This package implements the adaptive influence-based borrowing framework proposed by Qinwei Yang, Jingyi Li, Peng Wu, and Shu Yang (2026+) in the paper ``Improving Treatment Effect Estimation in Trials through Adaptive Borrowing of External Controls" <doi:10.48550/arXiv.2604.13973> for augmenting Randomized Controlled Trials (RCTs) with External Control (EC) data. This package provides a comprehensive workflow to: (1) quantify the comparability of external control samples using influence scores approximated via the influence function of the M-estimator; (2) construct candidate borrowing subsets and select the optimal subset that minimizes the Mean Squared Error (MSE); and (3) calibrate systematic differences in external outcomes using R-learner methods implemented via Ordinary Least Squares or Kernel Ridge Regression.

Biodiversity areas, especially primary forest, serve a multitude of functions for local economy, regional functionality of the ecosystems as well as the global health of our planet. Recently, adverse changes in human land use practices and climatic responses to increased greenhouse gas emissions, put these biodiversity areas under a variety of different threats. The present package helps to analyse a number of biodiversity indicators based on freely available geographical datasets. It supports computational efficient routines that allow the analysis of potentially global biodiversity portfolios. The primary use case of the package is to support evidence based reporting of an organization's effort to protect biodiversity areas under threat and to identify regions were intervention is most duly needed.

An implementation of a non-parametric statistical model using a parallelised Monte Carlo sampling scheme. The method implemented in this package allows non-parametric inference to be regularized for small sample sizes, while also being more accurate than approximations such as variational Bayes. The concentration parameter is an effective sample size parameter, determining the faith we have in the model versus the data. When the concentration is low, the samples are close to the exact Bayesian logistic regression method; when the concentration is high, the samples are close to the simplified variational Bayes logistic regression. The method is described in full in the paper Lyddon, Walker, and Holmes (2018), "Nonparametric learning from Bayesian models with randomized objective functions" <doi:10.48550/arXiv.1806.11544>.

Exploring time series for signal detection. It is specifically designed to detect possible outbreaks using infectious disease surveillance data at the European Union / European Economic Area or country level. Automatic detection tools used are presented in the paper "Monitoring count time series in R: aberration detection in public health surveillance", by Salmon (2016) <doi:10.18637/jss.v070.i10>. The package includes: - Signal Detection tool, an interactive shiny application in which the user can import external data and perform basic signal detection analyses; - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. This report can also be stratified by population characteristics (see Population variable). This project was funded by the European Centre for Disease Prevention and Control.

This package provides a user-friendly interactive Shiny interface for the BsplineQuantReg package, enabling quantile regression using B-splines with shape constraints, based on the method described in Abbes (2025). Almost all parameters of the main function quantile_spline() can be tuned. Features include interactive knot placement, per-region constraint specification, CSV data import, direct demo access, reproducible R code generation, and solver selection. The version 0.2.2 handles knots multiplicity, Bspline basis visualisation, mean-square regression, pp form visualisation under human readable form, in local or canonical bases, The GUI provides two modes, basic (compatible with BsplineQuantReg >= 0.2.2) and advanced (requires BsplineQuantReg >= 0.2.5 for stable multiplicity features). This GUI an improved version of the Python Tk version of BsplineQuantRegPy'.

Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.

Case-based reasoning is a problem-solving methodology that involves solving a new problem by referring to the solution of a similar problem in a large set of previously solved problems. The key aspect of Case Based Reasoning is to determine the problem that "most closely" matches the new problem at hand. This is achieved by defining a family of distance functions and using these distance functions as parameters for local averaging regression estimates of the final result. The optimal distance function is chosen based on a specific error measure used in regression estimation. This approach allows for efficient problem-solving by leveraging past experiences and adapting solutions from similar cases. The underlying concept is inspired by the work of Dippon J. et al. (2002) <doi:10.1016/S0167-9473(02)00058-0>.

This package implements a bootstrap-based heterogeneity test for standardized mean differences (d), Fisher-transformed Pearson's correlations (r), and natural-logarithm-transformed odds ratio (or) in meta-analysis studies. Depending on the presence of moderators, this Monte Carlo based test can be implemented in the random- or mixed-effects model. This package uses rma() function from the R package metafor to obtain parameter estimates and likelihoods, so installation of R package metafor is required. This approach refers to the studies of Anscombe (1956) <doi:10.2307/2332926>, Haldane (1940) <doi:10.2307/2332614>, Hedges (1981) <doi:10.3102/10769986006002107>, Hedges & Olkin (1985, ISBN:978-0123363800), Silagy, Lancaster, Stead, Mant, & Fowler (2004) <doi:10.1002/14651858.CD000146.pub2>, Viechtbauer (2010) <doi:10.18637/jss.v036.i03>, and Zuckerman (1994, ISBN:978-0521432009).

We provide comprehensive draft data for major professional sports leagues, including the National Football League (NFL), National Basketball Association (NBA), and National Hockey League (NHL). It offers access to both historical and current draft data, allowing for detailed analysis and research on player biases and player performance. The package is useful for sports fans and researchers interested in identifying biases and trends within scouting reports. Created by web scraping data from leading websites that cover professional sports player scouting reports, the package allows users to filter and summarize data for analytical purposes. For further details on the methods used, please refer to Wickham (2022) "rvest: Easily Harvest (Scrape) Web Pages" <https://CRAN.R-project.org/package=rvest> and Harrison (2023) "RSelenium: R Bindings for Selenium WebDriver" <https://CRAN.R-project.org/package=RSelenium>.

This package provides functions for imputing missing item responses for dichotomous and polytomous test and assessment data. This package enables missing imputation methods that are suitable for test and assessment data, including: listwise (LW) deletion (see De Ayala et al. 2001 <doi:10.1111/j.1745-3984.2001.tb01124.x>), treating as incorrect (IN, see Lord, 1974 <doi: 10.1111/j.1745-3984.1974.tb00996.x>; Mislevy & Wu, 1996 <doi: 10.1002/j.2333-8504.1996.tb01708.x>; Pohl et al., 2014 <doi: 10.1177/0013164413504926>), person mean imputation (PM), item mean imputation (IM), two-way (TW) and response function (RF) imputation, (see Sijtsma & van der Ark, 2003 <doi: 10.1207/s15327906mbr3804_4>), logistic regression (LR) imputation, predictive mean matching (PMM), and expectationâ maximization (EM) imputation (see Finch, 2008 <doi: 10.1111/j.1745-3984.2008.00062.x>).

Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.

Asciidoctor PDF is an extension for Asciidoctor that converts AsciiDoc documents to Portable Document Format (PDF) using the Prawn PDF library. It has features such as:

• Direct AsciiDoc to PDF conversion

• Configuration-driven theme (style and layout)

• Scalable Vector Graphics (SVG) support

• PDF document outline (i.e., bookmarks)

• Table of contents page(s)

• Document metadata (title, authors, subject, keywords, etc.)

• Internal cross reference links

• Syntax highlighting with Rouge, Pygments, or CodeRay

• Page numbering

• Customizable running content (header and footer)

• “Keep together” blocks (i.e., page breaks avoided in certain block content)

• Orphaned section titles avoided

• Autofit verbatim blocks (as permitted by base_font_size_min setting)

• Table border settings honored

• Font-based icons

• Custom TrueType (TTF) fonts

• Double-sided printing mode (margins alternate on recto and verso pages)

Extends the fable framework to support forecasting methods specifically designed for intermittent time series data, where demand occurs sporadically with many zero values. All methods produce probabilistic forecasts returned as distributional objects. The returned forecasts can be used to evaluate accuracy, plot and print the results seamlessly with fable'. The methods include: Harvey, Fernandes (1989) <doi:10.1080/07350015.1989.10509750>, Willemain, Smart, Schwarz (2004) <doi:10.1016/S0169-2070(03)00013-X>, Zhou, Viswanathan (2011) <doi:10.1016/j.ijpe.2010.09.021>, Snyder, Ord, Beaumont (2012) <doi:10.1016/j.ijforecast.2011.03.009>, Kolassa (2016) <doi:10.1016/j.ijforecast.2015.12.004>, Hasni, Aguir, Babai, Jemai (2019) <doi:10.1080/00207543.2018.1424375>, Damato, Azzimonti, Corani (2025) <doi:10.1016/j.ijforecast.2025.10.001>, Sbrana (2025) <doi:10.1080/01605682.2025.2569661>, Sbrana, Babai (2026) <doi:10.1016/j.ejor.2026.06.009>.

This package provides a fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2024) <doi:10.1007/s11749-024-00942-w> and Papastamoulis and Milienos (2024b) <doi:10.48550/arXiv.2409.10221>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of distributions. In both cases, user-defined families of distributions are allowed under some specific requirements. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of the target posterior distribution.

One key exploratory analysis step in single-cell genomics data analysis is the prediction of features with different activity levels. For example, we want to predict differentially expressed genes (DEGs) in single-cell RNA-seq data, spatial DEGs in spatial transcriptomics data, or differentially accessible regions (DARs) in single-cell ATAC-seq data. singleCellHaystack predicts differentially active features in single cell omics datasets without relying on the clustering of cells into arbitrary clusters. singleCellHaystack uses Kullback-Leibler divergence to find features (e.g., genes, genomic regions, etc) that are active in subsets of cells that are non-randomly positioned inside an input space (such as 1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For the theoretical background of singleCellHaystack we refer to our original paper Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3> and our update Vandenbon and Diez (Scientific Reports, 2023) <doi:10.1038/s41598-023-38965-2>.

Fit Bayesian graduation mortality using the Heligman-Pollard model, as seen in Heligman, L., & Pollard, J. H. (1980) <doi:10.1017/S0020268100040257> and Dellaportas, Petros, et al. (2001) <doi:10.1111/1467-985X.00202>, and dynamic linear model (Campagnoli, P., Petris, G., and Petrone, S. (2009) <doi:10.1007/b135794_2>). While Heligman-Pollard has parameters with a straightforward interpretation yielding some rich analysis, the dynamic linear model provides a very flexible adjustment of the mortality curves by controlling the discount factor value. Closing methods for both Heligman-Pollard and dynamic linear model were also implemented according to Dodd, Erengul, et al. (2018) <https://www.jstor.org/stable/48547511>. The Bayesian Lee-Carter model is also implemented to fit historical mortality tables time series to predict the mortality in the following years and to do improvement analysis, as seen in Lee, R. D., & Carter, L. R. (1992) <doi:10.1080/01621459.1992.10475265> and Pedroza, C. (2006) <doi:10.1093/biostatistics/kxj024>. Journal publication available at <doi:10.18637/jss.v113.i09>.

This package provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target values under change of support. This package extends the range of tools for spatial predictions available in R and provides an alternative to conditional simulation for non-linear spatial prediction problems with local change of support.

This package implements Importance Sampling (Sampling Importance Resampling, SIR) for Bayesian parameter estimation and Generalized Process Capability Indices (GPCIs) under progressive Type-II censored data. Evaluates classical and generalized capability indices including Cpy, Cp, Cpk, Cpu, Cpl, Cpm, Cpmk, Spmk, CpTk, Cpc, CNp, CNpk, CNpm, CNpmk, CNpmc, CNpmkc, and Vannman's Cp(u,v) family. Computes initial uncensored estimates, parameter MCMC chains, GPCI posterior chains, point estimates, posterior means, bias, mean squared error (MSE), Bayes risk under loss functions, Highest Posterior Density (HPD) credible intervals at 90%, 95%, and 99% levels, Heidelberger and Welch's MCMC convergence diagnostics, and convergence probabilities. Accommodates user-defined probability density/mass functions, cumulative distribution functions, and survival functions. Methods based on Balakrishnan and Aggarwala (2000) <doi:10.1007/978-1-4612-1186-0>, Maiti et al. (2010) <doi:10.1080/16843703.2010.11673233>, Dey and Saha (2019) <doi:10.1007/s41872-019-00081-4>, Alotaibi et al. (2022) <doi:10.1155/2022/3135264>, Saha et al. (2022) <doi:10.1080/02664763.2021.1971632>, and Saha et al. (2024) <doi:10.1142/S021853932450013X>.

Multisite causal mediation analysis using the methods proposed by Qin and Hong (2017) <doi:10.3102/1076998617694879>, Qin, Hong, Deutsch, and Bein (2019) <doi:10.1111/rssa.12446>, and Qin, Deutsch, and Hong (2021) <doi:10.1002/pam.22268>. It enables causal mediation analysis in multisite trials, in which individuals are assigned to a treatment or a control group at each site. It allows for estimation and hypothesis testing for not only the population average but also the between-site variance of direct and indirect effects transmitted through one single mediator or two concurrent (conditionally independent) mediators. This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. This package also provides a function that can further incorporate a sample weight and a nonresponse weight for multisite causal mediation analysis in the presence of complex sample and survey designs and non-random nonresponse, to enhance both the internal validity and external validity. The package also provides a weighting-based balance checking function for assessing the remaining overt bias.

Computes classical process capability indices (Cp, Cpk, Cpu, Cpl, Cpm, Cpmk, Pp, Ppk, Ppu, Ppl, Z) and the generalized process capability index Cpy (Maiti, Saha & Nanda, 2010) <doi:10.1080/16843703.2010.11673233> for any continuous or discrete quality characteristic. Users supply the probability density function (PDF) and cumulative distribution function (CDF) of the characteristic, and the package returns point estimates, bootstrap confidence intervals (percentile and BCa), and sensitivity tables/plots across ranges of short-term standard deviation (sigma), long-term standard deviation (s), desired yield (p0), and significance levels. Classical indices are recoverable as special cases under the normal distribution. The package follows the theory and notation of Kane (1986) <doi:10.1080/00224065.1986.11978984>, Chan, Cheng & Spiring (1988) <doi:10.1080/00224065.1988.11979102>, Pearn, Kotz & Johnson (1992) <doi:10.1080/00224065.1992.11979403>, Kotz & Johnson (2002) <doi:10.1080/00224065.2002.11980119>, Montgomery (2020, ISBN:978-1-119-39930-8), Juran (1974, ISBN:978-0-07-033176-1), Harry & Schroeder (2000, ISBN:978-0-385-49437-2), and the AIAG SPC Reference Manual (2005, ISBN:978-1-60534-026-3).

Evaluates Generalized Process Capability Indices (GPCIs) under Hybrid Type-II censored lifetime data using Importance Sampling (Sampling Importance Resampling, SIR). Implements Bayesian parameter estimation and evaluates classical and generalized capability indices including Cpy, Cp, Cpk, Cpu, Cpl, Cpm, Cpmk, Spmk, CpTk, Cpc, CNp, CNpk, CNpm, CNpmk, CNpmc, CNpmkc, and Vannman's Cp(u,v) family. Computes initial maximum likelihood estimates under Hybrid Type-II censoring, parameter MCMC chains, GPCI posterior chains, posterior point estimates, bias, mean squared error (MSE), Bayes risk, Highest Posterior Density (HPD) credible intervals at 90%, 95%, and 99% levels, Heidelberger and Welch's MCMC convergence diagnostics, and convergence probabilities. Accommodates user-defined probability density/mass functions, cumulative distribution functions, and survival functions. Goodness-of-fit testing for Hybrid Type-II censored data is supported via gofPHCS'. Methods are based on Childs et al. (2003) <doi:10.1080/0266476032000053637>, Kundu and Pradhan (2009) <doi:10.1016/j.spl.2008.09.006>, Maiti et al. (2010) <doi:10.1080/16843703.2010.11673233>, Dey and Saha (2019) <doi:10.1007/s41872-019-00081-4>, Alotaibi et al. (2022) <doi:10.1155/2022/3135264>, Saha et al. (2022) <doi:10.1080/02664763.2021.1971632>, and Saha et al. (2024) <doi:10.1142/S021853932450013X>.

In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of a continuous response. This package provides the setup and calculations needed to run a dose-finding trial with non-binary endpoints and performs simulations to assess designâ s operating characteristics under various scenarios. Three dose finding designs are included in this package: unified phase I design (Ivanova et al. (2009) <doi:10.1111/j.1541-0420.2008.01045.x>), Quasi-CRM/Robust-Quasi-CRM (Yuan et al. (2007) <doi:10.1111/j.1541-0420.2006.00666.x>, Pan et al. (2014) <doi:10.1371/journal.pone.0098147>) and generalized BOIN design (Mu et al. (2018) <doi:10.1111/rssc.12263>). The toxicity endpoints can be handled with these functions including equivalent toxicity score (ETS), total toxicity burden (TTB), general continuous toxicity endpoints, with incorporating ordinal grade toxicity information into dose-finding procedure. These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose-limiting toxicity (DLT) rates, discrete or continuous toxicity score, and incorporate safety and/or stopping rules.

This package provides several functions and datasets for area-level Small Area Estimation using the Hierarchical Bayesian (HB) method. Model-based estimators are designed for variables of interest that follow a Beta distribution (proportions bounded between 0 and 1). The package supports both non-spatial and spatial models based on Simultaneous Autoregressive (SAR) and Leroux Conditional Autoregressive (CAR) structures for area-level random effects, with optional survey design effect (DEFF) adjustments for sampling variances. In addition, it provides utility functions for constructing spatial weights matrices and performing spatial autocorrelation diagnostics. The runjags package is used to obtain posterior estimates via Markov Chain Monte Carlo (MCMC) with parallel computing capabilities. For references, see Rao and Molina (2015) <doi:10.1002/9781118735855>, Liu et al. (2014) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2014001/article/14030-eng.pdf>, Kubacki and Jedrzejczak (2016) <doi:10.59170/stattrans-2016-022>, Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>, Chung and Datta (2020) <https://www.census.gov/content/dam/Census/library/working-papers/2020/adrm/RRS2020-07.pdf>, Figueroa-Zúñiga et al. (2013) <doi:10.1016/j.csda.2012.12.002>, Denwood (2016) <doi:10.18637/jss.v071.i09>, Anselin (1988) <doi:10.1007/978-94-015-7799-1>, and Anselin and Morrison (2019) <https://spatialanalysis.github.io/lab_tutorials/Spatial_Weights_as_Distance_Functions.html>.

This package provides a comprehensive framework for estimating Generalized Process Capability Indices (GPCIs) under Hybrid Type-II censored lifetime data using Lindley's 3rd-order approximation method (Lindley, 1980 <doi:10.2307/2345271>). Supports user-supplied probability density/mass functions (PDF/PMF), cumulative distribution functions (CDF), survival functions (SF), and quantile functions. Computes Maximum Likelihood Estimates (MLE) using the MleCensoR package (Childs et al., 2003 <doi:10.1007/BF02517803>; Balakrishnan & Kundu, 2013 <doi:10.1002/nav.21545>) and Bayesian posterior expectations for classical and non-normal capability indices, including Cpy (Maiti et al., 2010 <doi:10.1080/16843703.2010.11673233>), Spmk (Dey & Saha, 2019 <doi:10.1007/s41872-019-00081-4>), CpTk (Saha et al., 2019), Cpc (Saha et al., 2022 <doi:10.1080/02664763.2021.1971632>), CNpmc (Alotaibi et al., 2022 <doi:10.1155/2022/3135264>), CNpmkc (Saha et al., 2024 <doi:10.1142/S021853932450013X>), CNpk (Saha et al., 2018 <doi:10.1080/21681015.2018.1437793>), and Vannman's Cp(u,v) family. Generates posterior parameter and GPCI chains via sampling with burn-in and thinning, calculating Bias, Mean Squared Error (MSE), Bayes Risk (SEL and Linex), Highest Posterior Density (HPD) credible intervals at 90%, 95%, and 99% levels, and Heidelberger and Welch's MCMC Convergence Diagnostics (Heidelberger & Welch, 1983 <doi:10.1287/opre.31.6.1109>) with convergence probabilities. Evaluates parametric and non-parametric bootstrap confidence intervals (Percentile, Normal, Basic, BCp, BCa) at 90%, 95%, and 99% levels of significance. Integrates goodness-of-fit testing for Hybrid Type-II censored data via the gofPHCS package.