Audits published or draft plant breeding tables for internal arithmetic consistency. Analysis of variance tables, precision statistics and genetic variability parameters are jointly over-determined by exact algebraic identities; BKVerify recomputes every derivable quantity using rounding-interval arithmetic and reports a value as inconsistent only when no combination of values inside the reported rounding intervals can satisfy the identity. The package deliberately restricts itself to relationships that hold irrespective of which variance-component definition an author adopted, so that flagged results reflect arithmetic inconsistency rather than methodological disagreement. Implemented checks cover analysis of variance internal structure, coefficient of variation, standard error of mean and critical difference, the genetic advance identity of Johnson, Robinson and Comstock (1955) <doi:10.2134/agronj1955.00021962004700070009x>, the relation between genotypic and phenotypic coefficients of variation and broad-sense heritability, and admissibility of reported correlation matrices.

Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

Stock, Options and Futures Trading Strategies for Traders and Investors with Bullish Outlook are represented here through their Graphs. The graphic indicators, strategies, calculations, functions and all the discussions are for academic, research, and educational purposes only and should not be construed as investment advice and come with absolutely no Liability. Guy Cohen (â The Bible of Options Strategies (2nd ed.)â , 2015, ISBN: 9780133964028). Zura Kakushadze, Juan A. Serur (â 151 Trading Strategiesâ , 2018, ISBN: 9783030027919). John C. Hull (â Options, Futures, and Other Derivatives (11th ed.)â , 2022, ISBN: 9780136939979).

This package provides statistical tools for Bayesian estimation of mixture distributions, mainly a mixture of Gamma, Normal, and t-distributions. The package is implemented based on the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.

Facilitates many of the analyses performed in studies of behavioral economic demand. The package supports commonly-used options for modeling operant demand including (1) data screening proposed by Stein, Koffarnus, Snider, Quisenberry, & Bickel (2015; <doi:10.1037/pha0000020>), (2) fitting models of demand such as linear (Hursh, Raslear, Bauman, & Black, 1989, <doi:10.1007/978-94-009-2470-3_22>), exponential (Hursh & Silberberg, 2008, <doi:10.1037/0033-295X.115.1.186>) and modified exponential (Koffarnus, Franck, Stein, & Bickel, 2015, <doi:10.1037/pha0000045>), and (3) calculating numerous measures relevant to applied behavioral economists (Intensity, Pmax, Omax). Also supports plotting and comparing data.

This package implements Bayesian Surprise methodology for data visualization, based on Correll and Heer (2017) <doi:10.1109/TVCG.2016.2598839> "Surprise! Bayesian Weighting for De-Biasing Thematic Maps". Provides tools to weight event data relative to spatio-temporal models, highlighting unexpected patterns while de-biasing against known factors like population density or sampling variation. Integrates seamlessly with sf for spatial data and ggplot2 for visualization. Supports temporal/streaming data analysis.

Arrays of structured data types can require large volumes of disk space to store. Blosc is a library that provides a fast and efficient way to compress such data. It is often applied in storage of n-dimensional arrays, such as in the case of the geo-spatial zarr file format. This package can be used to compress and decompress data using Blosc'.

This package provides a likelihood method is implemented to present evidence for evaluating bioequivalence (BE). The functions use bioequivalence data [area under the blood concentration-time curve (AUC) and peak concentration (Cmax)] from various crossover designs commonly used in BE studies including a fully replicated, a partially replicated design, and a conventional 2x2 crossover design. They will calculate the profile likelihoods for the mean difference, total standard deviation ratio, and within subject standard deviation ratio for a test and a reference drug. A plot of a standardized profile likelihood can be generated along with the maximum likelihood estimate and likelihood intervals, which present evidence for bioequivalence. See Liping Du and Leena Choi (2015) <doi:10.1002/pst.1661>.

Identifies genome-related molecular traits with significant evidence of genetic regulation and performs a bootstrap procedure to correct estimated effect sizes for over-estimation present in cis-QTL mapping studies (The "Winner's Curse"), described in Huang QQ *et al.* 2018 <doi: 10.1093/nar/gky780>.

This package provides functions for behavior genetics analysis, including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>], calculation of relatedness coefficients using path-tracing methods [Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>], inference of relatedness, pedigree conversion, and simulation of multi-generational family data [Lyu et al. (2025) <doi:10.1007/s10519-025-10225-1>]. For a full overview, see [Garrison et al. (2024) <doi:10.21105/joss.06203>]. For a big data application see [Burt et al. (2025) <doi: 10.1016/j.ebiom.2025.105911>.

This package provides functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.

Companion package, functions, data sets, examples for the book Patrice Bertail and Anna Dudek (2025), Bootstrap for Dependent Data, with an R package (by Bernard Desgraupes and Karolina Marek) - submitted. Kreiss, J.-P. and Paparoditis, E. (2003) <doi:10.1214/aos/1074290332> Politis, D.N., and White, H. (2004) <doi:10.1081/ETC-120028836> Patton, A., Politis, D.N., and White, H. (2009) <doi:10.1080/07474930802459016> Tsybakov, A. B. (2018) <doi:10.1007/b13794> Bickel, P., and Sakov, A. (2008) <doi:10.1214/18-AOS1803> Götze, F. and RaÄ kauskas, A. (2001) <doi:10.1214/lnms/1215090074> Politis, D. N., Romano, J. P., & Wolf, M. (1999, ISBN:978-0-387-98854-2) Carlstein E. (1986) <doi:10.1214/aos/1176350057> Künsch, H. (1989) <doi:10.1214/aos/1176347265> Liu, R. and Singh, K. (1992) <https://www.stat.purdue.edu/docs/research/tech-reports/1991/tr91-07.pdf> Politis, D.N. and Romano, J.P. (1994) <doi:10.1080/01621459.1994.10476870> Politis, D.N. and Romano, J.P. (1992) <https://www.stat.purdue.edu/docs/research/tech-reports/1991/tr91-07.pdf> Patrice Bertail, Anna E. Dudek. (2022) <doi:10.3150/23-BEJ1683> Dudek, A.E., LeÅ kow, J., Paparoditis, E. and Politis, D. (2014a) <https://ideas.repec.org/a/bla/jtsera/v35y2014i2p89-114.html> Beran, R. (1997) <doi:10.1023/A:1003114420352> B. Efron, and Tibshirani, R. (1993, ISBN:9780429246593) Bickel, P. J., Götze, F. and van Zwet, W. R. (1997) <doi:10.1007/978-1-4614-1314-1_17> A. C. Davison, D. Hinkley (1997) <doi:10.2307/1271471> Falk, M., & Reiss, R. D. (1989) <doi:10.1007/BF00354758> Lahiri, S. N. (2003) <doi:10.1007/978-1-4757-3803-2> Shimizu, K. .(2017) <doi:10.1007/978-3-8348-9778-7> Park, J.Y. (2003) <doi:10.1111/1468-0262.00471> Kirch, C. and Politis, D. N. (2011) <doi:10.48550/arXiv.1211.4732> Bertail, P. and Dudek, A.E. (2024) <doi:10.3150/23-BEJ1683> Dudek, A. E. (2015) <doi:10.1007/s00184-014-0505-9> Dudek, A. E. (2018) <doi:10.1080/10485252.2017.1404060> Bertail, P., Clémençon, S. (2006a) <https://ideas.repec.org/p/crs/wpaper/2004-47.html> Bertail, P. and Clémençon, S. (2006, ISBN:978-0-387-36062-1) RaduloviÄ , D. (2006) <doi:10.1007/BF02603005> Bertail, P. Politis, D. N. Rhomari, N. (2000) <doi:10.1080/02331880008802701> Nordman, D.J. Lahiri, S.N.(2004) <doi:10.1214/009053604000000779> Politis, D.N. Romano, J.P. (1993) <doi:10.1006/jmva.1993.1085> Hurvich, C. M. and Zeger, S. L. (1987, ISBN:978-1-4612-0099-4) Bertail, P. and Dudek, A. (2021) <doi:10.1214/20-EJS1787> Bertail, P., Clémençon, S. and Tressou, J. (2015) <doi:10.1111/jtsa.12105> Asmussen, S. (1987) <doi:10.1007/978-3-662-11657-9> Efron, B. (1979) <doi:10.1214/aos/1176344552> Gray, H., Schucany, W. and Watkins, T. (1972) <doi:10.2307/2335521> Quenouille, M.H. (1949) <doi:10.1111/j.2517-6161.1949.tb00023.x> Quenouille, M. H. (1956) <doi:10.2307/2332914> Prakasa Rao, B. L. S. and Kulperger, R. J. (1989) <https://www.jstor.org/stable/25050735> Rajarshi, M.B. (1990) <doi:10.1007/BF00050835> Dudek, A.E. Maiz, S. and Elbadaoui, M. (2014) <doi:10.1016/j.sigpro.2014.04.022> Beran R. (1986) <doi:10.1214/aos/1176349847> Maritz, J. S. and Jarrett, R. G. (1978) <doi:10.2307/2286545> Bertail, P., Politis, D., Romano, J. (1999) <doi:10.2307/2670177> Bertail, P. and Clémençon, S. (2006b) <doi:10.1007/0-387-36062-X_1> RaduloviÄ , D. (2004) <doi:10.1007/BF02603005> Hurd, H.L., Miamee, A.G. (2007) <doi:10.1002/9780470182833> Bühlmann, P. (1997) <doi:10.2307/3318584> Choi, E., Hall, P. (2000) <doi:10.1111/1467-9868.00244> Efron, B., Tibshirani, R. (1993, ISBN:9780429246593) Bertail, P., Clémençon, S. and Tressou, J. (2009) <doi:10.1007/s10687-009-0081-y> Bertail, P., Medina-Garay, A., De Lima-Medina, F. and Jales, I. (2024) <doi:10.1080/02331888.2024.2344670>.

This package provides methods for frontier analysis, Data Envelopment Analysis (DEA), under different technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+), and using different efficiency measures (input based, output based, hyperbolic graph, additive, super, and directional efficiency). Peers and slacks are available, partial price information can be included, and optimal cost, revenue and profit can be calculated. Evaluation of mergers is also supported. Methods for graphing the technology sets are also included. There is also support for comparative methods based on Stochastic Frontier Analyses (SFA) and for convex nonparametric least squares of convex functions (STONED). In general, the methods can be used to solve not only standard models, but also many other model variants. It complements the book, Bogetoft and Otto, Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of course also be used as a stand-alone package.

This package provides tools to visualize ordination results in R by adding covariance-based ellipses, centroids, vectors, and confidence regions to plots created with ggplot2'. The package extends the vegan framework and supports Principal Component Analysis (PCA), Redundancy Analysis (RDA), and Non-metric Multidimensional Scaling (NMDS). Ellipses can represent either group dispersion (standard deviation, SD) or centroid precision (standard error, SE), following Wang et al. (2015) <doi:10.1371/journal.pone.0118537>. Robust estimators of covariance are implemented, including the Minimum Covariance Determinant (MCD) method of Hubert et al. (2018) <doi:10.1002/wics.1421>. This approach reduces the influence of outliers. barrel is particularly useful for multivariate ecological datasets, promoting reproducible, publication-quality ordination graphics with minimal effort.

This package provides tools to deploy R web server applications that follow the _server.yml standard. This standard allows different R server frameworks ('plumber2', fiery', etc.) to be deployed using a common interface. The package supports deployment to DigitalOcean and includes validation tools to ensure _server.yml files are correctly formatted.

Calculate Bayesian marginal effects, average marginal effects, and marginal coefficients (also called population averaged coefficients) for models fit using the brms package including fixed effects, mixed effects, and location scale models. These are based on marginal predictions that integrate out random effects if necessary (see for example <doi:10.1186/s12874-015-0046-6> and <doi:10.1111/biom.12707>).

Fast Bayesian inference of marginal and conditional independence structures from high-dimensional data. Leday and Richardson (2019), Biometrics, <doi:10.1111/biom.13064>.

This package provides tools to create binary dosage files from either VCF or GEN files, merge binary dosage files, and read binary dosage files. Binary dosage files tend to have quicker read times than VCF and GEN formats. There is a small increase in size compared to compressed VCF and GEN files.

Bayesian MCPMod (Fleischer et al. (2022) <doi:10.1002/pst.2193>) is an innovative method that improves the traditional MCPMod by systematically incorporating historical data, such as previous placebo group data. This package offers functions for simulating, analyzing, and evaluating Bayesian MCPMod trials with normally and binary distributed endpoints. It enables the assessment of trial designs incorporating historical data across various true dose-response relationships and sample sizes. Robust mixture prior distributions, such as those derived with the Meta-Analytic-Predictive approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be specified for each dose group. Resulting mixture posterior distributions are used in the Bayesian Multiple Comparison Procedure and modeling steps. The modeling step also includes a weighted model averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>). Estimated dose-response relationships can be bootstrapped and visualized.

Finds the largest possible regression model that will still converge for various types of regression analyses (including mixed models and generalized additive models) and then optionally performs stepwise elimination similar to the forward and backward effect-selection methods in SAS, based on the change in log-likelihood or its significance, Akaike's Information Criterion, the Bayesian Information Criterion, the explained deviance, or the F-test of the change in R².

Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data or categorical data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data. All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks. References: J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>, N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>, J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>, M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>, D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>, P. Suter, J. Kuipers, G. Moffa, N.Beerenwinkel (2023) <doi:10.18637/jss.v105.i09>.

This package creates spatially or environmentally separated, or group-preserving, training and testing folds for k-fold, leave-group-out, and leave-one-out cross-validation. Provides spatial blocking, clustering, buffering, and nearest-neighbour distance-matching methods, together with tools to visualise folds, summarise fold sizes and class balance, and assess trainâ test separation and environmental novelty. Also estimates spatial autocorrelation ranges in point samples and continuous raster covariates to provide an initial distance scale for designing spatial folds. Methods are described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.

This package implements the Beta Kernel Process (BKP) for nonparametric modeling of covariate-dependent binomial probabilities, and the Dirichlet Kernel Process (DKP) for categorical or multinomial response data. Scalable global-local approximations are provided through TwinBKP and TwinDKP, using twinning-selected global subsets and local nearest-neighbour updates. Functions are included for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one- and two-dimensional input spaces. Gaussian, Matern 5/2, Matern 3/2, and Wendland kernels are supported, with hyperparameters selected by multi-start derivative-free optimization. For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.

This package provides a convenience package for use while drafting code. It facilitates making stand-out comment lines decorated with bands of characters. The input text strings are converted into R comment lines, suitably formatted. These are then displayed in a console window and, if possible, automatically transferred to a clipboard ready for pasting into an R script. Designed to save time when drafting R scripts that will need to be navigated and maintained by other programmers.