This package provides a programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.

It computes the Schmidt decomposition of bipartite quantum systems, discrete or continuous, and their respective entanglement metrics. See Artur Ekert, Peter L. Knight (1995) <doi:10.1119/1.17904> for more details.

Network-based regularization has achieved success in variable selection for high-dimensional biological data due to its ability to incorporate correlations among genomic features. This package provides procedures of network-based variable selection for generalized linear models (Ren et al. (2017) <doi:10.1186/s12863-017-0495-5> and Ren et al.(2019) <doi:10.1002/gepi.22194>). Continuous, binary, and survival response are supported. Robust network-based methods are available for continuous and survival responses.

This package provides an interface to the Vamp audio analysis plugin system <https://www.vamp-plugins.org/> developed by Queen Mary University of London's Centre for Digital Music. Enables loading and running Vamp plugins for various audio analysis tasks including tempo detection, onset detection, spectral analysis, and audio feature extraction. Supports mono and stereo audio with automatic channel adaptation and domain conversion.

Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about RAVE project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see citation("ravetools") for details.

This package provides a wrapper for the Deutsche Nationalbibliothek (German National Library) API', available at <https://www.dnb.de/EN/Home/home_node.html>. The German National Library is the German central archival library, collecting, archiving, bibliographically classifying all German and German-language publications, foreign publications about Germany, translations of German works, and the works of German-speaking emigrants published abroad between 1933 and 1945.

This package provides tools for creating data validation pipelines and tidy reports. This package offers a framework for exploring and validating data frame like objects using dplyr grammar of data manipulation.

This package provides a carbon-water coupled model (TRIPLEX-CW-Flux) is based on two well-established models, TRIPLEX-Flux model and Penmanâ Monteith model, integrates soil water and water vapor pressure deficits into the stomata conductance submodule to estimate net ecosystem production and evapotranspiration in forest ecosystems.<https://github.com/ShulanSun/rTRIPLEX_CW_Flux>.

An implementation of a stochastic heuristic method for performing multidimensional function optimization. The method is inspired in the Cross-Entropy Method. It does not relies on derivatives, neither imposes particularly strong requirements into the function to be optimized. Additionally, it takes profit from multi-core processing to enable optimization of time-consuming functions.

Code to facilitate simulation and inference when connectivity is defined by underlying random walks. Methods for spatially-correlated pairwise distance data are especially considered. This provides core code to conduct analyses similar to that in Hanks and Hooten (2013) <doi:10.1080/01621459.2012.724647>.

The renewal Hawkes (RHawkes) process (Wheatley, Filimonov, and Sornette, 2016 <doi:10.1016/j.csda.2015.08.007>) is an extension to the classical Hawkes self-exciting point process widely used in the modelling of clustered event sequence data. This package provides functions to simulate the RHawkes process with a given immigrant hazard rate function and offspring birth time density function, to compute the exact likelihood of a RHawkes process using the recursive algorithm proposed by Chen and Stindl (2018) <doi:10.1080/10618600.2017.1341324>, to compute the Rosenblatt residuals for goodness-of-fit assessment, and to predict future event times based on observed event times up to a given time. A function implementing the linear time RHawkes process likelihood approximation algorithm proposed in Stindl and Chen (2021) <doi:10.1007/s11222-021-10002-0> is also included.

This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).

This package provides functions for the complete analysis of respiratory data. Consists of a set of functions that allow to preprocessing respiratory data, calculate both regular statistics and nonlinear statistics, conduct group comparison and visualize the results. Especially, Power Spectral Density ('PSD') (A. Eke (2000) <doi:10.1007/s004249900135>), MultiScale Entropy(MSE) ('Madalena Costa(2002) <doi:10.1103/PhysRevLett.89.068102>) and MultiFractal Detrended Fluctuation Analysis(MFDFA) ('Jan W.Kantelhardt (2002) <doi:10.1016/S0378-4371(02)01383-3>) were applied for the analysis of respiratory data.

Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal . Details refer to (Peter Wittek, et al (2017)) <doi:10.18637/jss.v078.i09>.

This holds r markdown and quarto templates for academic papers and slide decks. It also has templates to create research projects which contain academic papers as vignettes.

Truncated Newton function minimization with bounds constraints based on the Matlab'/'Octave codes of Stephen Nash.

Access to some of the C level functions of the xts package. In its current state, the package is mostly a proof-of-concept to support adding useful functions, and does not yet add any of its own.

This package provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.

Simulation of random orthonormal matrices from linear and quadratic exponential family distributions on the Stiefel manifold. The most general type of distribution covered is the matrix-variate Bingham-von Mises-Fisher distribution. Most of the simulation methods are presented in Hoff(2009) "Simulation of the Matrix Bingham-von Mises-Fisher Distribution, With Applications to Multivariate and Relational Data" <doi:10.1198/jcgs.2009.07177>. The package also includes functions for optimization on the Stiefel manifold based on algorithms described in Wen and Yin (2013) "A feasible method for optimization with orthogonality constraints" <doi:10.1007/s10107-012-0584-1>.

This package provides a collection of programs for plotting SKEW-T,log p diagrams and wind profiles for data collected by radiosondes (the typical weather balloon-borne instrument). The format of this plot with companion lines to assess atmospheric stability are both standard in meteorology and difficult to create from basic graphics functions. Hence this package. One novel feature is being able add several profiles to the same plot for comparison. Use "help(ExampleSonde)" for an explanation of the variables needed and how they should be named in a data frame. See <https://github.com/dnychka/Radiosonde> for the package home page.

Many packages in the r-dcm family take similar arguments, which are checked for expected structures and values. Rather than duplicating code across several packages, commonly used check functions are included here. This package can then be imported to access the check functions in other packages.

Kiefer-Wolfowitz maximum likelihood estimation for mixture models and some other density estimation and regression methods based on convex optimization. See Koenker and Gu (2017) REBayes: An R Package for Empirical Bayes Mixture Methods, Journal of Statistical Software, 82, 1--26, <DOI:10.18637/jss.v082.i08>.

Allows loading and displaying an Observable notebook (online JavaScript notebooks powered by <https://observablehq.com>) as an HTML Widget in an R session, shiny application or rmarkdown document.

The visualization tool offers a nuanced understanding of regression dynamics, going beyond traditional per-unit interpretation of continuous variables versus categorical ones. It highlights the impact of unit changes as well as larger shifts like interquartile changes, acknowledging the distribution of empirical data. Furthermore, it generates visualizations depicting alterations in Odds Ratios for predictors across minimum, first quartile, median, third quartile, and maximum values, aiding in comprehending predictor-outcome interplay within empirical data distributions, particularly in logistic regression frameworks.