Spike and slab for prediction and variable selection in linear regression models. Uses a generalized elastic net for variable selection.

Load Avro Files into Apache Spark using sparklyr'. This allows to read files from Apache Avro <https://avro.apache.org/>.

Calculate change point based on spectral clustering with the option to automatically calculate the number of clusters if this information is not available.

Load WARC (Web ARChive) files into Apache Spark using sparklyr'. This allows to read files from the Common Crawl project <http://commoncrawl.org/>.

Estimate the internal consistency of your tasks with a permutation based split-half reliability approach. Unofficial release name: "I eat stickers all the time, dude!".

Spectra viewer, organizer, data preparation and property blocks from within R or stand-alone. Binary (application) part is installed separately using spnInstallApp() from spectrino package.

This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.

Import classification results from the RDP Classifier (Ribosomal Database Project), USEARCH sintax, vsearch sintax and the QIIME2 (Quantitative Insights into Microbial Ecology) classifiers into phyloseq tax_table objects.

Offers a fast algorithm for fitting solution paths of sparse SVM models with lasso or elastic-net regularization. Reference: Congrui Yi and Jian Huang (2017) <doi:10.1080/10618600.2016.1256816>.

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.

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

Models the nonnegative entries of a rectangular adjacency matrix using a sparse latent position model, as illustrated in Rastelli, R. (2018) "The Sparse Latent Position Model for nonnegative weighted networks" <arXiv:1808.09262>.

The sparse vector field consensus (SparseVFC) algorithm (Ma et al., 2013 <doi:10.1016/j.patcog.2013.05.017>) for robust vector field learning. Largely translated from the Matlab functions in <https://github.com/jiayi-ma/VFC>.

The SpectriPy package allows integration of Python-based MS analysis code with the Spectra package. Spectra objects can be converted into Python MS data structures. In addition, SpectriPy integrates and wraps the similarity scoring and processing/filtering functions from the Python matchms package into R.

This package provides a suite of functions that allow a full, fast, and efficient Bayesian treatment of the Bradley--Terry model. Prior assumptions about the model parameters can be encoded through a multivariate normal prior distribution. Inference is performed using a latent variable representation of the model.

spacetime provides classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal matching or aggregation, retrieving coordinates, print, summary, etc.

Test and estimates of location, tests of independence, tests of sphericity and several estimates of shape all based on spatial signs, symmetrized signs, ranks and signed ranks. For details, see Oja and Randles (2004) <doi:10.1214/088342304000000558> and Oja (2010) <doi:10.1007/978-1-4419-0468-3>.

The Robots Exclusion Protocol <https://www.robotstxt.org/orig.html> documents a set of standards for allowing or excluding robot/spider crawling of different areas of site content. Tools are provided which wrap The rep-cpp <https://github.com/seomoz/rep-cpp> C++ library for processing these robots.txt files.

It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, makes so-called spiral graph or spiral chart. It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high resolution. 2. It is efficient for time series data to reveal periodic patterns.

Efficient procedure for fitting regularization paths between L1 and L0, using the MC+ penalty of Zhang, C.H. (2010)<doi:10.1214/09-AOS729>. Implements the methodology described in Mazumder, Friedman and Hastie (2011) <DOI: 10.1198/jasa.2011.tm09738>. Sparsenet computes the regularization surface over both the family parameter and the tuning parameter by coordinate descent.

Visualization and analysis of spatially resolved transcriptomics data. The spatialGE R package provides methods for visualizing and analyzing spatially resolved transcriptomics data, such as 10X Visium, CosMx, or csv/tsv gene expression matrices. It includes tools for spatial interpolation, autocorrelation analysis, tissue domain detection, gene set enrichment, and differential expression analysis using spatial mixed models.

Fast computation of the required sample size or the achieved power, for GWAS studies with different types of covariate effects and different types of covariate-gene dependency structure. For the detailed description of the methodology, see Zhang (2022) "Power and Sample Size Computation for Genetic Association Studies of Binary Traits: Accounting for Covariate Effects" <arXiv:2203.15641>.

This package provides 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, plus the forward direction of the CIECAM02 color appearance model.

This package provides an implementation of the Sparse ICA method in Wang et al. (2024) <doi:10.1080/01621459.2024.2370593> for estimating sparse independent source components of cortical surface functional MRI data, by addressing a non-smooth, non-convex optimization problem through the relax-and-split framework. This method effectively balances statistical independence and sparsity while maintaining computational efficiency.