Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.

Calculate point estimates of and valid confidence intervals for longitudinal summaries of nonparametric, algorithm-agnostic variable importance measures. For more details, see Williamson et al. (2024) <doi:10.48550/arXiv.2311.01638>.

This package provides functions to prepare, visualize, and analyse diachronic network data on local political actors, with a particular focus on the development of local party systems and identification of actor groups. Formalizes and automates a continuity diagram method that has been previously applied in research on Czech local politics, e.g. Bubenicek and Kubalek (2010, ISSN:1803-8220), Kubalek and Bubenicek (2012, ISSN:1803-8220), and Cmejrek, Bubenicek, and Copik (2010, ISBN:978-80-247-3061-5). The package also includes several example datasets derived from Czech municipal elections, compiled from official election results, field research, and previously published case studies on Czech local politics.

Flexible procedures to compute local density-based outlier scores for ranking outliers. Both exact and approximate nearest neighbor search can be implemented, while also accommodating multiple neighborhood sizes and four different local density-based methods. It allows for referencing a random subsample of the input data or a user specified reference data set to compute outlier scores against, so both unsupervised and semi-supervised outlier detection can be implemented.

The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.

Implementation of the Swiss Confederation's standard analysis model for salary analyses <www.ebg.admin.ch/en/equal-pay-analysis-with-logib> in R. The analysis is run at company-level and the model is intended for medium-sized and large companies. It can technically be used with 50 or more employees (apprentices, trainees/interns and expats are not included in the analysis). Employees with at least 100 employees are required by the Gender Equality Act to conduct an equal pay analysis. This package allows users to run the equal salary analysis in R, providing additional transparency with respect to the methodology and simple automation possibilities.

This package provides a statistical learning method that tries to find the best set of predictors and interactions between predictors for modeling binary or quantitative response data in a decision tree. Several search algorithms and ensembling techniques are implemented allowing for finetuning the method to the specific problem. Interactions with quantitative covariables can be properly taken into account by fitting local regression models. Moreover, a variable importance measure for assessing marginal and interaction effects is provided. Implements the procedures proposed by Lau et al. (2024, <doi:10.1007/s10994-023-06488-6>).

Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear Poisson model where main row and column effects, as well as effects of known covariates and interaction terms can be fitted. The estimation procedure is based on the convex optimization of the Poisson loss penalized by a Lasso type penalty and a nuclear norm. LORI returns estimates of main effects, covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure. The methods are described in Robin, Josse, Moulines and Sardy (2019) <doi:10.1016/j.jmva.2019.04.004>.

This package provides a flexible approach, inspired by cosinor regression, for differential analysis of rhythmic transcriptome data. See Singer and Hughey (2018) <doi:10.1177/0748730418813785>.

Fit linear models based on periodic splines, moderate model coefficients using multivariate adaptive shrinkage, then compute properties of the moderated curves.

Given independent and identically distributed observations X(1), ..., X(n), allows to compute the maximum likelihood estimator (MLE) of probability mass function (pmf) under the assumption that it is log-concave, see Weyermann (2007) and Balabdaoui, Jankowski, Rufibach, and Pavlides (2012). The main functions of the package are logConDiscrMLE that allows computation of the log-concave MLE, logConDiscrCI that computes pointwise confidence bands for the MLE, and kInflatedLogConDiscr that computes a mixture of a log-concave PMF and a point mass at k.

Estimation of Latent Order Logistic (LOLOG) Models for Networks. LOLOGs are a flexible and fully general class of statistical graph models. This package provides functions for performing MOM, GMM and variational inference. Visual diagnostics and goodness of fit metrics are provided. See Fellows (2018) <doi:10.48550/arXiv.1804.04583> for a detailed description of the methods.

This package provides density, distribution and random generation functions for the Linear Ballistic Accumulation (LBA) model, a widely used choice response time model in cognitive psychology. The package supports model specifications, parameter estimation, and likelihood computation, facilitating simulation and statistical inference for LBA-based experiments. For details on the LBA model, see Brown and Heathcote (2008) <doi:10.1016/j.cogpsych.2007.12.002>.

Computes the probability density function, the cumulative distribution function, the hazard rate function, the quantile function and random generation for Lindley Power Series distributions, see Nadarajah and Si (2018) <doi:10.1007/s13171-018-0150-x>.

This package provides functions for validating and normalizing bibliographic codes such as ISBN, ISSN, and LCCN. Also includes functions to communicate with the WorldCat API, translate Call numbers (Library of Congress and Dewey Decimal) to their subject classifications or subclassifications, and provides various loadable data files such call number / subject crosswalks and code tables.

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.

Computational routines for estimating local Gaussian parameters. Local Gaussian parameters are useful for characterizing and testing for non-linear dependence within bivariate data. See e.g. Tjostheim and Hufthammer, Local Gaussian correlation: A new measure of dependence, Journal of Econometrics, 2013, Volume 172 (1), pages 33-48 <DOI:10.1016/j.jeconom.2012.08.001>.

This package implements Lagrangian multiplier smoothing splines for flexible nonparametric regression and function estimation. Provides tools for fitting, prediction, and inference using a constrained optimization approach to enforce smoothness. Supports generalized linear models, Weibull accelerated failure time (AFT) models, quadratic programming problems, and customizable arbitrary correlation structures. Options for fitting in parallel are provided. The method builds upon the framework described by Ezhov et al. (2018) <doi:10.1515/jag-2017-0029> using Lagrangian multipliers to fit cubic splines. For more information on correlation structure estimation, see Searle et al. (2009) <ISBN:978-0470009598>. For quadratic programming and constrained optimization in general, see Nocedal & Wright (2006) <doi:10.1007/978-0-387-40065-5>. For a comprehensive background on smoothing splines, see Wahba (1990) <doi:10.1137/1.9781611970128> and Wood (2006) <ISBN:978-1584884743> "Generalized Additive Models: An Introduction with R".

Implementations of Hurst exponent estimators based on the relationship between wavelet lifting scales and wavelet energy of Knight et al (2017) <doi:10.1007/s11222-016-9698-2>.

This package provides tools to retrieve and summarize taxonomic information and synonymy data for reptile species using data scraped from The Reptile Database website (<https://reptile-database.reptarium.cz/>). Outputs include clean and structured data frames useful for ecological, evolutionary, and conservation research.

An implementation of list comprehensions as purely syntactic sugar with a minor runtime overhead. It constructs nested for-loops and executes the byte-compiled loops to collect the results.

Assess the proportion of treatment effect explained by a longitudinal surrogate marker as described in Agniel D and Parast L (2021) <doi:10.1111/biom.13310>; and estimate the treatment effect on a longitudinal surrogate marker as described in Wang et al. (2025) <doi:10.1093/biomtc/ujaf104>. A tutorial for this package can be found at <https://www.laylaparast.com/longsurr>.

This package performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), and Bayesian optimal interval (BOIN) trials. For count data, it can design group sequential trials for negative binomial endpoints with censoring. Additionally, it facilitates group sequential equivalence trials for all supported data types. Moreover, it can design adaptive group sequential trials for changes in sample size, error spending function, number and spacing or future looks. Finally, it offers various options for adjusted p-values, including graphical and gatekeeping procedures.

This package implements a local indicator of stratified power to analyze local spatial stratified association and demonstrate how spatial stratified association changes spatially and in local regions, as outlined in Hu et al. (2024) <doi:10.1080/13658816.2024.2437811>.