R-universe search: algebra

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.

cpp

40.0 match 5 stars 6.71 score 4 scripts

robinhankin

freealg:The Free Algebra

The free algebra in R with non-commuting indeterminates. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2211.04002>.

Maintained by Robin K. S. Hankin. Last updated 5 days ago.

cpp

19.6 match 3 stars 7.07 score 10 dependents

mplex

multiplex:Algebraic Tools for the Analysis of Multiple Social Networks

Algebraic procedures for analyses of multiple social networks are delivered with this package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' makes possible, among other things, to create and manipulate multiplex, multimode, and multilevel network data with different formats. Effective ways are available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup with decomposition procedures or semiring structures with the relational bundles occurring in different types of multivariate networks. 'multiplex' provides also an algebraic approach for affiliation networks through Galois derivations between families of the pairs of subsets in the two domains of the network with visualization options.

Maintained by Antonio Rivero Ostoic. Last updated 2 months ago.

algebra network-analysis semigroup semiring

16.6 match 23 stars 8.12 score 69 scripts 2 dependents

robinhankin

weyl:The Weyl Algebra

A suite of routines for Weyl algebras. Notation follows Coutinho (1995, ISBN 0-521-55119-6, "A Primer of Algebraic D-Modules"). Uses 'disordR' discipline (Hankin 2022 <doi:10.48550/arXiv.2210.03856>). To cite the package in publications, use Hankin 2022 <doi:10.48550/arXiv.2212.09230>.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

23.6 match 3 stars 5.59 score 4 scripts

rudjer

SparseM:Sparse Linear Algebra

Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.

Maintained by Roger Koenker. Last updated 8 months ago.

fortran

10.3 match 3 stars 11.47 score 306 scripts 1.5k dependents

robinhankin

evitaicossa:Antiassociative Algebra

Methods to deal with the free antiassociative algebra over the reals with an arbitrary number of indeterminates. Antiassociativity means that (xy)z = -x(yz). Antiassociative algebras are nilpotent with nilindex four (Remm, 2022, <doi:10.48550/arXiv.2202.10812>) and this drives the design and philosophy of the package. Methods are defined to create and manipulate arbitrary elements of the antiassociative algebra, and to extract and replace coefficients. A vignette is provided.

Maintained by Robin K. S. Hankin. Last updated 5 days ago.

cpp

20.1 match 4.90 score

wrathematics

float:32-Bit Floats

R comes with a suite of utilities for linear algebra with "numeric" (double precision) vectors/matrices. However, sometimes single precision (or less!) is more than enough for a particular task. This package extends R's linear algebra facilities to include 32-bit float (single precision) data. Float vectors/matrices have half the precision of their "numeric"-type counterparts but are generally faster to numerically operate on, for a performance vs accuracy trade-off. The internal representation is an S4 class, which allows us to keep the syntax identical to that of base R's. Interaction between floats and base types for binary operators is generally possible; in these cases, type promotion always defaults to the higher precision. The package ships with copies of the single precision 'BLAS' and 'LAPACK', which are automatically built in the event they are not available on the system.

Maintained by Drew Schmidt. Last updated 7 days ago.

float-matrix hpc linear-algebra matrix fortran openblas openmp

8.3 match 46 stars 10.53 score 228 scripts 42 dependents

sciml

diffeqr:Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)

An interface to 'DifferentialEquations.jl' <https://diffeq.sciml.ai/dev/> from the R programming language. It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE), delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality, including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods. Supports GPUs, with support for CUDA (NVIDIA), AMD GPUs, Intel oneAPI GPUs, and Apple's Metal (M-series chip GPUs). 'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users. For more information, see Rackauckas and Nie (2017) <doi:10.5334/jors.151>.

Maintained by Christopher Rackauckas. Last updated 3 months ago.

dae dde delay-differential-equations differential-algebraic-equations differential-equations ode ordinary-differential-equations scientific-machine-learning sciml sde stochastic-differential-equations

10.0 match 143 stars 8.42 score 31 scripts

r-cas

Ryacas:R Interface to the 'Yacas' Computer Algebra System

Interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).

Maintained by Mikkel Meyer Andersen. Last updated 2 years ago.

cpp

7.7 match 40 stars 10.15 score 167 scripts 14 dependents

pachadotdev

cpp11armadillo:An 'Armadillo' Interface

Provides function declarations and inline function definitions that facilitate communication between R and the 'Armadillo' 'C++' library for linear algebra and scientific computing. This implementation is detailed in Vargas Sepulveda and Schneider Malamud (2024) <doi:10.48550/arXiv.2408.11074>.

Maintained by Mauricio Vargas Sepulveda. Last updated 26 days ago.

armadillo cpp cpp11 hacktoberfest linear-algebra

8.0 match 9 stars 9.14 score 1 scripts 16 dependents

rte-antares-rpackage

antaresRead:Import, Manipulate and Explore the Results of an 'Antares' Simulation

Import, manipulate and explore results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here : <https://antares-simulator.org/>).

Maintained by Tatiana Vargas. Last updated 3 days ago.

infrastructure dataimport adequacy bilan electricity energy hdf5 linear-algebra monte-carlo-simulation optimisation previsionnel rhdf5 rte simulation tyndp

7.5 match 13 stars 9.45 score 148 scripts 3 dependents

friendly

matlib:Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics

A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. Many of these functions are designed for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D and for rendering matrix expressions and equations in LaTeX.

Maintained by Michael Friendly. Last updated 2 days ago.

diagrams linear-equations matrix matrix-functions matrix-visualizer vector vignette

5.3 match 65 stars 12.89 score 900 scripts 11 dependents

beerda

lfl:Linguistic Fuzzy Logic

Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE). The package also contains basic fuzzy-related algebraic functions capable of handling missing values in different styles (Bochvar, Sobocinski, Kleene etc.), computation of Sugeno integrals and fuzzy transform.

Maintained by Michal Burda. Last updated 4 months ago.

association-rules forecast-model fuzzy-logic inference-rules cpp openmp

12.2 match 8 stars 5.35 score 28 scripts

davisvaughan

ivs:Interval Vectors

Provides a library for generic interval manipulations using a new interval vector class. Capabilities include: locating various kinds of relationships between two interval vectors, merging overlaps within a single interval vector, splitting an interval vector on its overlapping endpoints, and applying set theoretical operations on interval vectors. Many of the operations in this package were inspired by James Allen's interval algebra, Allen (1983) <doi:10.1145/182.358434>.

Maintained by Davis Vaughan. Last updated 2 years ago.

9.0 match 48 stars 7.05 score 39 scripts 2 dependents

rcppcore

RcppArmadillo:'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library

'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.

Maintained by Dirk Eddelbuettel. Last updated 6 days ago.

armadillo c-plus-plus rcpp rcpparmadillo openblas cpp openmp

3.4 match 197 stars 18.77 score 1.9k scripts 3.4k dependents

bioc

GenomAutomorphism:Compute the automorphisms between DNA's Abelian group representations

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

Maintained by Robersy Sanchez. Last updated 3 months ago.

mathematicalbiology comparativegenomics functionalgenomics multiplesequencealignment wholegenome genetic-code genetic-code-algebra genome genome-algebra

14.7 match 4.30 score 9 scripts

robinhankin

jordan:A Suite of Routines for Working with Jordan Algebras

A Jordan algebra is an algebraic object originally designed to study observables in quantum mechanics. Jordan algebras are commutative but non-associative; they satisfy the Jordan identity. The package follows the ideas and notation of K. McCrimmon (2004, ISBN:0-387-95447-3) "A Taste of Jordan Algebras". To cite the package in publications, please use Hankin (2023) <doi:10.48550/arXiv.2303.06062>.

Maintained by Robin K. S. Hankin. Last updated 8 months ago.

13.3 match 4.60 score 2 scripts

rcppcore

RcppEigen:'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library

R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.

Maintained by Dirk Eddelbuettel. Last updated 7 months ago.

algorithm c-plus-plus eigen eigen-library openblas cpp

3.4 match 112 stars 16.75 score 356 scripts 3.8k dependents

r-cas

caracas:Computer Algebra

Computer algebra via the 'SymPy' library (<https://www.sympy.org/>). This makes it possible to solve equations symbolically, find symbolic integrals, symbolic sums and other important quantities.

Maintained by Mikkel Meyer Andersen. Last updated 15 days ago.

8.3 match 24 stars 6.80 score 87 scripts 1 dependents

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 2 days ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

5.5 match 44 stars 9.45 score 472 scripts

rte-antares-rpackage

antaresProcessing:'Antares' Results Processing

Process results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions to create new columns like net load, load factors, upward and downward margins or to compute aggregated statistics like economic surpluses of consumers, producers and sectors.

Maintained by Tatiana Vargas. Last updated 3 months ago.

infrastructure dataimport adequacy antares bilan datatable energy linear-algebra margins monte-carlo-simulation optimization previsionnel rte simulation surplus tyndp

7.5 match 8 stars 6.70 score 35 scripts 1 dependents

archaeostat

ArchaeoPhases:Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling

Statistical analysis of archaeological dates and groups of dates. This package allows to post-process Markov Chain Monte Carlo (MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>, 'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal' <https://bcal.shef.ac.uk/>. It provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases) as described in Philippe and Vibet (2020) <doi:10.18637/jss.v093.c01>.

Maintained by Anne Philippe. Last updated 11 months ago.

archaeology bayesian-statistics geochronology markov-chain radiocarbon-dates

7.2 match 10 stars 6.90 score 66 scripts

krzjoa

matricks:Useful Tricks for Matrix Manipulation

Provides functions, which make matrix creation conciser (such as the core package's function m() for rowwise matrix definition or runifm() for random value matrices). Allows to set multiple matrix values at once, by using list of formulae. Provides additional matrix operators and dedicated plotting function.

Maintained by Krzysztof Joachimiak. Last updated 5 years ago.

algebra matrix matrix-manipulation cpp

11.0 match 4 stars 4.51 score 16 scripts

r-forge

deSolve:Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')

Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.

Maintained by Thomas Petzoldt. Last updated 1 years ago.

fortran openblas

3.9 match 12.33 score 8.0k scripts 427 dependents

tdaverse

ripserr:Calculate Persistent Homology with Ripser-Based Engines

Ports the Ripser <https://arxiv.org/abs/1908.02518> and Cubical Ripser <https://arxiv.org/abs/2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.

Maintained by Raoul Wadhwa. Last updated 2 days ago.

algebraic-topology cohomology cpp cubical-complex persistent-homology pixel point-cloud r-language r-programming rcpp rips-complex ripser simplicial-complex simplicial-homology topological-data-analysis topology vietoris-complex voxel cpp

7.5 match 7 stars 5.80 score 6 scripts

pachadotdev

cpp11eigen:An 'Eigen' Interface

Provides function declarations and inline function definitions that facilitate communication between R and the 'Eigen' 'C++' library for linear algebra and scientific computing.

Maintained by Mauricio Vargas Sepulveda. Last updated 5 months ago.

cpp cpp11 eigen hacktoberfest linear-algebra

8.0 match 2 stars 4.60 score 1 scripts

r-cas

Ryacas0:Legacy 'Ryacas' (Interface to 'Yacas' Computer Algebra System)

A legacy version of 'Ryacas', an interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).

Maintained by Mikkel Meyer Andersen. Last updated 2 years ago.

cpp

5.1 match 2 stars 7.11 score 36 scripts 6 dependents

vitormarquesr

qwalkr:Handle Continuous-Time Quantum Walks with R

Functions and tools for creating, visualizing, and investigating properties of continuous-time quantum walks, including efficient calculation of matrices such as the mixing matrix, average mixing matrix, and spectral decomposition of the Hamiltonian. E. Farhi (1997): <arXiv:quant-ph/9706062v2>; C. Godsil (2011) <arXiv:1103.2578v3>.

Maintained by Vitor Marques. Last updated 1 years ago.

linear-algebra probability-theory quantum-computing quantum-walk statistics

8.8 match 3.70 score 4 scripts

revelle

psych:Procedures for Psychological, Psychometric, and Personality Research

A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.

Maintained by William Revelle. Last updated 3 months ago.

2.3 match 52 stars 13.94 score 29k scripts 317 dependents

rcst

rim:Interface to 'Maxima', Enabling Symbolic Computation

An interface to the powerful and fairly complete computer algebra system 'Maxima'. It can be used to start and control 'Maxima' from within R by entering 'Maxima' commands. Results from 'Maxima' can be parsed and evaluated in R. It facilitates outputting results from 'Maxima' in 'LaTeX' and 'MathML'. 2D and 3D plots can be displayed directly. This package also registers a 'knitr'-engine enabling 'Maxima' code chunks to be written in 'RMarkdown' documents.

Maintained by Eric Stemmler. Last updated 5 months ago.

computer-algebra-system cpp

7.2 match 11 stars 4.34 score 10 scripts

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

3.3 match 7 stars 9.11 score 1.3k scripts 6 dependents

bartonicek

plotscaper:Explore Your Data with Interactive Figures

A framework for creating interactive figures for data exploration. All plots are automatically linked and support several kinds of interactive features, including selection, zooming, panning, and parameter manipulation. The figures can be interacted with either manually, using a mouse and a keyboard, or by running code from inside an active R session.

Maintained by Adam Bartonicek. Last updated 23 days ago.

3.8 match 16 stars 7.36 score 23 scripts

cran

conicfit:Algorithms for Fitting Circles, Ellipses and Conics Based on the Work by Prof. Nikolai Chernov

Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin.

Maintained by Jose Gama. Last updated 9 years ago.

15.4 match 1.78 score 2 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.sparse:Sparse Three-Dimensional Arrays and Linear Algebra Utilities

Defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.

Maintained by Adrian Baddeley. Last updated 8 months ago.

arrays sparse-matrix sparse-representations

2.9 match 2 stars 8.72 score 7 scripts 150 dependents

mjskay

ggblend:Blending and Compositing Algebra for 'ggplot2'

Algebra of operations for blending, copying, adjusting, and compositing layers in 'ggplot2'. Supports copying and adjusting the aesthetics or parameters of an existing layer, partitioning a layer into multiple pieces for re-composition, applying affine transformations to layers, and combining layers (or partitions of layers) using blend modes (including commutative blend modes, like multiply and darken). Blend mode support is particularly useful for creating plots with overlapping groups where the layer drawing order does not change the output; see Kindlmann and Scheidegger (2014) <doi:10.1109/TVCG.2014.2346325>.

Maintained by Matthew Kay. Last updated 2 years ago.

3.6 match 184 stars 6.29 score 71 scripts 1 dependents

snoweye

pbdSLAP:Programming with Big Data -- Scalable Linear Algebra Packages

Utilizing scalable linear algebra packages mainly including 'BLACS', 'PBLAS', and 'ScaLAPACK' in double precision via 'pbdMPI' based on 'ScaLAPACK' version 2.0.2.

Maintained by Wei-Chen Chen. Last updated 4 months ago.

fortran openmpi

5.1 match 4.30 score 4 scripts

reinhardfurrer

spam:SPArse Matrix

Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.

Maintained by Reinhard Furrer. Last updated 2 months ago.

fortran openblas cpp

2.3 match 1 stars 9.26 score 420 scripts 433 dependents

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

1.7 match 15 stars 12.60 score 7.7k scripts 295 dependents

hojsgaard

gRbase:A Package for Graphical Modelling in R

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.

Maintained by Søren Højsgaard. Last updated 4 months ago.

openblas cpp

2.3 match 3 stars 9.24 score 241 scripts 20 dependents

statnet

statnet.common:Common R Scripts and Utilities Used by the Statnet Project Software

Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.

Maintained by Pavel N. Krivitsky. Last updated 26 days ago.

1.7 match 8 stars 11.42 score 197 scripts 148 dependents

nashjc

nlsr:Functions for Nonlinear Least Squares Solutions - Updated 2022

Provides tools for working with nonlinear least squares problems. For the estimation of models reliable and robust tools than nls(), where the the Gauss-Newton method frequently stops with 'singular gradient' messages. This is accomplished by using, where possible, analytic derivatives to compute the matrix of derivatives and a stabilization of the solution of the estimation equations. Tools for approximate or externally supplied derivative matrices are included. Bounds and masks on parameters are handled properly.

Maintained by John C Nash. Last updated 27 days ago.

2.7 match 7.02 score 94 scripts 5 dependents

bioc

graph:graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Maintained by Bioconductor Package Maintainer. Last updated 11 days ago.

graphandnetwork

1.5 match 11.78 score 764 scripts 342 dependents

stla

EigenR:Complex Matrix Algebra with 'Eigen'

Matrix algebra using the 'Eigen' C++ library: determinant, rank, inverse, pseudo-inverse, kernel and image, QR decomposition, Cholesky decomposition, Schur decomposition, Hessenberg decomposition, linear least-squares problems. Also provides matrix functions such as exponential, logarithm, power, sine and cosine. Complex matrices are supported.

Maintained by Stéphane Laurent. Last updated 11 months ago.

eigen rcpp cpp

3.6 match 5 stars 4.78 score 27 scripts 1 dependents

covaruber

sommer:Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.

Maintained by Giovanny Covarrubias-Pazaran. Last updated 22 days ago.

average-information mixed-models rcpparmadillo openblas cpp openmp

1.3 match 43 stars 12.70 score 300 scripts 9 dependents

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 19 hours ago.

openblas cpp openmp

3.0 match 8 stars 5.51 score 15 scripts 9 dependents

david-cortes

MatrixExtra:Extra Methods for Sparse Matrices

Extends sparse matrix and vector classes from the 'Matrix' package by providing: (a) Methods and operators that work natively on CSR formats (compressed sparse row, a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(), mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag(); (b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types, including the 'float32' type from 'float'; (c) Coercion methods between pairs of classes which are not present in 'Matrix', such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions; (d) Utility functions for sparse matrices such as sorting the indices or removing zero-valued entries; (e) Fast transposes that work by outputting in the opposite storage format; (f) Faster replacements for many 'Matrix' methods for all sparse types, such as slicing and elementwise multiplication. (g) Convenience functions for sparse objects, such as 'mapSparse' or a shorter 'show' method.

Maintained by David Cortes. Last updated 9 months ago.

csr sparse-matrix openblas cpp openmp

1.8 match 20 stars 9.08 score 84 scripts 29 dependents

phillipbvetter

ctsmTMB:Continuous Time Stochastic Modelling using Template Model Builder

ctsmTMB is an R package for parameter and state estimation and forecasting in stochastic state space systems. These are partially observed state space systems that whose latent states evolve according to a system of stochastic differential equation. The package employs the R6 object for easy model construction, and uses the TMB/RTMB packages for its modern C++ implementations and algorithmic differentiation. The estimation methods implemented are variations of (non-linear) Kalman Filters in addition to the Laplace approximation.

Maintained by Phillip Brinck Vetter. Last updated 5 days ago.

cpp

3.0 match 2 stars 5.10 score

vjilmari

multid:Multivariate Difference Between Two Groups

Estimation of multivariate differences between two groups (e.g., multivariate sex differences) with regularized regression methods and predictive approach. See Lönnqvist & Ilmarinen (2021) <doi:10.1007/s11109-021-09681-2> and Ilmarinen et al. (2023) <doi:10.1177/08902070221088155>. Includes tools that help in understanding difference score reliability, predictions of difference score variables, conditional intra-class correlations, and heterogeneity of variance estimates. Package development was supported by the Academy of Finland research grant 338891.

Maintained by Ville-Juhani Ilmarinen. Last updated 6 months ago.

3.5 match 4.48 score 6 scripts

dkaschek

dMod:Dynamic Modeling and Parameter Estimation in ODE Models

The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.

Maintained by Daniel Kaschek. Last updated 10 days ago.

1.8 match 20 stars 8.35 score 251 scripts

fatelarico

FinNet:Quickly Build and Manipulate Financial Networks

Providing classes, methods, and functions to deal with financial networks. Users can easily store information about both physical and legal persons by using pre-made classes that are studied for integration with scraping packages such as 'rvest' and 'RSelenium'. Moreover, the package assists in creating various types of financial networks depending on the type of relation between its units depending on the relation under scrutiny (ownership, board interlocks, etc.), the desired tie type (valued or binary), and renders them in the most common formats (adjacency matrix, incidence matrix, edge list, 'igraph', 'network'). There are also ad-hoc functions for the Fiedler value, global network efficiency, and cascade-failure analysis.

Maintained by Fabio Ashtar Telarico. Last updated 5 months ago.

cpp

3.1 match 2 stars 4.78 score 7 scripts

coneill-math

m2r:Interface to 'Macaulay2'

Persistent interface to 'Macaulay2' <http://www.math.uiuc.edu/Macaulay2/> and front-end tools facilitating its use in the 'R' ecosystem. For details see Kahle et. al. (2020) <doi:10.18637/jss.v093.i09>.

Maintained by David Kahle. Last updated 5 years ago.

cpp

2.9 match 5 stars 5.23 score 34 scripts

inlabru-org

fmesher:Triangle Meshes and Related Geometry Tools

Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.

Maintained by Finn Lindgren. Last updated 2 days ago.

cpp

1.3 match 16 stars 11.18 score 261 scripts 26 dependents

clobatofern95

GPUmatrix:Basic Linear Algebra with GPU

GPUs are great resources for data analysis, especially in statistics and linear algebra. Unfortunately, very few packages connect R to the GPU, and none of them are transparent enough to run the computations on the GPU without substantial changes to the code. The maintenance of these packages is cumbersome: several of the earlier attempts have been removed from their respective repositories. It would be desirable to have a properly maintained R package that takes advantage of the GPU with minimal changes to the existing code. We have developed the GPUmatrix package (available on CRAN). GPUmatrix mimics the behavior of the Matrix package and extends R to use the GPU for computations. It includes single(FP32) and double(FP64) precision data types, and provides support for sparse matrices. It is easy to learn, and requires very few code changes to perform the operations on the GPU. GPUmatrix relies on either the Torch or Tensorflow R packages to perform the GPU operations. We have demonstrated its usefulness for several statistical applications and machine learning applications: non-negative matrix factorization, logistic regression and general linear models. We have also included a comparison of GPU and CPU performance on different matrix operations.

Maintained by Cesar Lobato-Fernandez. Last updated 1 years ago.

3.6 match 3.93 score 57 scripts 1 dependents

stla

RationalMatrix:Exact Matrix Algebra for Rational Matrices

Provides functions to deal with matrix algebra for matrices with rational entries: determinant, rank, image and kernel, inverse, Cholesky decomposition. All computations are exact.

Maintained by Stéphane Laurent. Last updated 2 years ago.

eigen gmp rcpp cpp

3.5 match 4.03 score 12 scripts 6 dependents

kurthornik

relations:Data Structures and Algorithms for Relations

Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.

Maintained by Kurt Hornik. Last updated 26 days ago.

2.8 match 5.04 score 58 scripts 14 dependents

astamm

roahd:Robust Analysis of High Dimensional Data

A collection of methods for the robust analysis of univariate and multivariate functional data, possibly in high-dimensional cases, and hence with attention to computational efficiency and simplicity of use. See the R Journal publication of Ieva et al. (2019) <doi:10.32614/RJ-2019-032> for an in-depth presentation of the 'roahd' package. See Aleman-Gomez et al. (2021) <arXiv:2103.08874> for details about the concept of depthgram.

Maintained by Aymeric Stamm. Last updated 3 years ago.

2.2 match 2 stars 6.29 score 164 scripts 2 dependents

joblion

rtkore:'STK++' Core Library Integration to 'R' using 'Rcpp'

'STK++' <http://www.stkpp.org> is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an 'Eigen'-like API), regression, dimension reduction, etc. The integration of the library to 'R' is using 'Rcpp'. The 'rtkore' package includes the header files from the 'STK++' core library. All files contain only template classes and/or inline functions. 'STK++' is licensed under the GNU LGPL version 2 or later. 'rtkore' (the 'stkpp' integration into 'R') is licensed under the GNU GPL version 2 or later. See file LICENSE.note for details.

Maintained by Serge Iovleff. Last updated 10 months ago.

cpp

3.5 match 3.90 score 25 scripts 2 dependents

ohdsi

CohortAlgebra:Use of Interval Algebra to Create New Cohort(s) from Existing Cohorts

This software tool is designed to generate new cohorts utilizing data from previously instantiated cohorts. It employs interval algebra operators such as UNION, INTERSECT, and MINUS to manipulate the data within the instantiated cohorts and create new cohorts.

Maintained by Gowtham Rao. Last updated 21 days ago.

openjdk

3.3 match 1 stars 4.00 score

ecor

blockmatrix:Tools to Solve Algebraic Systems with Partitioned Matrices

Some elementary matrix algebra tools are implemented to manage block matrices or partitioned matrix, i.e. "matrix of matrices" (http://en.wikipedia.org/wiki/Block_matrix). The block matrix is here defined as a new S3 object. In this package, some methods for "matrix" object are rewritten for "blockmatrix" object. New methods are implemented. This package was created to solve equation systems with block matrices for the analysis of environmental vector time series . Bugs/comments/questions/collaboration of any kind are warmly welcomed.

Maintained by Emanuele Cordano. Last updated 9 years ago.

3.4 match 3.82 score 22 scripts 2 dependents

statist7

sitar:Super Imposition by Translation and Rotation Growth Curve Analysis

Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales. The model was first described by Lindstrom (1995) <doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole et al (2010) <doi:10.1093/ije/dyq115>.

Maintained by Tim Cole. Last updated 2 months ago.

1.5 match 13 stars 8.69 score 58 scripts 3 dependents

kenaho1

asbio:A Collection of Statistical Tools for Biologists

Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.

Maintained by Ken Aho. Last updated 2 months ago.

1.8 match 5 stars 7.32 score 310 scripts 3 dependents

jrmccombs

RHPCBenchmark:Benchmarks for High-Performance Computing Environments

Microbenchmarks for determining the run time performance of aspects of the R programming environment and packages relevant to high-performance computation. The benchmarks are divided into three categories: dense matrix linear algebra kernels, sparse matrix linear algebra kernels, and machine learning functionality.

Maintained by James McCombs. Last updated 8 years ago.

4.2 match 3.02 score 21 scripts

cran

scaRabee:Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

A port of the Scarabee toolkit originally written as a Matlab-based application. scaRabee provides a framework for simulation and optimization of pharmacokinetic-pharmacodynamic models at the individual and population level. It is built on top of the neldermead package, which provides the direct search algorithm proposed by Nelder and Mead for model optimization.

Maintained by Sebastien Bihorel. Last updated 3 years ago.

4.5 match 2.70 score 3 scripts

earowang

sugrrants:Supporting Graphs for Analysing Time Series

Provides 'ggplot2' graphics for analysing time series data. It aims to fit into the 'tidyverse' and grammar of graphics framework for handling temporal data.

Maintained by Earo Wang. Last updated 1 years ago.

statistical-graphics time-series

1.6 match 82 stars 7.42 score 214 scripts 1 dependents

cran

redcas:An Interface to the Computer Algebra System 'REDUCE'

'REDUCE' is a portable general-purpose computer algebra system supporting scalar, vector, matrix and tensor algebra, symbolic differential and integral calculus, arbitrary precision numerical calculations and output in 'LaTeX' format. 'REDUCE' is based on 'Lisp' and is available on the two dialects 'Portable Standard Lisp' ('PSL') and 'Codemist Standard Lisp' ('CSL'). The 'redcas' package provides an interface for executing arbitrary 'REDUCE' code interactively from 'R', returning output as character vectors. 'R' code and 'REDUCE' code can be interspersed. It also provides a specialized function for calling the 'REDUCE' feature for solving systems of equations, returning the output as an 'R' object designed for the purpose. A further specialized function uses 'REDUCE' features to generate 'LaTeX' output and post-processes this for direct use in 'LaTeX' documents, e.g. using 'Sweave'.

Maintained by Martin Gregory. Last updated 4 months ago.

5.6 match 2.15 score 28 scripts

stla

giacR:Interface to the Computer Algebra System 'Giac'

'Giac' <https://www-fourier.ujf-grenoble.fr/~parisse/giac/doc/en/cascmd_en/cascmd_en.html> is a general purpose symbolic algebra software. It powers the graphical interface 'Xcas'. This package allows to execute 'Giac' commands in 'R'.

Maintained by Stéphane Laurent. Last updated 12 months ago.

giac

3.5 match 3.06 score 23 scripts

tidyverse

lubridate:Make Dealing with Dates a Little Easier

Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

Maintained by Vitalie Spinu. Last updated 3 months ago.

date date-time

0.5 match 757 stars 20.95 score 135k scripts 1.9k dependents

lme4

lme4:Linear Mixed-Effects Models using 'Eigen' and S4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

Maintained by Ben Bolker. Last updated 3 days ago.

cpp

0.5 match 647 stars 20.69 score 35k scripts 1.5k dependents

sn248

sundialr:An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers

Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.

Maintained by Satyaprakash Nayak. Last updated 2 months ago.

ode-solver sundials cpp

1.7 match 10 stars 6.26 score 9 scripts

benubah

control:A Control Systems Toolbox

Solves control systems problems relating to time/frequency response, LTI systems design and analysis, transfer function manipulations, and system conversion.

Maintained by Ben C. Ubah. Last updated 5 years ago.

1.8 match 19 stars 5.86 score 76 scripts

robinhankin

stokes:The Exterior Calculus

Provides functionality for working with tensors, alternating forms, wedge products, Stokes's theorem, and related concepts from the exterior calculus. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/arXiv.2210.03856>). The canonical reference would be M. Spivak (1965, ISBN:0-8053-9021-9) "Calculus on Manifolds". To cite the package in publications please use Hankin (2022) <doi:10.48550/arXiv.2210.17008>.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

1.5 match 3 stars 6.62 score

robinhankin

freegroup:The Free Group

The free group in R; juxtaposition is represented by a plus. Includes inversion, multiplication by a scalar, group-theoretic power operation, and Tietze forms. To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2212.05883>.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

1.9 match 5.06 score 33 scripts

cran

wPerm:Permutation Tests

Supplies permutation-test alternatives to traditional hypothesis-test procedures such as two-sample tests for means, medians, and standard deviations; correlation tests; tests for homogeneity and independence; and more. Suitable for general audiences, including individual and group users, introductory statistics courses, and more advanced statistics courses that desire an introduction to permutation tests.

Maintained by Neil A. Weiss. Last updated 9 years ago.

7.2 match 1.30 score

r-spatial

RPyGeo:ArcGIS Geoprocessing via Python

Provides access to ArcGIS geoprocessing tools by building an interface between R and the ArcPy Python side-package via the reticulate package.

Maintained by Alexander Brenning. Last updated 5 years ago.

1.5 match 29 stars 6.19 score 54 scripts

kylecaudle

rTensor2:MultiLinear Algebra

A set of tools for basic tensor operators. A tensor in the context of data analysis in a multidimensional array. The tools in this package rely on using any discrete transformation (e.g. Fast Fourier Transform (FFT)). Standard tools included are the Eigenvalue decomposition of a tensor, the QR decomposition and LU decomposition. Other functionality includes the inverse of a tensor and the transpose of a symmetric tensor. Functionality in the package is outlined in Kernfeld et al. (2015) <https://www.sciencedirect.com/science/article/pii/S0024379515004358>.

Maintained by Kyle Caudle. Last updated 12 months ago.

3.8 match 2.48 score 2 scripts 1 dependents

f-rousset

spaMM:Mixed-Effect Models, with or without Spatial Random Effects

Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.

Maintained by François Rousset. Last updated 9 months ago.

gsl cpp openmp

1.9 match 4.94 score 208 scripts 5 dependents

cran

SDAResources:Datasets and Functions for 'Sampling: Design and Analysis, 3rd Edition'

Includes all the datasets of 'Sampling: Design and Analysis' (3rd edition by Sharon Lohr) in R format and additional functions for analyzing and graphing probability samples.

Maintained by Yan Lu. Last updated 3 years ago.

4.5 match 2.00 score

permaverse

nevada:Network-Valued Data Analysis

A flexible statistical framework for network-valued data analysis. It leverages the complexity of the space of distributions on graphs by using the permutation framework for inference as implemented in the 'flipr' package. Currently, only the two-sample testing problem is covered and generalization to k samples and regression will be added in the future as well. It is a 4-step procedure where the user chooses a suitable representation of the networks, a suitable metric to embed the representation into a metric space, one or more test statistics to target specific aspects of the distributions to be compared and a formula to compute the permutation p-value. Two types of inference are provided: a global test answering whether there is a difference between the distributions that generated the two samples and a local test for localizing differences on the network structure. The latter is assumed to be shared by all networks of both samples. References: Lovato, I., Pini, A., Stamm, A., Vantini, S. (2020) "Model-free two-sample test for network-valued data" <doi:10.1016/j.csda.2019.106896>; Lovato, I., Pini, A., Stamm, A., Taquet, M., Vantini, S. (2021) "Multiscale null hypothesis testing for network-valued data: Analysis of brain networks of patients with autism" <doi:10.1111/rssc.12463>.

Maintained by Aymeric Stamm. Last updated 3 months ago.

openblas cpp

1.9 match 6 stars 4.48 score 7 scripts

simonlabcode

bakR:Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

Several implementations of a novel Bayesian hierarchical statistical model of nucleotide recoding RNA-seq experiments (NR-seq; TimeLapse-seq, SLAM-seq, TUC-seq, etc.) for analyzing and comparing NR-seq datasets (see 'Vock and Simon' (2023) <doi:10.1261/rna.079451.122>). NR-seq is a powerful extension of RNA-seq that provides information about the kinetics of RNA metabolism (e.g., RNA degradation rate constants), which is notably lacking in standard RNA-seq data. The statistical model makes maximal use of these high-throughput datasets by sharing information across transcripts to significantly improve uncertainty quantification and increase statistical power. 'bakR' includes a maximally efficient implementation of this model for conservative initial investigations of datasets. 'bakR' also provides more highly powered implementations using the probabilistic programming language 'Stan' to sample from the full posterior distribution. 'bakR' performs multiple-test adjusted statistical inference with the output of these model implementations to help biologists separate signal from background. Methods to automatically visualize key results and detect batch effects are also provided.

Maintained by Isaac Vock. Last updated 4 months ago.

cpp

1.3 match 6 stars 6.12 score 21 scripts

stan-dev

StanHeaders:C++ Header Files for Stan

The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.

Maintained by Ben Goodrich. Last updated 1 days ago.

bayesian-data-analysis bayesian-inference bayesian-statistics mcmc stan

0.5 match 1.1k stars 15.52 score 291 scripts 344 dependents

bioc

IRanges:Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Maintained by Hervé Pagès. Last updated 1 months ago.

infrastructure datarepresentation bioconductor-package core-package

0.5 match 22 stars 15.09 score 2.1k scripts 1.8k dependents

kylecaudle

TensorTools:Multilinear Algebra

A set of tools for basic tensor operators. A tensor in the context of data analysis in a multidimensional array. The tools in this package rely on using any discrete transformation (e.g. Fast Fourier Transform (FFT)). Standard tools included are the Eigenvalue decomposition of a tensor, the QR decomposition and LU decomposition. Other functionality includes the inverse of a tensor and the transpose of a symmetric tensor. Functionality in the package is outlined in Kernfeld, E., Kilmer, M., and Aeron, S. (2015) <doi:10.1016/j.laa.2015.07.021>.

Maintained by Kyle Caudle. Last updated 5 months ago.

3.8 match 2.00 score

cran

AlgebraicHaploPackage:Haplotype Two Snips Out of a Paired Group of Patients

Two unordered pairs of data of two different snips positions is haplotyped by resolving a small number ob closed equations.

Maintained by Jan Wolfertz. Last updated 9 years ago.

3.3 match 2.00 score

pegeler

samplesizeCMH:Power and Sample Size Calculation for the Cochran-Mantel-Haenszel Test

Calculates the power and sample size for Cochran-Mantel-Haenszel tests. There are also several helper functions for working with probability, odds, relative risk, and odds ratio values.

Maintained by Paul Egeler. Last updated 1 months ago.

categorical-data cmh-test sample-size statistical-power statistics

1.1 match 4 stars 5.94 score 36 scripts

hwborchers

pracma:Practical Numerical Math Functions

Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Maintained by Hans W. Borchers. Last updated 1 years ago.

0.5 match 29 stars 12.34 score 6.6k scripts 931 dependents

uislambekov

TDAvec:Vector summaries of persistence diagrams

Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency, all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages

Maintained by Umar Islambekov. Last updated 7 days ago.

openblas cpp openmp

1.8 match 3.52 score 11 scripts

barnhilldave

TML:Tropical Geometry Tools for Machine Learning

Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>, Barnhill and Yoshida (2023) <doi:10.3390/math11153433>, Aliatimis et al. (2023) <arXiv:2306.08796>, Yoshida et al. (2022) <arXiv:2206.04206>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.

Maintained by David Barnhill. Last updated 8 months ago.

1.6 match 3 stars 3.65 score 1 scripts

stephenslab

mashr:Multivariate Adaptive Shrinkage

Implements the multivariate adaptive shrinkage (mash) method of Urbut et al (2019) <DOI:10.1038/s41588-018-0268-8> for estimating and testing large numbers of effects in many conditions (or many outcomes). Mash takes an empirical Bayes approach to testing and effect estimation; it estimates patterns of similarity among conditions, then exploits these patterns to improve accuracy of the effect estimates. The core linear algebra is implemented in C++ for fast model fitting and posterior computation.

Maintained by Peter Carbonetto. Last updated 4 months ago.

openblas gsl cpp openmp

0.5 match 91 stars 11.04 score 624 scripts 3 dependents

mlampros

ClusterR:Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering

Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.

Maintained by Lampros Mouselimis. Last updated 9 months ago.

affinity-propagation cpp11 gmm kmeans kmedoids-clustering mini-batch-kmeans rcpparmadillo openblas cpp openmp

0.5 match 84 stars 11.08 score 640 scripts 24 dependents

kaskr

RTMB:'R' Bindings for 'TMB'

Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.

Maintained by Kasper Kristensen. Last updated 1 months ago.

openblas cpp

0.5 match 54 stars 10.49 score 394 scripts 9 dependents

alfinurrahmah

fakmct:Fuzzy Adaptive Resonance Theory K-Means Clustering Technique

A set of function for clustering data observation with hybrid method Fuzzy ART and K-Means by Sengupta, Ghosh & Dan (2011) <doi:10.1080/0951192X.2011.602362>.

Maintained by Alfi Nurrahmah. Last updated 3 years ago.

1.9 match 1 stars 2.70 score 4 scripts

alexeckert

parallelDist:Parallel Distance Matrix Computation using Multiple Threads

A fast parallelized alternative to R's native 'dist' function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of 41 predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user- defined functions written in C++. For ease of use, the 'parDist' function extends the signature of the 'dist' function and uses the same parameter naming conventions as distance methods of existing R packages. The package is mainly implemented in C++ and leverages the 'RcppParallel' package to parallelize the distance computations with the help of the 'TinyThread' library. Furthermore, the 'Armadillo' linear algebra library is used for optimized matrix operations during distance calculations. The curiously recurring template pattern (CRTP) technique is applied to avoid virtual functions, which improves the Dynamic Time Warping calculations while the implementation stays flexible enough to support different DTW step patterns and normalization methods.

Maintained by Alexander Eckert. Last updated 3 years ago.

data-science distance-computations matrices openblas cpp

0.5 match 51 stars 9.92 score 432 scripts 14 dependents

cran

tropAlgebra:Tropical Algebraic Functions

It includes functions like tropical addition, tropical multiplication for vectors and matrices. In tropical algebra, the tropical sum of two numbers is their minimum and the tropical product of two numbers is their ordinary sum. For more information see also I. Simon (1988) Recognizable sets with multiplicities in the tropical semi ring: Volume 324 Lecture Notes I Computer Science, pages 107-120 <doi: 10.1007/BFb0017135>.

Maintained by Muhammad Kashif Hanif. Last updated 7 years ago.

3.8 match 2 stars 1.30 score

winvector

rquery:Relational Query Generator for Data Manipulation at Scale

A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.

Maintained by John Mount. Last updated 2 years ago.

0.5 match 110 stars 9.53 score 126 scripts 3 dependents

resc0059

QuantumOps:Performs Common Linear Algebra Operations Used in Quantum Computing and Implements Quantum Algorithms

Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>. Can be used with the gridsynth algorithm <arXiv:1212.6253> to perform decomposition into the Clifford+T set.

Maintained by Salonik Resch. Last updated 5 years ago.

2.7 match 1 stars 1.72 score 52 scripts

projectmosaic

mosaicCalc:R-Language Based Calculus Operations for Teaching

Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.

Maintained by Daniel Kaplan. Last updated 20 days ago.

0.5 match 13 stars 8.68 score 546 scripts

dirkschumacher

ompr:Model and Solve Mixed Integer Linear Programs

Model mixed integer linear programs in an algebraic way directly in R. The model is solver-independent and thus offers the possibility to solve a model with different solvers. It currently only supports linear constraints and objective functions. See the 'ompr' website <https://dirkschumacher.github.io/ompr/> for more information, documentation and examples.

Maintained by Dirk Schumacher. Last updated 2 years ago.

integer-programming linear-programming milp mip optimization

0.5 match 268 stars 8.33 score 321 scripts 6 dependents

winvector

rqdatatable:'rquery' for 'data.table'

Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.

Maintained by John Mount. Last updated 2 years ago.

0.5 match 38 stars 8.10 score 142 scripts 2 dependents

tomkellygenetics

matrixcalc:Collection of Functions for Matrix Calculations

A collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics. This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201. Horn, R.A. (1990) Matrix Analysis. ISBN 978-0521386326. Lancaster, P. (1969) Theory of Matrices. ISBN 978-0124355507. Lay, D.C. (1995) Linear Algebra: And Its Applications. ISBN 978-0201845563.

Maintained by S. Thomas Kelly. Last updated 4 years ago.

0.5 match 8.32 score 1.7k scripts 149 dependents

geobosh

sarima:Simulation and Prediction with Seasonal ARIMA Models

Functions, classes and methods for time series modelling with ARIMA and related models. The aim of the package is to provide consistent interface for the user. For example, a single function autocorrelations() computes various kinds of theoretical and sample autocorrelations. This is work in progress, see the documentation and vignettes for the current functionality. Function sarima() fits extended multiplicative seasonal ARIMA models with trends, exogenous variables and arbitrary roots on the unit circle, which can be fixed or estimated (for the algebraic basis for this see <arXiv:2208.05055>, a paper on the methodology is being prepared).

Maintained by Georgi N. Boshnakov. Last updated 12 months ago.

arima kalman-filter reg-sarima sarima sarimax seasonal time-series xarima openblas cpp

0.5 match 3 stars 6.71 score 112 scripts 1 dependents

pachadotdev

economiccomplexity:Computational Methods for Economic Complexity

A wrapper of different methods from Linear Algebra for the equations introduced in The Atlas of Economic Complexity and related literature. This package provides standard matrix and graph output that can be used seamlessly with other packages. See <doi:10.21105/joss.01866> for a summary of these methods and its evolution in literature.

Maintained by Mauricio Vargas Sepulveda. Last updated 3 months ago.

economic-complexity eigenvalues eigenvectors graphs international-trade matrix networks recursive-algorithm openblas cpp openmp

0.5 match 39 stars 6.32 score 18 scripts

kaskr

RTMBp:'R' Bindings for 'TMB'

Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMBp' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.

Maintained by Kasper Kristensen. Last updated 1 months ago.

openblas cpp openmp

0.5 match 51 stars 6.44 score 1 scripts

waternumbers

FKF:Fast Kalman Filter

This is a fast and flexible implementation of the Kalman filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in BLAS and LAPACK. Due to the speed of the filter, the fitting of high-dimensional linear state space models to large datasets becomes possible. This package also contains a plot function for the visualization of the state vector and graphical diagnostics of the residuals.

Maintained by Paul Smith. Last updated 6 months ago.

openblas

0.5 match 12 stars 6.31 score 57 scripts 2 dependents

glenndavis52

colorSpec:Color Calculations with Emphasis on Spectral Data

Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners. Build complex systems from simpler parts using a spectral product algebra. For light sources, compute CCT, CRI, SSI, and IES TM-30 reports. For object colors, compute optimal colors and Logvinenko coordinates. Work with the standard CIE illuminants and color matching functions, and read spectra from text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.

Maintained by Glenn Davis. Last updated 1 months ago.

0.5 match 2 stars 6.34 score 73 scripts 5 dependents

accarniel

fsr:Handling Fuzzy Spatial Data

Support for fuzzy spatial objects, their operations, and fuzzy spatial inference models based on Spatial Plateau Algebra. It employs fuzzy set theory and fuzzy logic as foundation to deal with spatial fuzziness. It mainly implements underlying concepts defined in the following research papers: (i) "Spatial Plateau Algebra: An Executable Type System for Fuzzy Spatial Data Types" <doi:10.1109/FUZZ-IEEE.2018.8491565>; (ii) "A Systematic Approach to Creating Fuzzy Region Objects from Real Spatial Data Sets" <doi:10.1109/FUZZ-IEEE.2019.8858878>; (iii) "Spatial Data Types for Heterogeneously Structured Fuzzy Spatial Collections and Compositions" <doi:10.1109/FUZZ48607.2020.9177620>; (iv) "Fuzzy Inference on Fuzzy Spatial Objects (FIFUS) for Spatial Decision Support Systems" <doi:10.1109/FUZZ-IEEE.2017.8015707>; (v) "Evaluating Region Inference Methods by Using Fuzzy Spatial Inference Models" <doi:10.1109/FUZZ-IEEE55066.2022.9882658>.

Maintained by Anderson Carniel. Last updated 1 years ago.

fuzzy-inference-system fuzzy-logic fuzzy-spatial-data spatial-data spatial-data-science

0.8 match 10 stars 4.18 score

gams-dev

gamstransfer:A Data Interface Between 'GAMS' and R

Read, analyze, modify, and write 'GAMS' (General Algebraic Modeling System) data. The main focus of 'gamstransfer' is the highly efficient transfer of data with 'GAMS' <https://www.gams.com/>, while keeping these operations as simple as possible for the user. The transfer of data usually takes place via an intermediate GDX (GAMS Data Exchange) file. Additionally, 'gamstransfer' provides utility functions to get an overview of 'GAMS' data and to check its validity.

Maintained by Atharv Bhosekar. Last updated 6 months ago.

zlib cpp

0.5 match 2 stars 6.18 score 26 scripts 13 dependents

robinhankin

onion:Octonions and Quaternions

Quaternions and Octonions are four- and eight- dimensional extensions of the complex numbers. They are normed division algebras over the real numbers and find applications in spatial rotations (quaternions), and string theory and relativity (octonions). The quaternions are noncommutative and the octonions nonassociative. See the package vignette for more details.

Maintained by Robin K. S. Hankin. Last updated 1 months ago.

0.5 match 6 stars 5.97 score 43 scripts 3 dependents

mlysy

mniw:The Matrix-Normal Inverse-Wishart Distribution

Density evaluation and random number generation for the Matrix-Normal Inverse-Wishart (MNIW) distribution, as well as the the Matrix-Normal, Matrix-T, Wishart, and Inverse-Wishart distributions. Core calculations are implemented in a portable (header-only) C++ library, with matrix manipulations using the 'Eigen' library for linear algebra. Also provided is a Gibbs sampler for Bayesian inference on a random-effects model with multivariate normal observations.

Maintained by Martin Lysy. Last updated 6 months ago.

cpp

0.5 match 4 stars 6.03 score 30 scripts 3 dependents

albersonmiranda

fio:Friendly Input-Output Analysis

Simplifies the process of importing and managing input-output matrices from 'Microsoft Excel' into R, and provides a suite of functions for analysis. It leverages the 'R6' class for clean, memory-efficient object-oriented programming. Furthermore, all linear algebra computations are implemented in 'Rust' to achieve highly optimized performance.

Maintained by Alberson da Silva Miranda. Last updated 1 months ago.

economics rust cargo

0.5 match 12 stars 5.98 score 1 scripts

cran

tensorA:Advanced Tensor Arithmetic with Named Indices

Provides convenience functions for advanced linear algebra with tensors and computation with data sets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, parallel computations on sequences of tensors.

Maintained by K. Gerald van den Boogaart. Last updated 1 years ago.

0.5 match 5.83 score 399 dependents

drelliesmall

smallstuff:Dr. Small's Functions

Functions used in courses taught by Dr. Small at Drew University.

Maintained by Ellie Small. Last updated 1 years ago.

1.9 match 1.48 score 2 scripts 1 dependents

japilo

colorednoise:Simulate Temporally Autocorrelated Populations

Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one. This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.

Maintained by July Pilowsky. Last updated 11 months ago.

openblas cpp

0.5 match 10 stars 5.43 score 18 scripts

covaruber

lme4breeding:Relationship-Based Mixed-Effects Models

Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.

Maintained by Giovanny Covarrubias-Pazaran. Last updated 22 days ago.

0.5 match 6 stars 5.23 score 7 scripts

mbertolacci

WoodburyMatrix:Fast Matrix Operations via the Woodbury Matrix Identity

A hierarchy of classes and methods for manipulating matrices formed implicitly from the sums of the inverses of other matrices, a situation commonly encountered in spatial statistics and related fields. Enables easy use of the Woodbury matrix identity and the matrix determinant lemma to allow computation (e.g., solving linear systems) without having to form the actual matrix. More information on the underlying linear algebra can be found in Harville, D. A. (1997) <doi:10.1007/b98818>.

Maintained by Michael Bertolacci. Last updated 2 years ago.

0.5 match 3 stars 4.22 score 11 scripts

stla

resultant:Utilities for Multivariate Polynomials with Rational Coefficients

Computation of resultant, subresultants, greatest common divisor, integral division (aka division without remainder) of two multivariate polynomials with rational coefficients, Sturm-Habicht sequence and square-free factorization of a multivariate polynomial with rational coefficients. The computations are performed by the 'C++' library 'CGAL' (<https://www.cgal.org/>). Resultants have applications in polynomial systems solving, number theory, and algebraic geometry. The package also contains some functions computing the number of real roots of a univariate polynomial with rational coefficients, and a function computing the division with remainder of two univariate polynomials with rational coefficients.

Maintained by Stéphane Laurent. Last updated 8 months ago.

cgal multivariate-polynomials gmp cpp

0.5 match 4.23 score 42 scripts

stla

cyclotomic:The Field of Cyclotomic Numbers

The cyclotomic numbers are complex numbers that can be thought of as the rational numbers extended with the roots of unity. They are represented exactly, enabling exact computations. They contain the Gaussian rationals (complex numbers with rational real and imaginary parts) as well as the square roots of all rational numbers. They also contain the sine and cosine of all rational multiples of pi. The algorithms implemented in this package are taken from the 'Haskell' package 'cyclotomic', whose algorithms are adapted from code by Martin Schoenert and Thomas Breuer in the 'GAP' project (<https://www.gap-system.org/>). Cyclotomic numbers have applications in number theory, algebraic geometry, algebraic number theory, coding theory, and in the theory of graphs and combinatorics. They have connections to the theory of modular functions and modular curves.

Maintained by Stéphane Laurent. Last updated 1 years ago.

arithmetic cyclotomic-numbers

0.8 match 1 stars 2.70 score 9 scripts

cdeterman

RViennaCL:'ViennaCL' C++ Header Files

'ViennaCL' is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports 'CUDA', 'OpenCL', and 'OpenMP' (including switches at runtime). I have placed these libraries in this package as a more efficient distribution system for CRAN. The idea is that you can write a package that depends on the 'ViennaCL' library and yet you do not need to distribute a copy of this code with your package.

Maintained by Charles Determan Jr. Last updated 6 years ago.

0.5 match 19 stars 3.98 score 2 scripts

francescobartolucci

extRC:Extended RC Models for Contingency Tables

Maximum likelihood estimation of an extended class of row-column (RC) association models for two-dimensional contingency tables, which are formulated by a condition of reduced rank on a matrix of extended association parameters; see Forcina (2019) <arXiv:1910.13848>. These parameters are defined by choosing the logit type for the row and column variables among four different options and a transformation derived from suitable divergence measures.

Maintained by Francesco Bartolucci. Last updated 4 years ago.

2.0 match 1.00 score 10 scripts

rosarialo

CAvariants:Correspondence Analysis Variants

Provides six variants of two-way correspondence analysis (ca): simple ca, singly ordered ca, doubly ordered ca, non symmetrical ca, singly ordered non symmetrical ca, and doubly ordered non symmetrical ca.

Maintained by Rosaria Lombardo. Last updated 1 years ago.

1.7 match 1.18 score 15 scripts

predict-epfl

piqp:R Interface to Proximal Interior Point Quadratic Programming Solver

An embedded proximal interior point quadratic programming solver, which can solve dense and sparse quadratic programs, described in Schwan, Jiang, Kuhn, and Jones (2023) <doi:10.48550/arXiv.2304.00290>. Combining an infeasible interior point method with the proximal method of multipliers, the algorithm can handle ill-conditioned convex quadratic programming problems without the need for linear independence of the constraints. The solver is written in header only 'C++ 14' leveraging the 'Eigen' library for vectorized linear algebra. For small dense problems, vectorized instructions and cache locality can be exploited more efficiently. Allocation free problem updates and re-solves are also provided.

Maintained by Balasubramanian Narasimhan. Last updated 2 years ago.

cpp

0.5 match 3.70 score 9 scripts

cufesam

fasterElasticNet:An Amazing Fast Way to Fit Elastic Net

Fit Elastic Net, Lasso, and Ridge regression and do cross-validation in a fast way. We build the algorithm based on Least Angle Regression by Bradley Efron, Trevor Hastie, Iain Johnstone, etc. (2004)(<doi:10.1214/009053604000000067 >) and some algorithms like Givens rotation and Forward/Back Substitution. In this way, many matrices to be computed are retained as triangular matrices which can eventually speed up the computation. The fitting algorithm for Elastic Net is written in C++ using Armadillo linear algebra library.

Maintained by Linyu Zuo. Last updated 6 years ago.

elastic-net openblas cpp openmp

0.5 match 8 stars 3.60 score 4 scripts

cran

biganalytics:Utilities for 'big.matrix' Objects from Package 'bigmemory'

Extend the 'bigmemory' package with various analytics. Functions 'bigkmeans' and 'binit' may also be used with native R objects. For 'tapply'-like functions, the bigtabulate package may also be helpful. For linear algebra support, see 'bigalgebra'. For mutex (locking) support for advanced shared-memory usage, see 'synchronicity'.

Maintained by Michael J. Kane. Last updated 12 months ago.

cpp

0.5 match 1 stars 3.37 score 196 scripts 4 dependents

yannrichet-asnr

rlibkriging:Kriging Models using the 'libKriging' Library

Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should provide most standard Kriging / Gaussian process regression features (like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages). 'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson, 'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.

Maintained by Yann Richet. Last updated 2 months ago.

openblas arpack cpp

0.5 match 3.40 score 126 scripts

ecor

rasterList:A Raster Where Cells are Generic Objects

A S4 class has been created such that complex operations can be executed on each cell of a raster map. The raster of objects contains a raster map with the addition of a list of generic objects: one object for each raster cells. It allows to write few lines of R code for complex map algebra. Two environmental applications about frequency analysis of raster map of precipitation and creation of a raster map of soil water retention curves have been presented.

Maintained by Emanuele Cordano. Last updated 2 years ago.

climate hydrology hydrology-statistical hydrology-stormwater-analysis

0.5 match 1 stars 3.34 score 22 scripts

rned

blocksdesign:Nested and Crossed Block Designs for Factorial and Unstructured Treatment Sets

Constructs treatment and block designs for linear treatment models with crossed or nested block factors. The treatment design can be any feasible linear model and the block design can be any feasible combination of crossed or nested block factors. The block design is a sum of one or more block factors and the block design is optimized sequentially with the levels of each successive block factor optimized conditional on all previously optimized block factors. D-optimality is used throughout except for square or rectangular lattice block designs which are constructed algebraically using mutually orthogonal Latin squares. Crossed block designs with interaction effects are optimized using a weighting scheme which allows for differential weighting of first and second-order block effects. Outputs include a table showing the allocation of treatments to blocks and tables showing the achieved D-efficiency factors for each block and treatment design. Edmondson, R.N. Multi-level Block Designs for Comparative Experiments. JABES 25, 500–522 (2020) <doi:10.1007/s13253-020-00416-0>.

Maintained by Rodney Edmondson. Last updated 4 years ago.

0.5 match 1 stars 3.31 score 23 scripts 2 dependents

dkahle

latte:Interface to 'LattE' and '4ti2'

Back-end connections to 'LattE' (<https://www.math.ucdavis.edu/~latte>) for counting lattice points and integration inside convex polytopes and '4ti2' (<http://www.4ti2.de/>) for algebraic, geometric, and combinatorial problems on linear spaces and front-end tools facilitating their use in the 'R' ecosystem.

Maintained by David Kahle. Last updated 2 years ago.

0.5 match 3 stars 3.18 score 1 scripts

zichongli5

PRIMAL:Parametric Simplex Method for Sparse Learning

Implements a unified framework of parametric simplex method for a variety of sparse learning problems (e.g., Dantzig selector (for linear regression), sparse quantile regression, sparse support vector machines, and compressive sensing) combined with efficient hyper-parameter selection strategies. The core algorithm is implemented in C++ with Eigen3 support for portable high performance linear algebra. For more details about parametric simplex method, see Haotian Pang (2017) <https://papers.nips.cc/paper/6623-parametric-simplex-method-for-sparse-learning.pdf>.

Maintained by Zichong Li. Last updated 5 years ago.

cpp

0.5 match 3.00 score 3 scripts

ptaranti

coppeCosenzaR:COPPE-Cosenza Fuzzy Hierarchy Model

The program implements the COPPE-Cosenza Fuzzy Hierarchy Model. The model was based on the evaluation of local alternatives, representing regional potentialities, so as to fulfill demands of economic projects. After defining demand profiles in terms of their technological coefficients, the degree of importance of factors is defined so as to represent the productive activity. The method can detect a surplus of supply without the restriction of the distance of classical algebra, defining a hierarchy of location alternatives. In COPPE-Cosenza Model, the distance between factors is measured in terms of the difference between grades of memberships of the same factors belonging to two or more sets under comparison. The required factors are classified under the following linguistic variables: Critical (CR); Conditioning (C); Little Conditioning (LC); and Irrelevant (I). And the alternatives can assume the following linguistic variables: Excellent (Ex), Good (G), Regular (R), Weak (W), Empty (Em), Zero (Z) and Inexistent (In). The model also provides flexibility, allowing different aggregation rules to be performed and defined by the Decision Maker. Such feature is considered in this package, allowing the user to define other aggregation matrices, since it considers the same linguistic variables mentioned.

Maintained by Pier Taranti. Last updated 5 years ago.

coppe-cosenza

0.5 match 3.00 score 20 scripts

dnychka

LatticeKrig:Multi-Resolution Kriging Based on Markov Random Fields

Methods for the interpolation of large spatial datasets. This package uses a basis function approach that provides a surface fitting method that can approximate standard spatial data models. Using a large number of basis functions allows for estimates that can come close to interpolating the observations (a spatial model with a small nugget variance.) Moreover, the covariance model for this method can approximate the Matern covariance family but also allows for a multi-resolution model and supports efficient computation of the profile likelihood for estimating covariance parameters. This is accomplished through compactly supported basis functions and a Markov random field model for the basis coefficients. These features lead to sparse matrices for the computations and this package makes of the R spam package for sparse linear algebra. An extension of this version over previous ones ( < 5.4 ) is the support for different geometries besides a rectangular domain. The Markov random field approach combined with a basis function representation makes the implementation of different geometries simple where only a few specific R functions need to be added with most of the computation and evaluation done by generic routines that have been tuned to be efficient. One benefit of this package's model/approach is the facility to do unconditional and conditional simulation of the field for large numbers of arbitrary points. There is also the flexibility for estimating non-stationary covariances and also the case when the observations are a linear combination (e.g. an integral) of the spatial process. Included are generic methods for prediction, standard errors for prediction, plotting of the estimated surface and conditional and unconditional simulation. See the 'LatticeKrigRPackage' GitHub repository for a vignette of this package. Development of this package was supported in part by the National Science Foundation Grant 1417857 and the National Center for Atmospheric Research.

Maintained by Douglas Nychka. Last updated 5 months ago.

fortran

0.5 match 2.89 score 130 scripts 1 dependents

sgsokol

r2sundials:Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem

Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:10.1145/1089014.1089020>.

Maintained by Serguei Sokol. Last updated 8 months ago.

cpp

0.5 match 2 stars 2.78 score 3 scripts

cran

epandist:Statistical Functions for the Censored and Uncensored Epanechnikov Distribution

Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.

Maintained by Mathias Borritz Milfeldt. Last updated 9 years ago.

0.5 match 2.70 score

aaronjfisher

bootSVD:Fast, Exact Bootstrap Principal Component Analysis for High Dimensional Data

Implements fast, exact bootstrap Principal Component Analysis and Singular Value Decompositions for high dimensional data, as described in <doi:10.1080/01621459.2015.1062383> (see also <arXiv:1405.0922> ). For data matrices that are too large to operate on in memory, users can input objects with class 'ff' (see the 'ff' package), where the actual data is stored on disk. In response, this package will implement a block matrix algebra procedure for calculating the principal components (PCs) and bootstrap PCs. Depending on options set by the user, the 'parallel' package can be used to parallelize the calculation of the bootstrap PCs.

Maintained by Aaron Fisher. Last updated 4 years ago.

0.5 match 1 stars 2.54 score 23 scripts 1 dependents

nmartinkova

fuzzyreg:Fuzzy Linear Regression

Estimators for fuzzy linear regression. The functions estimate parameters of fuzzy linear regression models with crisp or fuzzy independent variables (triangular fuzzy numbers are supported). Implements multiple methods for parameter estimation and algebraic operations with triangular fuzzy numbers. Includes functions for summarising, printing and plotting the model fit. Calculates predictions from the model and total error of fit. Individual methods are described in Diamond (1988) <doi:10.1016/0020-0255(88)90047-3>, Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004>, Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98>, Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008>, Skrabanek, Marek & Pozdilkova (2021) <doi:10.3390/math9060685>, Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>, Zeng, Feng & Li (2017) <doi:10.1016/j.asoc.2016.09.029>.

Maintained by Natalia Martinkova. Last updated 2 years ago.

0.5 match 2.38 score 24 scripts

cran

cPCG:Efficient and Customized Preconditioned Conjugate Gradient Method for Solving System of Linear Equations

Solves system of linear equations using (preconditioned) conjugate gradient algorithm, with improved efficiency using Armadillo templated 'C++' linear algebra library, and flexibility for user-specified preconditioning method. Please check <https://github.com/styvon/cPCG> for latest updates.

Maintained by Yongwen Zhuang. Last updated 6 years ago.

openblas cpp

0.5 match 2.28 score 19 scripts

cran

vecsets:Like Set Tools in 'Base' Package but Keeps Duplicate Elements

The 'base' tools union() intersect(), etc., follow the algebraic definition that each element of a set must be unique. Since it's often helpful to compare all elements of two vectors, this toolset treats every element as unique for counting purposes. For ease of use, all functions in vecsets have an argument 'multiple' which, when set to FALSE, reverts them to the base::sets (alias for all the items) tools functionality.

Maintained by Carl Witthoft. Last updated 1 years ago.

0.5 match 1.94 score 29 scripts 1 dependents

cran

probs:Elementary Probability on Finite Sample Spaces

Performs elementary probability calculations on finite sample spaces, which may be represented by data frames or lists. This package is meant to rescue some widely used functions from the archived 'prob' package (see <https://cran.r-project.org/src/contrib/Archive/prob/>). Functionality includes setting up sample spaces, counting tools, defining probability spaces, performing set algebra, calculating probability and conditional probability, tools for simulation and checking the law of large numbers, adding random variables, and finding marginal distributions. Characteristic functions for all base R distributions are included.

Maintained by Joe gr. Schlarmann. Last updated 9 months ago.

0.5 match 1.70 score

cran

sparkhail:A 'Sparklyr' Extension for 'Hail'

'Hail' is an open-source, general-purpose, 'python' based data analysis tool with additional data types and methods for working with genomic data, see <https://hail.is/>. 'Hail' is built to scale and has first-class support for multi-dimensional structured data, like the genomic data in a genome-wide association study (GWAS). 'Hail' is exposed as a 'python' library, using primitives for distributed queries and linear algebra implemented in 'scala', 'spark', and increasingly 'C++'. The 'sparkhail' is an R extension using 'sparklyr' package. The idea is to help R users to use 'hail' functionalities with the well-know 'tidyverse' syntax, see <https://www.tidyverse.org/>.

Maintained by Samuel Macêdo. Last updated 5 years ago.

0.5 match 1.70 score

cran

Tex4exams:Generating 'Sweave' Code for 'R/exams' Questions in Mathematics

When using the R package 'exams' to write mathematics questions in 'Sweave' files, the output of a lot of R functions need to be adjusted for display in mathematical formulas. Specifically, the functions were accumulated when writing questions for the topics of the mathematics courses College Algebra, Precalculus, Calculus, Differential Equations, Introduction to Probability, and Linear Algebra. The output of the developed functions can be used in 'Sweave' files.

Maintained by Qingwen Hu. Last updated 2 years ago.

0.8 match 1.00 score

shchurch

countland:Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq

A set of functions for applying a restricted linear algebra to the analysis of count-based data. See the accompanying preprint manuscript: "Normalizing need not be the norm: count-based math for analyzing single-cell data" Church et al (2022) <doi:10.1101/2022.06.01.494334> This tool is specifically designed to analyze count matrices from single cell RNA sequencing assays. The tools implement several count-based approaches for standard steps in single-cell RNA-seq analysis, including scoring genes and cells, comparing cells and clustering, calculating differential gene expression, and several methods for rank reduction. There are many opportunities for further optimization that may prove useful in the analysis of other data. We provide the source code freely available at <https://github.com/shchurch/countland> and encourage users and developers to fork the code for their own purposes.

Maintained by Church Samuel H.. Last updated 1 years ago.

0.5 match 1.32 score 21 scripts

davidealtomare

FBFsearch:Algorithm for Searching the Space of Gaussian Directed Acyclic Graph Models Through Moment Fractional Bayes Factors

We propose an objective Bayesian algorithm for searching the space of Gaussian directed acyclic graph (DAG) models. The algorithm proposed makes use of moment fractional Bayes factors (MFBF) and thus it is suitable for learning sparse graph. The algorithm is implemented by using Armadillo: an open-source C++ linear algebra library.

Maintained by Davide Altomare. Last updated 3 years ago.

openblas cpp

0.5 match 1.00 score 3 scripts

kundupro

GENMETA:Implements Generalized Meta-Analysis Using Iterated Reweighted Least Squares Algorithm

Generalized meta-analysis is a technique for estimating parameters associated with a multiple regression model through meta-analysis of studies which may have information only on partial sets of the regressors. It estimates the effects of each variable while fully adjusting for all other variables that are measured in at least one of the studies. Using algebraic relationships between regression parameters in different dimensions, a set of moment equations is specified for estimating the parameters of a maximal model through information available on sets of parameter estimates from a series of reduced models available from the different studies. The specification of the equations requires a reference dataset to estimate the joint distribution of the covariates. These equations are solved using the generalized method of moments approach, with the optimal weighting of the equations taking into account uncertainty associated with estimates of the parameters of the reduced models. The proposed framework is implemented using iterated reweighted least squares algorithm for fitting generalized linear regression models. For more details about the method, please see pre-print version of the manuscript on generalized meta-analysis by Prosenjit Kundu, Runlong Tang and Nilanjan Chatterjee (2018) <doi:10.1093/biomet/asz030>.The current version (0.2.0) is updated to address some of the stability issues in the previous version (0.1).

Maintained by Prosenjit Kundu. Last updated 2 years ago.

0.5 match 1.00 score 6 scripts