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r-spatialcovariance
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Functions that compute the spatial covariance matrix for the matern and power classes of spatial models, for data that arise on rectangular units. This code can also be used for the change of support problem and for spatial data that arise on irregularly shaped regions like counties or zipcodes by laying a fine grid of rectangles and aggregating the integrals in a form of Riemann integration.
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2025-03-25 |
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r-spatialacc
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Provides a set of spatial accessibility measures from a set of locations (demand) to another set of locations (supply). It aims, among others, to support research on spatial accessibility to health care facilities. Includes the locations and some characteristics of major public hospitals in Greece.
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2025-03-25 |
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r-spatest
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Performs score test using saddlepoint approximation to estimate the null distribution. Also prepares summary statistics for meta-analysis and performs meta-analysis to combine multiple association results. For the latest version, please check <https://github.com/leeshawn/SPAtest>.
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2025-03-25 |
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r-sparsestep
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Implements the SparseStep model for solving regression problems with a sparsity constraint on the parameters. The SparseStep regression model was proposed in Van den Burg, Groenen, and Alfons (2017) <arXiv:1701.06967>. In the model, a regularization term is added to the regression problem which approximates the counting norm of the parameters. By iteratively improving the approximation a sparse solution to the regression problem can be obtained. In this package both the standard SparseStep algorithm is implemented as well as a path algorithm which uses golden section search to determine solutions with different values for the regularization parameter.
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2025-03-25 |
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r-sparsepp
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Provides interface to 'sparsepp' - fast, memory efficient hash map. It is derived from Google's excellent 'sparsehash' implementation. We believe 'sparsepp' provides an unparalleled combination of performance and memory usage, and will outperform your compiler's unordered_map on both counts. Only Google's 'dense_hash_map' is consistently faster, at the cost of much greater memory usage (especially when the final size of the map is not known in advance).
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2025-03-25 |
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r-sparsemvn
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Computes multivariate normal (MVN) densities, and samples from MVN distributions, when the covariance or precision matrix is sparse.
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2025-03-25 |
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r-sparsemse
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Implements the routines and algorithms developed and analysed in "Multiple Systems Estimation for Sparse Capture Data: Inferential Challenges when there are Non-Overlapping Lists" Chan, L, Silverman, B. W., Vincent, K (2019) <arXiv:1902.05156>. This package explicitly handles situations where there are pairs of lists which have no observed individuals in common. It deals correctly with parameters whose estimated values can be considered as being negative infinity. It also addresses other possible issues of non-existence and non-identifiability of maximum likelihood estimates.
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2025-03-25 |
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r-sparsemdc
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Implements the algorithm described in Barron, M., and Li, J. (Not yet published). This algorithm clusters samples from multiple ordered populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseMDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.
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2025-03-25 |
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r-sparseindextracking
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Computation of sparse portfolios for financial index tracking, i.e., joint selection of a subset of the assets that compose the index and computation of their relative weights (capital allocation). The level of sparsity of the portfolios, i.e., the number of selected assets, is controlled through a regularization parameter. Different tracking measures are available, namely, the empirical tracking error (ETE), downside risk (DR), Huber empirical tracking error (HETE), and Huber downside risk (HDR). See vignette for a detailed documentation and comparison, with several illustrative examples. The package is based on the paper: K. Benidis, Y. Feng, and D. P. Palomar, "Sparse Portfolios for High-Dimensional Financial Index Tracking," IEEE Trans. on Signal Processing, vol. 66, no. 1, pp. 155-170, Jan. 2018. <doi:10.1109/TSP.2017.2762286>.
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2025-03-25 |
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r-sparsegrid
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SparseGrid is a package to create sparse grids for numerical integration, based on code from www.sparse-grids.de
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2025-03-25 |
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r-sparseeigen
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Computation of sparse eigenvectors of a matrix (aka sparse PCA) with running time 2-3 orders of magnitude lower than existing methods and better final performance in terms of recovery of sparsity pattern and estimation of numerical values. Can handle covariance matrices as well as data matrices with real or complex-valued entries. Different levels of sparsity can be specified for each individual ordered eigenvector and the method is robust in parameter selection. See vignette for a detailed documentation and comparison, with several illustrative examples. The package is based on the paper: K. Benidis, Y. Sun, P. Babu, and D. P. Palomar (2016). "Orthogonal Sparse PCA and Covariance Estimation via Procrustes Reformulation," IEEE Transactions on Signal Processing <doi:10.1109/TSP.2016.2605073>.
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2025-03-25 |
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r-sparsedc
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Implements the algorithm described in Barron, M., Zhang, S. and Li, J. 2017, "A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data", Nucleic Acids Research, gkx1113, <doi:10.1093/nar/gkx1113>. This algorithm clusters samples from two different populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.
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2025-03-25 |
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r-sparsebnutils
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A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data, as described in Aragam, Gu, and Zhou (2017) <arXiv:1703.04025>.
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2025-03-25 |
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r-sparql
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Use SPARQL to pose SELECT or UPDATE queries to an end-point.
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2025-03-25 |
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r-sparktex
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Generate syntax for use with the sparklines package for LaTeX.
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2025-03-25 |
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r-sparkr
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Provides an R Front end for 'Apache Spark' <https://spark.apache.org>.
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2025-03-25 |
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r-sparkline
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Include interactive sparkline charts <http://omnipotent.net/jquery.sparkline> in all R contexts with the convenience of 'htmlwidgets'.
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2025-03-25 |
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r-spar
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This package performs robust nonparametric tests for rare variants association analysis using summation of partition approaches that incorporate gene-gene and gene-environmental interactions
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2025-03-25 |
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r-spanish
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Character vector to numerical translation in Euros from Spanish spelled monetary quantities. Reverse translation from integer to Spanish. Upper limit is up to the millions range. Geocoding via Cadastral web site.
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2025-03-25 |
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r-spanel
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Fit the spatial panel data models: the fixed effects, random effects and between models.
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2025-03-25 |
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r-spaero
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Implements methods for anticipating the emergence and eradication of infectious diseases from surveillance time series. Also provides support for computational experiments testing the performance of such methods.
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2025-03-25 |
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r-spader
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Estimation of various biodiversity indices and related (dis)similarity measures based on individual-based (abundance) data or sampling-unit-based (incidence) data taken from one or multiple communities/assemblages.
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2025-03-25 |
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r-spaddins
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A set of RStudio addins that are designed to be used in combination with user-defined RStudio keyboard shortcuts. These addins either: 1) insert text at a cursor position (e.g. insert operators %>%, <<-, %$%, etc.), 2) replace symbols in selected pieces of text (e.g., convert backslashes to forward slashes which results in stings like "c:\data\" converted into "c:/data/") or 3) enclose text with special symbols (e.g., converts "bold" into "**bold**") which is convenient for editing R Markdown files.
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2025-03-25 |
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r-spacyr
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An R wrapper to the 'Python' 'spaCy' 'NLP' library, from <http://spacy.io>.
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2025-03-25 |
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r-spacesxyz
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Functions for converting among CIE XYZ, xyY, Lab, and Luv. Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci. The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included. Three standard color difference metrics are included.
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2025-03-25 |
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r-spacesrgb
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Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
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2025-03-25 |
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r-spaa
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Miscellaneous functions for analysing species association and niche overlap.
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2025-03-25 |
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r-spa3g
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The package implements the model-based kernel machine method for detecting gene-centric gene-gene interactions of Li and Cui (2012).
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2025-03-25 |
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r-sp23design
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Provides methods for generating, exploring and executing seamless Phase II-III designs of Lai, Lavori and Shih using generalized likelihood ratio statistics. Includes pdf and source files that describe the entire R implementation with the relevant mathematical details.
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2025-03-25 |
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r-source.gist
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Analogous to source(), but works when given a Gist URL or ID.
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2025-03-25 |
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r-sound
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Basic functions for dealing with wav files and sound samples.
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2025-03-25 |
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r-sotu
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The President of the United States is constitutionally obligated to provide a report known as the 'State of the Union'. The report summarizes the current challenges facing the country and the president's upcoming legislative agenda. While historically the State of the Union was often a written document, in recent decades it has always taken the form of an oral address to a joint session of the United States Congress. This package provides the raw text from every such address with the intention of being used for meaningful examples of text analysis in R. The corpus is well suited to the task as it is historically important, includes material intended to be read and material intended to be spoken, and it falls in the public domain. As the corpus spans over two centuries it is also a good test of how well various methods hold up to the idiosyncrasies of historical texts. Associated data about each address, such as the year, president, party, and format, are also included.
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2025-03-25 |
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r-sotkanet
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Access statistical information on welfare and health in Finland from the Sotkanet open data portal <https://sotkanet.fi/sotkanet/fi/index>.
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2025-03-25 |
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r-sortablehtmltables
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SortableHTMLTables writes a data frame to an HTML file that contains a sortable table. The sorting is done using the jQuery plugin Tablesorter. The appearance is controlled through a CSS file and several GIF's.
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2025-03-25 |
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r-sorptionanalysis
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Provides tools to efficiently analyze and visualize laboratory data from aqueous static adsorption experiments. The package provides functions to plot Langmuir, Freundlich, and Temkin isotherms and functions to determine the statistical conformity of data points to the Langmuir, Freundlich, and Temkin adsorption models through statistical characterization of the isothermic least squares regressions lines. Scientific Reference: Dada, A.O, Olalekan, A., Olatunya, A. (2012) <doi:10.9790/5736-0313845>.
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2025-03-25 |
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r-sor
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Estimation for longitudinal data following outcome dependent sampling using the sequential offsetted regression technique. Includes support for binary, count, and continuous data. The first regression is a logistic regression, which uses a known ratio (the probability of being sampled given that the subject/observation was referred divided by the probability of being sampled given that the subject/observation was no referred) as an offset to estimate the probability of being referred given outcome and covariates. The second regression uses this estimated probability to calculate the mean population response given covariates.
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2025-03-25 |
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r-soql
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Used to construct the URLs and parameters of 'Socrata Open Data API' <https://dev.socrata.com> calls, using the API's 'SoQL' parameter format. Has method-chained and sensical syntax. Plays well with pipes.
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2025-03-25 |
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r-sopie
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Provides functions to non-parametrically estimate the off-pulse interval of a source function originating from a pulsar. The technique is based on a sequential application of P-values obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov, Cramer-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.
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2025-03-25 |
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r-soniclength
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Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.
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2025-03-25 |
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r-sonar
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Formulas for calculating sound velocity, water pressure, depth, density, absorption and sonar equations.
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2025-03-25 |
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r-somplot
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The package provides the plot function som.plot() to create high quality visualisations of hexagonal Kohonen maps (self-organising maps).
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2025-03-25 |
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r-somemtp
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It's a collection of functions for Multiplicity Correction and Multiple Testing.
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2025-03-25 |
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r-somekfwer
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This package collects some procedures controlling the Generalized Familywise Error Rate.
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2025-03-25 |
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r-somebm
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some Brownian motions simulation functions
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2025-03-25 |
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r-solverationalmatrixequation
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Given a symmetric positive definite matrix Q and a non-singular matrix L, find symmetric positive definite solution X such that X = Q + L (X inv) L^T. Reference: Benner, P., Faßbender, H. On the Solution of the Rational Matrix Equation. Benner, Faßbender (2007) <doi:10.1155/2007/21850>.
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2025-03-25 |
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r-solrad
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For surface energy models and estimation of solar positions and components with varying topography, time and locations. The functions calculate solar top-of-atmosphere, open, diffuse and direct components, atmospheric transmittance and diffuse factors, day length, sunrise and sunset, solar azimuth, zenith, altitude, incidence, and hour angles, earth declination angle, equation of time, and solar constant. Details about the methods and equations are explained in Seyednasrollah, Bijan, Mukesh Kumar, and Timothy E. Link. 'On the role of vegetation density on net snow cover radiation at the forest floor.' Journal of Geophysical Research: Atmospheres 118.15 (2013): 8359-8374, <doi:10.1002/jgrd.50575>.
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2025-03-25 |
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r-solomon
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Parentage analysis using Bayes' theorem
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2025-03-25 |
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r-solartime
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Provide utilities to work with solar time, i.e. where noon is exactly when sun culminates. Provides functions for computing sun position and times of sunrise and sunset.
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2025-03-25 |
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r-solarpos
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Calculation of solar zenith and azimuth angles.
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2025-03-25 |
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r-solar
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Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
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2025-03-25 |
