Settings and functions to extend the knitr Stata engine.

Model age schedules of mortality, nqx, suitable for a life table. This package implements the SVD-Comp mortality model indexed by either child or child/adult mortality. Given input value(s) of either 5q0 or (5q0, 45q15), the qx() function generates single-year 1qx or 5-year 5qx conditional age-specific probabilities of dying. See Clark (2016) <doi:10.48550/arXiv.1612.01408> and Clark (2019) <doi:10.1007/s13524-019-00785-3>.

Density, distribution function, quantile function and random generation for the skewed t distribution of Fernandez and Steel.

Design a Bayesian seamless multi-arm biomarker-enriched phase II/III design with the survival endpoint with allowing sample size re-estimation. James M S Wason, Jean E Abraham, Richard D Baird, Ioannis Gournaris, Anne-Laure Vallier, James D Brenton, Helena M Earl, Adrian P Mander (2015) <doi:10.1038/bjc.2015.278>. Guosheng Yin, Nan Chen, J. Jack Lee (2018) <doi:10.1007/s12561-017-9199-7>. Ying Yuan, Beibei Guo, Mark Munsell, Karen Lu, Amir Jazaeri (2016) <doi:10.1002/sim.6971>.

An implementation of the stratification index proposed by Zhou (2012) <DOI:10.1177/0081175012452207>. The package provides two functions, srank, which returns stratum-specific information, including population share and average percentile rank; and strat, which returns the stratification index and its approximate standard error. When a grouping factor is specified, strat also provides a detailed decomposition of the overall stratification into between-group and within-group components.

Produce small area population estimates by fitting census data to survey data.

This package implements the following approaches for multidimensional scaling (MDS) based on stress minimization using majorization (smacof): ratio/interval/ordinal/spline MDS on symmetric dissimilarity matrices, MDS with external constraints on the configuration, individual differences scaling (idioscal, indscal), MDS with spherical restrictions, and ratio/interval/ordinal/spline unfolding (circular restrictions, row-conditional). Various tools and extensions like jackknife MDS, bootstrap MDS, permutation tests, MDS biplots, gravity models, unidimensional scaling, drift vectors (asymmetric MDS), classical scaling, and Procrustes are implemented as well.

Unsupervised text tokenizer allowing to perform byte pair encoding and unigram modelling. Wraps the sentencepiece library <https://github.com/google/sentencepiece> which provides a language independent tokenizer to split text in words and smaller subword units. The techniques are explained in the paper "SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing" by Taku Kudo and John Richardson (2018) <doi:10.18653/v1/D18-2012>. Provides as well straightforward access to pretrained byte pair encoding models and subword embeddings trained on Wikipedia using word2vec', as described in "BPEmb: Tokenization-free Pre-trained Subword Embeddings in 275 Languages" by Benjamin Heinzerling and Michael Strube (2018) <http://www.lrec-conf.org/proceedings/lrec2018/pdf/1049.pdf>.

Single-index mixture cure models allow estimating the probability of cure and the latency depending on a vector (or functional) covariate, avoiding the curse of dimensionality. The vector of parameters that defines the model can be estimated by maximum likelihood. A nonparametric estimator for the conditional density of the susceptible population is provided. For more details, see Piñeiro-Lamas (2024) (<https://ruc.udc.es/dspace/handle/2183/37035>). Funding: This work, integrated into the framework of PERTE for Vanguard Health, has been co-financed by the Spanish Ministry of Science, Innovation and Universities with funds from the European Union NextGenerationEU, from the Recovery, Transformation and Resilience Plan (PRTR-C17.I1) and from the Autonomous Community of Galicia within the framework of the Biotechnology Plan Applied to Health.

This package provides a graphical user interface (GUI) for fitting Bayesian regression models using the package brms which in turn relies on Stan (<https://mc-stan.org/>). The shinybrms GUI is a shiny app.

This package provides tools to calculate the alpha parameter of the Weibull distribution, given beta and the age-specific fertility of a species, so that the population remains stable and stationary. Methods are inspired by "Survival profiles from linear models versus Weibull models: Estimating stable and stationary population structures for Pleistocene large mammals" (Martà n-González et al. 2019) <doi:10.1016/j.jasrep.2019.03.031>.

Encapsulates a number of spatially balanced sampling algorithms, namely, Balanced Acceptance Sampling (equal, unequal, seed point, panels), Halton frames (for discretizing a continuous resource), Halton Iterative Partitioning (equal probability) and Simple Random Sampling. Robertson, B. L., Brown, J. A., McDonald, T. and Jaksons, P. (2013) <doi:10.1111/biom.12059>. Robertson, B. L., McDonald, T., Price, C. J. and Brown, J. A. (2017) <doi:10.1016/j.spl.2017.05.004>. Robertson, B. L., McDonald, T., Price, C. J. and Brown, J. A. (2018) <doi:10.1007/s10651-018-0406-6>. Robertson, B. L., van Dam-Bates, P. and Gansell, O. (2021a) <doi:10.1007/s10651-020-00481-1>. Robertson, B. L., Davies, P., Gansell, O., van Dam-Bates, P., McDonald, T. (2025) <doi:10.1111/anzs.12435>.

Uncertainty propagation analysis in spatial environmental modelling following methodology described in Heuvelink et al. (2007) <doi:10.1080/13658810601063951> and Brown and Heuvelink (2007) <doi:10.1016/j.cageo.2006.06.015>. The package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model outputs. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques. Uncertain variables are described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is accommodated for. The MC realizations may be used as input to the environmental models called from R, or externally.

This package provides a comprehensive toolkit for extracting latent signals from panel data through multivariate time series analysis. Implements spectral decomposition methods including wavelet multiresolution analysis via maximal overlap discrete wavelet transform, Percival and Walden (2000) <doi:10.1017/CBO9780511841040>, empirical mode decomposition for non-stationary signals, Huang et al. (1998) <doi:10.1098/rspa.1998.0193>, and Bayesian trend extraction via the Grant-Chan embedded Hodrick-Prescott filter, Grant and Chan (2017) <doi:10.1016/j.jedc.2016.12.007>. Features Bayesian variable selection through regularized Horseshoe priors, Piironen and Vehtari (2017) <doi:10.1214/17-EJS1337SI>, for identifying structurally relevant predictors from high-dimensional candidate sets. Includes dynamic factor model estimation, principal component analysis with bootstrap significance testing, and automated technical interpretation of signal morphology and variance topology.

Approximate Bayesian regularization using Gaussian approximations. The input is a vector of estimates and a Gaussian error covariance matrix of the key parameters. Bayesian shrinkage is then applied to obtain parsimonious solutions. The method is described on Karimova, van Erp, Leenders, and Mulder (2024) <DOI:10.31234/osf.io/2g8qm>. Gibbs samplers are used for model fitting. The shrinkage priors that are supported are Gaussian (ridge) priors, Laplace (lasso) priors (Park and Casella, 2008 <DOI:10.1198/016214508000000337>), and horseshoe priors (Carvalho, et al., 2010; <DOI:10.1093/biomet/asq017>). These priors include an option for grouped regularization of different subsets of parameters (Meier et al., 2008; <DOI:10.1111/j.1467-9868.2007.00627.x>). F priors are used for the penalty parameters lambda^2 (Mulder and Pericchi, 2018 <DOI:10.1214/17-BA1092>). This correspond to half-Cauchy priors on lambda (Carvalho, Polson, Scott, 2010 <DOI:10.1093/biomet/asq017>).

Track and record the use of applications and the user's interactions with Shiny inputs. Allows to trace the inputs with which the user interacts, the outputs generated, as well as the errors displayed in the interface.

This package implements methods for variable selection in linear regression based on the "Sum of Single Effects" (SuSiE) model, as described in Wang et al (2020) <DOI:10.1101/501114> and Zou et al (2021) <DOI:10.1101/2021.11.03.467167>. These methods provide simple summaries, called "Credible Sets", for accurately quantifying uncertainty in which variables should be selected. The methods are motivated by genetic fine-mapping applications, and are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse. The fitting algorithm, a Bayesian analogue of stepwise selection methods called "Iterative Bayesian Stepwise Selection" (IBSS), is simple and fast, allowing the SuSiE model be fit to large data sets (thousands of samples and hundreds of thousands of variables).

This package provides a set of functions to build a scoring model from beginning to end, leading the user to follow an efficient and organized development process, reducing significantly the time spent on data exploration, variable selection, feature engineering, binning and model selection among other recurrent tasks. The package also incorporates monotonic and customized binning, scaling capabilities that transforms logistic coefficients into points for a better business understanding and calculates and visualizes classic performance metrics of a classification model.

Enables small area estimation (SAE) of health and demographic indicators in low- and middle-income countries (LMICs). It powers an R shiny application for generating subnational estimates and prevalence maps of 150+ binary indicators from Demographic and Health Surveys (DHS). It builds on the SAE analysis workflow from the surveyPrev package. For documentation, visit <https://sae4health.stat.uw.edu/>. Methodological details can be found at Wu et al. (2025) <doi:10.48550/arXiv.2505.01467>.

This package implements several methods to estimate effects of generalized time-varying treatment strategies on the mean of an outcome at one or more selected follow-up times of interest. Specifically, the package implements the time-smoothed inverse probability weighted estimators described in McGrath et al. (2025) <doi:10.48550/arXiv.2509.13971>. Outcomes may be repeatedly, non-monotonically, informatively, and sparsely measured in the data source. The package also supports settings where outcomes are truncated by death, i.e. some individuals die during follow-up which renders the outcome of interest undefined at the follow-up time of interest.

Streamlines the creation of descriptive frequency tables ('Table 1'), diagnostic test accuracy evaluations (sensitivity, specificity, predictive values), and multi-outcome regression summaries. Features automatic tables, prevalence and odds ratio calculations, and seamless integration with flextable for exporting results to Microsoft Word and PowerPoint'.

This package provides a shiny interface for a simpler use of the sbm R package. It also contains useful functions to easily explore the sbm package results. With this package you should be able to use the stochastic block model without any knowledge in R, get automatic reports and nice visuals, as well as learning the basic functions of sbm'.

This package provides a minimalist implementation of model stacking by Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1> for boosted tree models. A classic, two-layer stacking model is implemented, where the first layer generates features using gradient boosting trees, and the second layer employs a logistic regression model that uses these features as inputs. Utilities for training the base models and parameters tuning are provided, allowing users to experiment with different ensemble configurations easily. It aims to provide a simple and efficient way to combine multiple gradient boosting models to improve predictive model performance and robustness.

This package contains functions to perform various models and methods for test equating (Kolen and Brennan, 2014 <doi:10.1007/978-1-4939-0317-7> ; Gonzalez and Wiberg, 2017 <doi:10.1007/978-3-319-51824-4> ; von Davier et. al, 2004 <doi:10.1007/b97446>). It currently implements the traditional mean, linear and equipercentile equating methods. Both IRT observed-score and true-score equating are also supported, as well as the mean-mean, mean-sigma, Haebara and Stocking-Lord IRT linking methods. It also supports newest methods such that local equating, kernel equating (using Gaussian, logistic, Epanechnikov, uniform and adaptive kernels) with presmoothing, and IRT parameter linking methods based on asymmetric item characteristic functions. Functions to obtain both standard error of equating (SEE) and standard error of equating differences between two equating functions (SEED) are also implemented for the kernel method of equating.