An implementation of representation-dependent gene level operations for genetic algorithms with genes representing permutations: Initialization of genes, mutation, and crossover. The crossover operation provided is position-based crossover (Syswerda, G., Chap. 21 in Davis, L. (1991, ISBN:0-442-00173-8). For mutation, several variants are included: Order-based mutation (Syswerda, G., Chap. 21 in Davis, L. (1991, ISBN:0-442-00173-8), randomized Lin-Kernighan heuristics (Croes, G. A. (1958) <doi:10.1287/opre.6.6.791> and Lin, S. and Kernighan. B. W. (1973) <doi:10.1287/opre.21.2.498>), and randomized greedy operators. A random mix operator for mutation selects a mutation variant randomly.

This package implements a probabilistic approach to time series forecasting combining XGBoost regression with conformal inference methods. The package provides functionality for generating predictive distributions, evaluating uncertainty, and optimizing hyperparameters using Bayesian, coarse-to-fine, or random search strategies.

Institutional performance assessment remains a key challenge to a multitude of stakeholders. Existing indicators such as h-type indicators, g-type indicators, and many others do not reflect expertise of institutions that defines their research portfolio. The package offers functionality to compute and visualise two novel indices: the x-index and the xd-index. The x-index evaluates an institution's scholarly expertise within a specific discipline or field, while the xd-index provides a broader assessment of overall scholarly expertise considering an institution's publication pattern and strengths across coarse thematic areas. These indices offer a nuanced understanding of institutional research capabilities, aiding stakeholders in research management and resource allocation decisions. Lathabai, H.H., Nandy, A., and Singh, V.K. (2021) <doi:10.1007/s11192-021-04188-3>. Nandy, A., Lathabai, H.H., and Singh, V.K. (2023) <doi:10.5281/zenodo.8305585>. This package provides the h-, g-, x-, xd-indices, and their variants for use with standard format of Web of Science (WoS) scrapped datasets.

Based on STATA xtsum command, it is used to compute summary statistics for a panel data set. It generates overall, between-group, and within-group statistics for specified variables in a panel data set, as presented in S. Porter (2023) <https://stephenporter.org/files/xtsum_handout.pdf>, StataCorp (2023) <https://www.stata.com/manuals/xtxtsum.pdf>.

Read and write XES Files to create event log objects used by the bupaR framework. XES (Extensible Event Stream) is the `IEEE` standard for storing and sharing event data (see <http://standards.ieee.org/findstds/standard/1849-2016.html> for more info).

This collection of gene representation-independent mechanisms for evolutionary and genetic algorithms for the R-package xega <https://CRAN.R-project.org/package=xega> contains four groups of functions: First, functions for selecting a gene in a population of genes according to its fitness value and for adaptive scaling of the fitness values as well as for performance optimization and measurement offer several variants for implementing the survival of the fittest. Second, evaluation functions for deterministic functions avoid recomputation. Evaluation of stochastic functions incrementally improve the estimation of the mean and variance of fitness values at almost no additional cost. Evaluation functions for gene repair handle error-correcting decoders. Third, timing and counting functions for profiling the algorithm pipeline are provided to assess bottlenecks in the algorithms. Fourth, a small collection of problem environments for function optimization, combinatorial optimization, and grammar-based genetic programming and grammatical evolution is provided for tutorial examples. For xega's architecture, see Geyer-Schulz, A. (2025) <doi:10.5445/IR/1000187255>. The methods in the package are described by the following references: Baker, James E. (1987, ISBN:978-08058-0158-8), De Jong, Kenneth A. (1975) <https://deepblue.lib.umich.edu/handle/2027.42/4507>, Geyer-Schulz, Andreas (1997, ISBN:978-3-7908-0830-X), Grefenstette, John J. (1987, ISBN:978-08058-0158-8), Grefenstette, John J. and Baker, James E. (1989, ISBN:1-55860-066-3), Holland, John (1975, ISBN:0-472-08460-7), Lau, H. T. (1986) <doi:10.1007/978-3-642-61649-5>, Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005) <doi:10.1007/3-540-31306-0>, Reynolds, J. C. (1993) <doi:10.1007/BF01019459>, Schaffer, J. David (1989, ISBN:1-55860-066-3), Wenstop, Fred (1980) <doi:10.1016/0165-0114(80)90031-7>, Whitley, Darrell (1989, ISBN:1-55860-066-3), Wickham, Hadley (2019, ISBN:978-815384571).

Representation-dependent gene-level operations for genetic and evolutionary algorithms with real-coded genes used in the R-package xega <https://CRAN.R-project.org/package=xega> are collected in this package. The common feature of the gene operations is that all of them are useful for derivation-free optimization algorithms. At the moment the package implements initialization, mutation, crossover, and replication operations for differential evolution as described in Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005) <doi:10.1007/3-540-31306-0>. In addition, several (more recent) methods for determining the scale factor are provided. For xega''s architecture, see Geyer-Schulz, A. (2025) <doi:10.5445/IR/1000187255>.

XML package for creating and reading and manipulating XML', with an object model based on Reference Classes'.

This package provides a consistent interface for common feature importance methods as described in Ewald et al. (2024) <doi:10.1007/978-3-031-63797-1_22>, including permutation feature importance (PFI), conditional and relative feature importance (CFI, RFI), leave one covariate out (LOCO), and Shapley additive global importance (SAGE), as well as feature sampling mechanisms to support conditional importance methods.

Allows to provide live interpretations and explanations of statistical functions in R. These interpretations and explanations are shown when the explained function is called by the user. They can interact with the values of the explained function's actual results to offer relevant, meaningful insights. The xplain interpretations and explanations are based on an easy-to-use XML format that allows to include R code to interact with the returns of the explained function.

An implementation of the RuleFit algorithm as described in Friedman & Popescu (2008) <doi:10.1214/07-AOAS148>. eXtreme Gradient Boosting ('XGBoost') is used to build rules, and glmnet is used to fit a sparse linear model on the raw and rule features. The result is a model that learns similarly to a tree ensemble, while often offering improved interpretability and achieving improved scoring runtime in live applications. Several algorithms for reducing rule complexity are provided, most notably hyperrectangle de-overlapping. All algorithms scale to several million rows and support sparse representations to handle tens of thousands of dimensions.

This package implements panel cointegration tests allowing for structural breaks and cross-section dependence following the methodology of Banerjee and Carrion-i-Silvestre (2015) <doi:10.1002/jae.2348>. The package provides iterative factor-break estimation, individual ADF tests on defactored residuals, standardized panel test statistics, and the Bai and Ng (2004) <doi:10.1111/j.1468-0262.2004.00528.x> MQ test for identifying common stochastic trends. Supports five model specifications with varying deterministic components and break structures.

This package provides a few functions which provide a quick way of subsetting genomic admixture data and generating customizable stacked barplots.

This is a collection of some useful functions when dealing with text data. Currently it only contains a very efficient function of decoding HTML entities in character vectors by Rcpp routine.

Estimation of Panel Quantile Autoregressive Distributed Lag (PQARDL) models that combine panel ARDL methodology with quantile regression. Supports Pooled Mean Group (PMG), Mean Group (MG), and Dynamic Fixed Effects (DFE) estimators across multiple quantiles. Computes long-run cointegrating parameters, error correction term speed of adjustment, half-life of adjustment, and performs Wald tests for parameter equality across quantiles. Based on the econometric frameworks of Pesaran, Shin, and Smith (1999) <doi:10.1080/01621459.1999.10474156>, Cho, Kim, and Shin (2015) <doi:10.1016/j.jeconom.2015.02.030>, and Bildirici and Kayikci (2022) <doi:10.1016/j.energy.2022.124303>.

Reading and writing sheets of a single Excel file into and from a list of data frames. Eases I/O of tabular data in bioinformatics while keeping them in a human readable format.

This package provides support for transformations of numeric aggregates between statistical classifications (e.g. occupation or industry categorisations) using the Crossmaps framework. Implements classes for representing transformations between a source and target classification as graph structures, and methods for validating and applying crossmaps to transform data collected under the source classification into data indexed using the target classification codes. Documentation about the Crossmaps framework is provided in the included vignettes and in Huang (2024, <doi:10.48550/arXiv.2406.14163>).

Extras and extensions for xaringan slides. Navigate your slides with tile view. Make your slides editable, live! Announce slide changes with subtle tones. Animate slide transitions with animate.css'. Add tabbed panels to slides with panelset'. Use the Tachyons CSS utility toolkit for rapid slide development. Scribble on your slides. Add a copy button to your code chunks with clipboard'. Add a logo or top or bottom banner to every slide. Broadcast slides to stay in sync with remote viewers. Include yourself in your slides with webcam'. Plus a whole lot more!

This tool enables in-database scoring of XGBoost models built in R, by translating trained model objects into SQL query. XGBoost <https://github.com/dmlc/xgboost> provides parallel tree boosting (also known as gradient boosting machine, or GBM) algorithms in a highly efficient, flexible and portable way. GBM algorithm is introduced by Friedman (2001) <doi:10.1214/aos/1013203451>, and more details on XGBoost can be found in Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.

Hamiltonian Monte Carlo for both continuous and discontinuous posterior distributions with a customizable trajectory length termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for the original Discontinuous Hamiltonian Monte Carlo; Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016) <doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian Monte Carlo termination criteria.

Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.

This package provides a high-level interface for creating and exporting summary tables to Excel'. Built on dplyr and openxlsx', it provides tools for generating one-way to n-way tables, and summarizing multiple response questions and question blocks. Tables are exported with native Excel formatting, including titles, footnotes, and basic styling options.

Helpers for transforming XML content into number of tables while preserving parent to child relationships.

This package implements the bootstrap slope heterogeneity test for panel data based on Blomquist and Westerlund (2015) <doi:10.1007/s00181-015-0978-z>. Tests the null hypothesis that slope coefficients are homogeneous across cross-sectional units. Provides both standard and adjusted Delta statistics with bootstrap p-values. Supports partialling out of control variables and cross-sectional averages for dealing with cross-sectional dependence.