This package implements three bias-correction techniques from Battaglia et al. (2025 <doi:10.48550/arXiv.2402.15585>) to improve inference in regression models with covariates generated by AI or machine learning.

These guidelines are meant to provide a pragmatic, yet rigorous, help to drug developers and decision makers, since they are shaped by three fundamental ingredients: the clinically determined margin of detriment on OS that is unacceptably high (delta null); the benefit on OS that is plausible given the mechanism of action of the novel intervention (delta alt); and the quantity of information (i.e. survival events) it is feasible to accrue given the clinical and drug development setting. The proposed guidelines facilitate transparent discussions between stakeholders focusing on the risks of erroneous decisions and what might be an acceptable trade-off between power and the false positive error rate.

This package provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.

Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.

Extends the mlr3 package with a backend to transparently work with databases such as SQLite', DuckDB', MySQL', MariaDB', or PostgreSQL'. The package provides three additional backends: DataBackendDplyr relies on the abstraction of package dbplyr to interact with most DBMS. DataBackendDuckDB operates on DuckDB data bases and also on Apache Parquet files. DataBackendPolars operates on Polars data frames.

Fast imputations under the object-oriented programming paradigm. Moreover there are offered a few functions built to work with popular R packages such as data.table or dplyr'. The biggest improvement in time performance can be achieved for a calculation where a grouping variable is used. A single evaluation of a quantitative model for the multiple imputations is another major enhancement. A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.

This package provides tools for likelihood-based inference in one-dimensional stochastic differential equations with mixed effects using expectationâ maximization (EM) algorithms. The package supports Wiener and Ornsteinâ Uhlenbeck diffusion processes with user-specified drift functions, allowing flexible parametric forms including polynomial, exponential, and trigonometric structures. Estimation is performed via Markov chain Monte Carlo EM.

Researchers often need to calculate body-size growth rates for individuals that do not have associated age data. These growth rates are based on mark-recapture data where an individual was captured and measured at time 1 then recaptured and measured at time 2. The sizes at each time and amount of time between captures can be used to calculate growth rates. MRgrowth follows the approach in Edmonds et al. (2021) <doi:10.1371/journal.pone.0259978> and provides functions to calculate growth using three formulas, the Faben's reformulation of the von Bertalanffy formula, the Gompertz formula, and a logistic formula.

This package provides functionality to generate compound optimal designs for targeting the multiple experimental objectives directly, ensuring that the full set of research questions is answered as economically as possible. Designs can be found using point or coordinate exchange algorithms combining estimation, inference and lack-of-fit criteria that account for model inadequacy. Details and examples are given by Koutra et al. (2024) <doi:10.48550/arXiv.2412.17158>.

This package implements methodologies for modelling interval data by Normal and Skew-Normal distributions, considering appropriate parameterizations of the variance-covariance matrix that takes into account the intrinsic nature of interval data, and lead to four different possible configuration structures. The Skew-Normal parameters can be estimated by maximum likelihood, while Normal parameters may be estimated by maximum likelihood or robust trimmed maximum likelihood methods.

Function ModEstM() is the only one of this package, it estimates the modes of an empirical univariate distribution. It relies on the stats::density() function, even for input control. Due to very good performance of the density estimation, computation time is not an issue. The multiple modes are handled using dplyr::group_by(). For conditions and rates of convergences, see Eddy (1980) <doi:10.1214/aos/1176345080>.

Mask ranges based on expert knowledge or remote sensing layers. These tools can be combined to quantitatively and reproducibly generate a new map or to update an existing map. Methods include expert opinion and data-driven tools to generate thresholds for binary masks.

This package implements a general interface for model-based estimations for a wide variety of models, used in the computation of marginal means, contrast analysis and predictions. For a list of supported models, see insight::supported_models()'.

This package implements a high dimensional mediation analysis algorithm using Local False Discovery Rates. The methodology is described in Roy and Zhang (2024) <doi:10.48550/arXiv.2402.13933>.

User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis model; - generalised linear mixed model; - logistic regression with penalised likelihood for rare events; - Hartung-Knapp method for random effects model; - Kenward-Roger method for random effects model; - prediction interval and density of the prediction distribution; - expected proportion of comparable studies with clinically important benefit or harm; - statistical tests for funnel plot asymmetry; - trim-and-fill method to evaluate bias in meta-analysis; - meta-regression; - cumulative meta-analysis and leave-one-out meta-analysis; - import data from RevMan 5'; - produce forest plot summarising several (subgroup) meta-analyses.

This package provides a formula-driven framework for maximizing target functions via the minorization-maximization (MM) algorithm. The package represents the target as a symbolic expression tree, infers its curvature via disciplined-convex-programming rules, and constructs a separable surrogate at each iterate using only Jensen's inequality and the supporting hyperplane. The driver maximizes the surrogate via block-coordinate Newton with line search, falling back to a multivariate step on any non-separable residue. A formula interface accepts standard R expressions (including `sum()` reductions and `X %*% theta` design-matrix products) so statistical models such as Poisson regression can be written in one line.

Mass-balance-adjusted Regression algorithm for streamflow reconstruction at sub-annual resolution (e.g., seasonal or monthly). The algorithm implements a penalty term to minimize the differences between the total sub-annual flows and the annual flow. The method is described in Nguyen et al (2020) <DOI:10.1002/essoar.10504791.1>.

This package provides a minimal-dependency client for the Matrix Client-Server HTTP API <https://spec.matrix.org/>, suitable for talking to a Synapse <https://element-hq.github.io/synapse/> or Conduit <https://conduit.rs/> homeserver. Covers login, room management, message send and history, media upload or download, and the transport endpoints needed to coordinate end-to-end encryption (device-key and one-time-key publication, key query and claim, to-device events). Encryption itself is out of scope; pair with a separate crypto package.

Inference of a multi-states birth-death model from a phylogeny, comprising a number of states N, birth and death rates for each state and on which edges each state appears. Inference is done using a hybrid approach: states are progressively added in a greedy approach. For a fixed number of states N the best model is selected via maximum likelihood. Reference: J. Barido-Sottani, T. G. Vaughan and T. Stadler (2018) <doi:10.1098/rsif.2018.0512>.

This group of functions simplifies the creation of linked micromap plots. Please see <https://www.jstatsoft.org/v63/i02/> for additional details.

This package provides estimation and leave-one-cluster-out jackknife standard errors for four longitudinal cluster-randomized trial estimands: horizontal individual average treatment effect (h-iATE), horizontal cluster average treatment effect (h-cATE), vertical individual average treatment effect (v-iATE), and vertical cluster-period average treatment effect (v-cATE), using unadjusted and augmented (model-robust standardization) estimators. The working model may be fit using linear mixed models for continuous outcomes or generalized estimating equations and generalized linear mixed models for binary outcomes. Period inclusion for aggregation is determined automatically: only periods with both treated and control clusters are included in the construction of the marginal means and treatment effect contrasts. See Fang et al. (2025) <doi:10.48550/arXiv.2507.17190>.

Estimates Variable Length Markov Chains (VLMC) models and VLMC with covariates models from discrete sequences. Supports model selection via information criteria and simulation of new sequences from an estimated model. See Bühlmann, P. and Wyner, A. J. (1999) <doi:10.1214/aos/1018031204> for VLMC and Zanin Zambom, A., Kim, S. and Lopes Garcia, N. (2022) <doi:10.1111/jtsa.12615> for VLMC with covariates.

Fit and plot macroecological patterns predicted by the Maximum Entropy Theory of Ecology (METE).

Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, Roberts et al. (2023) <doi:10.1002/eap.2788>, and Hostetler et al. (2025) <doi:10.1111/2041-210X.14467> for details on some of these methods.