Eases the use of ecotoxicological effect models. Can simulate common toxicokinetic-toxicodynamic (TK/TD) models such as General Unified Threshold models of Survival (GUTS) and Lemna. It can derive effects and effect profiles (EPx) from scenarios. It supports the use of tidyr workflows employing the pipe symbol. Time-consuming tasks can be parallelized.

This package provides a fast and general implementation of the Elston-Stewart algorithm that can calculate the likelihoods of large and complex pedigrees. References for the Elston-Stewart algorithm are Elston & Stewart (1971) <doi:10.1159/000152448>, Lange & Elston (1975) <doi:10.1159/000152714> and Cannings et al. (1978) <doi:10.2307/1426718>.

We provide the main R functions to compute the posterior interval for the noncentrality parameter of the chi-squared distribution. The skewness estimate of the posterior distribution is also available to improve the coverage rate of posterior intervals. Details can be found in Du and Hu (2022) <doi:10.1080/01621459.2020.1777137>.

This package provides a neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is described in Dahl, Johnson, and Andros (2023) "Comparison and Bayesian Estimation of Feature Allocations" <doi:10.1080/10618600.2023.2204136>.

Make computer vision tasks approachable in R by leveraging Large Language Models. Providing fine-tuned prompts, boilerplate functions, and input/output helpers for common computer vision workflows, such as classifying and describing images. Functions are designed to take images as input and return structured data, helping users build practical applications with minimal code.

Generate concentration-time profiles from linear pharmacokinetic (PK) systems, possibly with first-order absorption or zero-order infusion, possibly with one or more peripheral compartments, and possibly under steady-state conditions. Single or multiple doses may be specified. Secondary (derived) PK parameters (e.g. Cmax, Ctrough, AUC, Tmax, half-life, etc.) are computed.

Given a postulated model and a set of data, the comparison density is estimated and the deviance test is implemented in order to assess if the data distribution deviates significantly from the postulated model. Finally, the results are summarized in a CD-plot as described in Algeri S. (2019) <arXiv:1906.06615>.

Compose generic monadic function pipelines with %>>% and %>-% based on implementing the S7 generics fmap() and bind(). Methods are provided for the built-in list type and the maybe class from the maybe package. The concepts are modelled directly after the Monad typeclass in Haskell, but adapted for idiomatic use in R.

Automates and standardizes the import of raw data from Oregon RFID (radio-frequency identification) ORMR (Oregon RFID Multi-Reader) and ORSR (Oregon RFID Single Reader) antenna readers. Compiled data can then be combined within multi-reader arrays for further analysis, including summarizing tag and reader detections, determining tag direction, and calculating antenna efficiency.

This package implements a simulation study to assess the strengths and weaknesses of causal inference methods for estimating policy effects using panel data. See Griffin et al. (2021) <doi:10.1007/s10742-022-00284-w> and Griffin et al. (2022) <doi:10.1186/s12874-021-01471-y> for a description of our methods.

Computes optimal axis-aligned hyperrectangles for discrete binary arrays and continuous regions defined by quadratic response functions. The package provides methods for discrete optimization, grid classification, continuous refinement, and exact global extrema calculations. Applications include the identification of practical operating regions within multivariate design spaces, including pharmaceutical development settings related to ICH Q8.

Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.

Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.

Build and run metaheuristic optimization algorithms as serializable component graphs executed by a Rust core, with reproducible, bit-exact trajectories shared across the R and Python frontends. Includes population and local-search algorithm presets, standard benchmark suites (BBOB, CEC 2014/2017/2022, TSP), multi-objective indicators, structural-bias diagnostics and statistical comparison tools.

This package provides a method to explore the treatment-covariate interactions in survival or generalized linear model (GLM) for continuous, binomial and count data arising from two or more treatment arms of a clinical trial. A permutation distribution approach to inference is implemented, based on permuting the covariate values within each treatment group.

Likelihood ratio and maximum likelihood statistics are provided that can be used as alternatives to p-values Colquhoun (2017) <doi:10.1098/rsos.171085>. Arguments can be either p-values or t-statistics. together with degrees of freedom. For the function tTOlr', the argument twoSided has the default twoSided = TRUE'.

Obtain United States map data frames of varying region types (e.g. county, state). The map data frames include Alaska and Hawaii conveniently placed to the bottom left, as they appear in most maps of the US. Convenience functions for plotting choropleths, visualizing spatial data, and working with FIPS codes are also provided.

Nonparametric estimation of discount functions and yield curves from transaction data of coupon paying bonds. Koo, B., La Vecchia, D., & Linton, O. B. (2021) <doi:10.1016/j.jeconom.2020.04.014> describe an application of this package using the Center for Research in Security Prices (CRSP) Bond Data and document its implementation.

This package provides a framework for Bayesian meta-analysis, including model estimation, prior specification, model comparison, prediction, summaries, visualizations, and diagnostics. The package fits single and model-averaged meta-analytic, meta-regression, multilevel and multivariate, publication bias adjusted, and generalized linear mixed models. The model-averaged meta-analytic models combine competing models based on their predictive performance, weight inference by posterior model probabilities, and test model components using Bayes factors (e.g., effect vs. no effect; Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022, <doi:10.1037/met0000405>; Bartoš et al., 2025, <doi:10.1037/met0000737>). Users can specify flexible prior distributions for effect sizes, heterogeneity, publication bias (including selection models and PET-PEESE), and moderators.

This package provides a proof of concept implementation of regularized non-negative matrix factorization optimization. A non-negative matrix factorization factors non-negative matrix Y approximately as L R, for non-negative matrices L and R of reduced rank. This package supports such factorizations with weighted objective and regularization penalties. Allowable regularization penalties include L1 and L2 penalties on L and R, as well as non-orthogonality penalties. This package provides multiplicative update algorithms, which are a modification of the algorithm of Lee and Seung (2001) <http://papers.nips.cc/paper/1861-algorithms-for-non-negative-matrix-factorization.pdf>, as well as an additive update derived from that multiplicative update. See also Pav (2024) <doi:10.48550/arXiv.2410.22698>.

This package provides a compact R interface for performing tensor calculations. This is achieved by allowing (upper and lower) index labeling of arrays and making use of Ricci calculus conventions to implicitly trigger contractions and diagonal subsetting. Explicit tensor operations, such as addition, subtraction and multiplication of tensors via the standard operators, raising and lowering indices, taking symmetric or antisymmetric tensor parts, as well as the Kronecker product are available. Common tensors like the Kronecker delta, Levi Civita epsilon, certain metric tensors, the Christoffel symbols, the Riemann as well as Ricci tensors are provided. The covariant derivative of tensor fields with respect to any metric tensor can be evaluated. An effort was made to provide the user with useful error messages.

This package is an interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.

Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R.

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.