An implementation of EDM algorithms based on research software developed at the Sugihara Lab ('UCSD/SIO'). Primary methods include Simplex projection from Sugihara & May (1990) <doi:10.1038/344734a0>, Sequential locally-weighted global linear maps S-map': Sugihara (1994) <doi:10.1098/rsta.1994.0106>, Convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, Multiview embedding from Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.

Implementation of an alternating direction method of multipliers algorithm for fitting a linear model with tree-based lasso regularization, which is proposed in Algorithm 1 of Yan and Bien (2020) <doi:10.1080/01621459.2020.1796677>. The package allows efficient model fitting on the entire 2-dimensional regularization path for large datasets. The complete set of functions also makes the entire process of tuning regularization parameters and visualizing results hassle-free.

Generates pseudo-random vectors that follow an arbitrary von Mises-Fisher distribution on a sphere. This method is fast and efficient when generating a large number of pseudo-random vectors. Functions to generate random variates and compute density for the distribution of an inner product between von Mises-Fisher random vector and its mean direction are also provided. Details are in Kang and Oh (2024) <doi:10.1007/s11222-024-10419-3>.

This package provides a Perl interface (Perl::Rename) as well as a command-line utility (rename) that can rename multiple files at once based on a Perl regular expression.

Rdfind is a command line tool that finds duplicate files based on their content instead of their file names. It is useful for compressing backup directories or just finding duplicate files.

This package provides an interface to Amazon Web Services, including storage, database, and compute services, such as Simple Storage Service (S3), DynamoDB NoSQL database, and Lambda functions-as-a-service.

UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.

Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community <https://docs.airr-community.org>.

This package provides a wrapper for ada-url', a WHATWG compliant and fast URL parser written in modern C++'. Also contains auxiliary functions such as a public suffix extractor.

This package provides functions for Maximum Likelihood Estimation, Markov Chain Monte Carlo, finding confidence intervals. The implementation is heavily based on the original Fortran source code translated to R.

This package provides a toolkit for computing and visualizing CAPL-2 (Canadian Assessment of Physical Literacy, Second Edition; <https://www.capl-eclp.ca>) scores and interpretations from raw data.

Estimating the number of factors in Exploratory Factor Analysis (EFA) with out-of-sample prediction errors using a cross-validation scheme. Haslbeck & van Bork (Preprint) <https://psyarxiv.com/qktsd>.

This package implements a path algorithm for the Fused Lasso Signal Approximator. For more details see the help files or the article by Hoefling (2009) <arXiv:0910.0526>.

Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://www.scienceverse.org/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.

The gene-set distance analysis of omic data is implemented by generalizing distance correlations to evaluate the association of a gene set with categorical and censored event-time variables.

Supplies a set of functions to interface with bikeshare data following the General Bikeshare Feed Specification, allowing users to query and accumulate tidy datasets for specified cities/bikeshare programs.

Tool for diagnosing table joins. It combines the speed of `collapse` and `data.table`, the flexibility of `dplyr`, and the diagnosis and features of the `merge` command in `Stata`.

To test if a tensor time series following a Tucker-decomposition factor model has a Kronecker product structure. Supplementary functions for tensor reshape and its reversal are also included.

This is a Neural Network regression model implementation using Keras', consisting of 10 Long Short-Term Memory layers that are fully connected along with the rest of the inputs.

An interface for interacting with OSF (<https://osf.io>). osfr enables you to access open research materials and data, or create and manage your own private or public projects.

Permutation based Kolmogorov-Smirnov test for paired samples. The test was proposed by Wang W.S., Amsler C. and Schmidt, P. (2025) <doi:10.1007/s00181-025-02779-0>.

The Penn World Table 9.x (<http://www.ggdc.net/pwt/>) provides information on relative levels of income, output, inputs, and productivity for 182 countries between 1950 and 2017.

This package provides quasi-Newton methods to minimize partially separable functions. The methods are largely described by Nocedal and Wright (2006) <doi:10.1007/978-0-387-40065-5>.

This package provides a set of consistent, opinionated functions to quickly check objects, convert them to the desired configuration, or deliver informative error messages when that is not possible.