This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

This package conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.

This package provides an infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). It also provides C implementations of the association mining algorithms Apriori and Eclat.

This package provides key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.

RESTinio is a header-only C++14 library that gives you an embedded HTTP/Websocket server. It is based on standalone version of ASIO and targeted primarily for asynchronous processing of HTTP-requests.

RESTinio is a header-only C++14 library that gives you an embedded HTTP/Websocket server. It is based on standalone version of ASIO and targeted primarily for asynchronous processing of HTTP-requests.

Spy is a mocking library. By default, it will raise an error if you attempt to stub a method that doesn't exist or call the stubbed method with the wrong arity.

ruby-unf is a wrapper library to bring Unicode Normalization Form support to both Ruby and JRuby. It uses unf_ext on CRuby and java.text.Normalizer on JRuby.

This is a meta-package designed to support the installation of Rmosek (>= 6.0) and bring the optimization facilities of MOSEK (>= 6.0) to the R-language. The interface supports large-scale optimization of many kinds: Mixed-integer and continuous linear, second-order cone, exponential cone and power cone optimization, as well as continuous semidefinite optimization. Rmosek and the R-language are open-source projects. MOSEK is a proprietary product, but unrestricted trial and academic licenses are available.

Implementation of a variety of methods to compute the robustness of ecological interaction networks with binary interactions as described in <doi:10.1002/env.2709>. In particular, using the Stochastic Block Model and its bipartite counterpart, the Latent Block Model to put a parametric model on the network, allows the comparison of the robustness of networks differing in species richness and number of interactions. It also deals with networks that are partially sampled and/or with missing values.

Rserve acts as a socket server (TCP/IP or local sockets) which allows binary requests to be sent to R. Every connection has a separate workspace and working directory. Client-side implementations are available for popular languages such as C/C++ and Java, allowing any application to use facilities of R without the need of linking to R code. Rserve supports remote connection, user authentication and file transfer. A simple R client is included in this package as well.

rg is an Emacs search package based on the ripgrep command line tool. It allows one to interactively search based on the editing context then refine or modify the search results.

This package provides a fast and intuitive batch effect removal tool for single-cell data. BBKNN is originally used in the scanpy python package, and now can be used with Seurat seamlessly.

R client for Bender Hyperparameters optimizer : <https://bender.dreem.com> The R client allows you to communicate with the Bender API and therefore submit some new trials within your R script itself.

The Bloom Detecting Algorithm enables the detection of blooms within a time series of species abundance and extracts 22 phenological variables. For details, see Karasiewicz et al. (2022) <doi:10.3390/jmse10020174>.

R/C++ implementation of the model proposed by Primiceri ("Time Varying Structural Vector Autoregressions and Monetary Policy", Review of Economic Studies, 2005), with functionality for computing posterior predictive distributions and impulse responses.

This package provides a way to reduce model objects to necessary parts, making them easier to work with, store, share and simulate multiple values for new responses while allowing for parameter uncertainty.

The implementation of bias-corrected sandwich variance estimators for the analysis of cluster randomized trials with time-to-event outcomes using the marginal Cox model, proposed by Wang et al. (under review).

Fast and memory-efficient (or cheap') tools to facilitate efficient programming, saving time and memory. It aims to provide cheaper alternatives to common base R functions, as well as some additional functions.

Evaluates the performance of binary classifiers. Computes confusion measures (TP, TN, FP, FN), derived measures (TPR, FDR, accuracy, F1, DOR, ..), and area under the curve. Outputs are well suited for nested dataframes.

Chat with large language models from a range of providers including Claude <https://claude.ai>, OpenAI <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.

This package provides probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).

Command-line and shiny GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.

To create the multiple polygonal point layer for easily discernible shapes, we developed the package, it is like the geom_point of ggplot2'. It can be used to draw the scatter plot.