match 1.00 scorecran
MNM:Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks
Multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score are provided. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components. The methodology is described in Oja (2010) <doi:10.1007/978-1-4419-0468-3> and Nordhausen and Oja (2011) <doi:10.18637/jss.v043.i05>.
Maintained by Klaus Nordhausen. Last updated 1 years ago.
1.9 match 2.88 score 25 scripts 1 dependentscran
cmaes:Covariance Matrix Adapting Evolutionary Strategy
Single objective optimization using a CMA-ES.
Maintained by Olaf Mersmann. Last updated 3 years ago.
2.3 match 1 stars 2.19 score 13 scripts 4 dependentsnano-optics
cda:Coupled-Dipole Approximation for Electromagnetic Scattering by Three- Dimensional Clusters of Sub-Wavelength Particles
Coupled-dipole simulations for electromagnetic scattering of light by sub-wavelength particles in arbitrary 3-dimensional configurations. Scattering and absorption spectra are simulated by inversion of the interaction matrix, or by an order-of-scattering approximation scheme. High-level functions are provided to simulate spectra with varying angles of incidence, as well as with full angular averaging.
Maintained by Baptiste Auguie. Last updated 3 years ago.
1.8 match 2 stars 2.78 score 60 scripts
somakd
fad:Factor Analysis for Data
Compute maximum likelihood estimators of parameters in a Gaussian factor model using the the matrix-free methodology described in Dai et al. (2020) <doi:10.1080/10618600.2019.1704296>. In contrast to the factanal() function from 'stats' package, fad() can handle high-dimensional datasets where number of variables exceed the sample size and is also substantially faster than the EM algorithms.
Maintained by Somak Dutta. Last updated 1 years ago.
1.7 match 3 stars 2.78 score 4 scripts
obreschkow
rglplus:Extension of the 'rgl' 3D Visualization Package
Provides 3D plotting routines that facilitate the use of the 'rgl' package and extend its functionality. For example, the routines allow the user to directly control the camera position & orientation, as well as to generate 3D movies with a moving observer.
Maintained by Danail Obreschkow. Last updated 5 months ago.
1.8 match 2 stars 2.60 score 1 scriptsjpnolan
mvmesh:Multivariate Meshes and Histograms in Arbitrary Dimensions
Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes. Directional and other multivariate histograms are provided.
Maintained by John P. Nolan. Last updated 5 years ago.
2.2 match 2.08 score 1 scripts 4 dependentscran
ManifoldOptim:An R Interface to the 'ROPTLIB' Library for Riemannian Manifold Optimization
An R interface to version 0.3 of the 'ROPTLIB' optimization library (see <https://www.math.fsu.edu/~whuang2/> for more information). Optimize real- valued functions over manifolds such as Stiefel, Grassmann, and Symmetric Positive Definite matrices. For details see Martin et. al. (2020) <doi:10.18637/jss.v093.i01>. Note that the optional ldr package used in some of this package's examples can be obtained from either JSS <https://www.jstatsoft.org/index.php/jss/article/view/v061i03/2886> or from the CRAN archives <https://cran.r-project.org/src/contrib/Archive/ldr/ldr_1.3.3.tar.gz>.
Maintained by Sean R. Martin. Last updated 3 years ago.
2.0 match 2.23 score 28 scripts 2 dependents
klauschn
SpatialNP:Multivariate Nonparametric Methods Based on Spatial Signs and Ranks
Test and estimates of location, tests of independence, tests of sphericity and several estimates of shape all based on spatial signs, symmetrized signs, ranks and signed ranks. For details, see Oja and Randles (2004) <doi:10.1214/088342304000000558> and Oja (2010) <doi:10.1007/978-1-4419-0468-3>.
Maintained by Klaus Nordhausen. Last updated 3 years ago.
2.0 match 2.18 score 10 scripts 5 dependents
gvalentini58
RANKS:Ranking of Nodes with Kernelized Score Functions
Implementation of Kernelized score functions and other semi-supervised learning algorithms for node label ranking to analyze biomolecular networks. RANKS can be easily applied to a large set of different relevant problems in computational biology, ranging from automatic protein function prediction, to gene disease prioritization and drug repositioning, and more in general to any bioinformatics problem that can be formalized as a node label ranking problem in a graph. The modular nature of the implementation allows to experiment with different score functions and kernels and to easily compare the results with baseline network-based methods such as label propagation and random walk algorithms, as well as to enlarge the algorithmic scheme by adding novel user-defined score functions and kernels.
Maintained by Giorgio Valentini. Last updated 2 years ago.
2.0 match 1.90 score 7 scripts
rogiersbart
morphology:Morphological description of 3D categorical arrays
The {morphology} package implements a flexible API for the calculation of nearest-neighbour based morphological quantities for one-, two- or three-dimensional categorical arrays.
Maintained by Bart Rogiers. Last updated 9 months ago.
1.9 match 2.00 score 3 scripts
mthrun
ScatterDensity:Density Estimation and Visualization of 2D Scatter Plots
The user has the option to utilize the two-dimensional density estimation techniques called smoothed density published by Eilers and Goeman (2004) <doi:10.1093/bioinformatics/btg454>, and pareto density which was evaluated for univariate data by Thrun, Gehlert and Ultsch, 2020 <doi:10.1371/journal.pone.0238835>. Moreover, it provides visualizations of the density estimation in the form of two-dimensional scatter plots in which the points are color-coded based on increasing density. Colors are defined by the one-dimensional clustering technique called 1D distribution cluster algorithm (DDCAL) published by Lux and Rinderle-Ma (2023) <doi:10.1007/s00357-022-09428-6>.
Maintained by Michael Thrun. Last updated 29 days ago.
1.8 match 2.00 score 1 scriptscran
radar:Fundamental Formulas for Radar
Fundamental formulas for Radar, for attenuation, range, velocity, effectiveness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick Guy's Python package PyRadarMet
Maintained by Jose Gama. Last updated 10 years ago.
3.4 match 1 stars 1.00 scorecran
assist:A Suite of R Functions Implementing Spline Smoothing Techniques
Fit various smoothing spline models. Includes an ssr() function for smoothing spline regression, an nnr() function for nonparametric nonlinear regression, an snr() function for semiparametric nonlinear regression, an slm() function for semiparametric linear mixed-effects models, and an snm() function for semiparametric nonlinear mixed-effects models. See Wang (2011) <doi:10.1201/b10954> for an overview.
Maintained by Yuedong Wang. Last updated 2 years ago.
3.3 match 1.00 score
cdueben
spaths:Shortest Paths Between Points in Grids
Shortest paths between points in grids. Optional barriers and custom transition functions. Applications regarding planet Earth, as well as generally spheres and planes. Optimized for computational performance, customizability, and user friendliness. Graph-theoretical implementation tailored to gridded data. Currently focused on Dijkstra's (1959) <doi:10.1007/BF01386390> algorithm. Future updates broaden the scope to other least cost path algorithms and to centrality measures.
Maintained by Christian Düben. Last updated 10 days ago.
0.5 match 4 stars 5.15 score 7 scripts
cran
manifold:Operations for Riemannian Manifolds
Implements operations for Riemannian manifolds, e.g., geodesic distance, Riemannian metric, exponential and logarithm maps, etc. Also incorporates random object generator on the manifolds. See Dai, Lin, and Müller (2021) <doi:10.1111/biom.13385>.
Maintained by Xiongtao Dai. Last updated 2 years ago.
1.8 match 1 stars 1.48 score 5 scripts 1 dependentskisungyou
RiemBase:Functions and C++ Header Files for Computation on Manifolds
We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007, ISBN:9780691132983) on computational aspects of optimization on matrix manifolds.
Maintained by Kisung You. Last updated 4 years ago.
0.5 match 3 stars 4.40 score 28 scripts 2 dependents
mrmarjan
nemBM:Using Network Evolution Models to Generate Networks with Selected Blockmodel Type
To study network evolution models and different blockmodeling approaches. Various functions enable generating (temporal) networks with a selected blockmodel type, taking into account selected local network mechanisms. The development of this package is financially supported the Slovenian Research Agency (www.arrs.gov.si) within the research program P5<96>0168 and the research project J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Maintained by Marjan Cugmas. Last updated 2 years ago.
2.0 match 1.00 scorecran
sonar:Fundamental Formulas for Sonar
Formulas for calculating sound velocity, water pressure, depth, density, absorption and sonar equations.
Maintained by Jose Gama. Last updated 9 years ago.
2.0 match 1.00 score
steffenkriewald
osc:Orthodromic Spatial Clustering
Allows distance based spatial clustering of georeferenced data by implementing the City Clustering Algorithm - CCA. Multiple versions allow clustering for a matrix, raster and single coordinates on a plain (Euclidean distance) or on a sphere (great-circle or orthodromic distance).
Maintained by Steffen Kriewald. Last updated 5 years ago.
0.5 match 3.81 score 13 scripts
synx21
SCOR:Spherically Constrained Optimization Routine
A non-convex optimization package that optimizes any function under the criterion, combination of variables are on the surface of a unit sphere.
Maintained by Debsurya De. Last updated 5 years ago.
0.5 match 2 stars 3.30 score 3 scriptscran
InspectChangepoint:High-Dimensional Changepoint Estimation via Sparse Projection
Provides a data-driven projection-based method for estimating changepoints in high-dimensional time series. Multiple changepoints are estimated using a (wild) binary segmentation scheme.
Maintained by Tengyao Wang. Last updated 3 years ago.
1.7 match 1 stars 1.00 scorecran
RPointCloud:Visualizing Topological Loops and Voids
Visualizations to explain the results of a topological data analysis. The goal of topological data analysis is to identify persistent topological structures, such as loops (topological circles) and voids (topological spheres), in data sets. The output of an analysis using the 'TDA' package is a Rips diagram (named after the mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in these holes in the data by providing tools to visualize the features that help explain the structures found in the Rips diagram. See McGee and colleagues (2024) <doi:10.1101/2024.05.16.593927>.
Maintained by Kevin R. Coombes. Last updated 7 months ago.
0.5 match 2.78 score