Bayesian trophic position models using stan by leveraging brms for stable isotope data. Trophic position models are derived by using equations from Post (2002) <doi:10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2>, Vander Zanden and Vadeboncoeur (2002) <doi:10.1890/0012-9658(2002)083[2152:FAIOBA]2.0.CO;2>, and Heuvel et al. (2024) <doi:10.1139/cjfas-2024-0028>.

Analyze Peptide Array Data and characterize peptide sequence space. Allows for high level visualization of global signal, Quality control based on replicate correlation and/or relative Kd, calculation of peptide Length/Charge/Kd parameters, Hits selection based on RFU Signal, and amino acid composition/basic motif recognition with RFU signal weighting. Basic signal trends can be used to generate peptides that follow the observed compositional trends.

The Zarr specification is widely used to build libraries for the storage and retrieval of n-dimensional array data from data stores ranging from local file systems to the cloud. This package is a native Zarr implementation in R with support for all required features of Zarr version 3. It is designed to be extensible such that new stores, codecs and extensions can be added easily.

Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics.

This package lets you analyze response times and accuracies from psychological experiments with the linear ballistic accumulator (LBA) model from Brown and Heathcote (2008). The LBA model is optionally fitted with explanatory variables on the parameters such as the drift rate, the boundary and the starting point parameters. A log-link function on the linear predictors can be used to ensure that parameters remain positive when needed.

Enables binary package installations on Linux distributions. Provides functions to manage packages via the distribution's package manager. Also provides transparent integration with R's install.packages() and a fallback mechanism. When installed as a system package, interacts with the system's package manager without requiring administrative privileges via an integrated D-Bus service; otherwise, uses sudo. Currently, the following backends are supported: DNF, APT, ALPM.

Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models. Provides tools to analyse intraspecific trait variability and its consequences for community assembly. Implements a framework using individual-level trait data to decompose variance at the population, species, and community levels. Methods are described in Taudiere and Violle (2016) <doi:10.1111/ecog.01433>.

This package provides a shortcut procedure is proposed to implement closed testing for large-scale multiple testings, especially with the global test. This shortcut is asymptotically equivalent to closed testing and post hoc. Users could detect any possible sets of features or pathways with family-wise error rate controlled. The global test is powerful to detect associations between a group of features and an outcome of interest.

This package provides a Bayesian hierarchical model for clustering dissimilarity data using the Dirichlet process. The latent configuration of objects and the number of clusters are automatically inferred during the fitting process. The package supports multiple models which are available to detect clusters of various shapes and sizes using different covariance structures. Additional functions are included to ensure adequate model fits through prior and posterior predictive checks.

This package provides a revision to the stats::ks.test() function and the associated ks.test.Rd help page. With one minor exception, it does not change the existing behavior of ks.test(), and it adds features necessary for doing one-sample tests with hypothesized discrete distributions. The package also contains cvm.test(), for doing one-sample Cramer-von Mises goodness-of-fit tests.

Wrapper functions that interface with FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used neuroimaging software, using system commands. The goal is to be able to interface with FSL completely in R, where you pass R objects of class nifti', implemented by package oro.nifti', and the function executes an FSL command and returns an R object of class nifti if desired.

Penalised likelihood estimation of a covariance matrix via the ridge-regularised covglasso estimator described in Cibinel et al. (2024) <doi:10.48550/arXiv.2410.02403>. Based on the C++ code of the R package covglasso (by Michael Fop, <https://orcid.org/0000-0003-3936-2757>) and the R code of icf (by Mathias Drton, <https://orcid.org/0000-0001-5614-3025>) within the R package ggm'.

Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects. Inputs are : data frame, RDA (package vegan') and PCA (package FactoMineR') objects. Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.

Implementation of the GTE (Group Technical Effects) model for single-cell data. GTE is a quantitative metric to assess batch effects for individual genes in single-cell data. For a single-cell dataset, the user can calculate the GTE value for individual features (such as genes), and then identify the highly batch-sensitive features. Removing these highly batch-sensitive features results in datasets with low batch effects.

The haversine is a function used to calculate the distance between a pair of latitude and longitude points while accounting for the assumption that the points are on a spherical globe. This package provides a fast, dataframe compatible, haversine function. For the first publication on the haversine calculation see Joseph de Mendoza y RÃ os (1795) <https://books.google.cat/books?id=030t0OqlX2AC> (In Spanish).

Miscellaneous functions for classification and visualization, e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes, an interface to svmlight and stepclass() wrapper variable selection for supervised classification, partimat() visualization of classification rules and shardsplot() of cluster results as well as kmodes() clustering for categorical data, corclust() variable clustering, variable extraction from different variable clustering models and weight of evidence preprocessing.

Density evaluation and random number generation for the Matrix-Normal Inverse-Wishart (MNIW) distribution, as well as the the Matrix-Normal, Matrix-T, Wishart, and Inverse-Wishart distributions. Core calculations are implemented in a portable (header-only) C++ library, with matrix manipulations using the Eigen library for linear algebra. Also provided is a Gibbs sampler for Bayesian inference on a random-effects model with multivariate normal observations.

Test whether equality and order constraints hold for all individuals simultaneously by comparing Bayesian mixed models through Bayes factors. A tutorial style vignette and a quickstart guide are available, via vignette("manual", "quid"), and vignette("quickstart", "quid") respectively. See Haaf and Rouder (2017) <doi:10.1037/met0000156>; Haaf, Klaassen and Rouder (2019) <doi:10.31234/osf.io/a4xu9>; and Rouder & Haaf (2021) <doi:10.5334/joc.131>.

This package creates stratum orthogonal arrays (also known as strong orthogonal arrays). These are arrays with more levels per column than the typical orthogonal array, and whose low order projections behave like orthogonal arrays, when collapsing levels to coarser strata. Details are described in Groemping (2022) "A unifying implementation of stratum (aka strong) orthogonal arrays" <http://www1.bht-berlin.de/FB_II/reports/Report-2022-002.pdf>.

Markov chain Monte Carlo samplers for posterior simulations of conjugate Bayesian nonparametric mixture models. Functionality is provided for Gibbs sampling as in Algorithm 3 of Neal (2000) <DOI:10.1080/10618600.2000.10474879>, restricted Gibbs merge-split sampling as described in Jain & Neal (2004) <DOI:10.1198/1061860043001>, and sequentially-allocated merge-split sampling <DOI:10.1080/00949655.2021.1998502>, as well as summary and utility functions.

We utilize approximate Bayesian machinery to fit two-level conjugate hierarchical models on overdispersed Gaussian, Poisson, and Binomial data and evaluates whether the resulting approximate Bayesian interval estimates for random effects meet the nominal confidence levels via frequency coverage evaluation. The data that Rgbp assumes comprise observed sufficient statistic for each random effect, such as an average or a proportion of each group, without population-level data. The approximate Bayesian tool equipped with the adjustment for density maximization produces approximate point and interval estimates for model parameters including second-level variance component, regression coefficients, and random effect. For the Binomial data, the package provides an option to produce posterior samples of all the model parameters via the acceptance-rejection method. The package provides a quick way to evaluate coverage rates of the resultant Bayesian interval estimates for random effects via a parametric bootstrapping, which we call frequency method checking.

The Ziggurat pseudo-random number generator (or PRNG) offers a lightweight and very fast PRNG for the normal, exponential, and uniform distributions. It is provided here in a small zero-dependency package. It can be used from R as well as from C/C++ code in other packages as is demonstrated by four included sample packages using four distinct methods to use the PRNG presented here in client package.

Rapidly create a GUI for a function you created by automatically creating widgets for arguments of the function. This package automatically parses help routines for context-sensitive help to these arguments. The interface is essentially a wrapper to some Tcl/Tk routines to both simplify and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be incorporated into the interface for greater customization for the more experienced.

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).