This package performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".

This package provides a data set of the Portuguese NHS hospitals.

Interface to H2O4GPU <https://github.com/h2oai/h2o4gpu>, a collection of GPU solvers for machine learning algorithms.

Tracks elapsed clock time using a `hms::hms()` scalar. It was was originally developed to time Bayesian model runs. It should not be used to estimate how long extremely fast code takes to execute as the package code adds a small time cost.

Higher-order latent trait theory (item response theory). We implement the generalized partial credit model with a second-order latent trait structure. Latent regression can be done on the second-order latent trait. For a pre-print of the methods, see, "Latent Regression in Higher-Order Item Response Theory with the R Package hlt" <https://mkleinsa.github.io/doc/hlt_proof_draft_brmic.pdf>.

Simulate and analyze hierarchical composite endpoints with univariate distributions by Gasparyan, Koch, Brunner in (2025) in â The Univariate Distribution of Hierarchical Composite Endpoints and the Condorcet Non-transitivity Paradox.â (Biometrical Journal 68 (3), <doi:10.1002/bimj.70140>). Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) â Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progressionâ (Journal of the American Society of Nephrology 34 (2): 2025â 2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method, but other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in â An unbiased rank-based estimator of the Mannâ Whitney variance including the case of tiesâ (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Includes implementation of a new Wilson-type, compatible confidence interval for the win odds, as proposed by Schüürhuis, Konietschke, Brunner (2025) in â A new approach to the nonparametric Behrensâ Fisher problem with compatible confidence intervals.â (Biometrical Journal 67 (6), <doi:10.1002/bimj.70096>). Stratification and covariate adjustment are performed based on the methodology presented by Koch GG et al. in â Issues for covariance analysis of dichotomous and ordered categorical data from randomized clinical trials and non-parametric strategies for addressing themâ (Statistics in Medicine 17 (15-16): 1863â 92). For a review, see Gasparyan SB et al (2021) â Adjusted win ratio with stratification: Calculation methods and interpretationâ (Statistical Methods in Medical Research 30 (2): 580â 611, <doi:10.1177/0962280220942558>).

This package provides a collection of functions for sampling and simulating 3D surfaces and objects and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity, second moments of area and volume, and more.

This package provides a toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA GitHub repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.

This package contains functions to construct high-dimensional orthogonal maximin distance designs in two, four, eight, and sixteen levels from rotating the Kronecker product of sub-Hadamard matrices.

Higher order likelihood inference is a promising approach for analyzing small sample size data. The holi package provides web applications for higher order likelihood inference. It currently supports linear, logistic, and Poisson generalized linear models through the rstar_glm() function, based on Pierce and Bellio (2017) <doi:10.1111/insr.12232> and likelihoodAsy'. The package offers two main features: LA_rstar(), which launches an interactive shiny application allowing users to fit models with rstar_glm() through their web browser, and sim_rstar_glm_pgsql(), which streamlines the process of launching a web-based shiny simulation application that saves results to a user-created PostgreSQL database.

This package implements some item response models for multiple ratings, including the hierarchical rater model, conditional maximum likelihood estimation of linear logistic partial credit model and a wrapper function to the commercial FACETS program. See Robitzsch and Steinfeld (2018) for a description of the functionality of the package. See Wang, Su and Qiu (2014; <doi:10.1111/jedm.12045>) for an overview of modeling alternatives.

This package implements Interpretable Boosted Linear Models (IBLMs). These combine a conventional generalized linear model (GLM) with a machine learning component, such as XGBoost. The package also provides tools within for explaining and analyzing these models. For more details see Gawlowski and Wang (2025) <https://ifoa-adswp.github.io/IBLM/reference/figures/iblm_paper.pdf>.

Two functions for running and then post-estimating an Interrupted Time Series Analysis model. This is a solution for running time series analyses on temporally short data. See English (2019) The its.analysis R package - Modelling short time series data <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3398189> for an overview of the method.

Fast and multi-threaded implementation of isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>), extended isolation forest (Hariri, Kind, Brunner (2018) <doi:10.48550/arXiv.1811.02141>), SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>), fair-cut forest (Cortes (2021) <doi:10.48550/arXiv.2110.13402>), robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>), and customizable variations of them, for isolation-based outlier detection, clustered outlier detection, distance or similarity approximation (Cortes (2019) <doi:10.48550/arXiv.1910.12362>), isolation kernel calculation (Ting, Zhu, Zhou (2018) <doi:10.1145/3219819.3219990>), and imputation of missing values (Cortes (2019) <doi:10.48550/arXiv.1911.06646>), based on random or guided decision tree splitting, and providing different metrics for scoring anomalies based on isolation depth or density (Cortes (2021) <doi:10.48550/arXiv.2111.11639>). Provides simple heuristics for fitting the model to categorical columns and handling missing data, and offers options for varying between random and guided splits, and for using different splitting criteria.

Computes individual causes of death and population cause-specific mortality fractions using the InSilicoVA algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used InterVA method. This package provides general model fitting and customization for InSilicoVA algorithm and basic graphical visualization of the output.

Computes bilateral and multilateral index numbers. It has support for many standard bilateral indexes as well as multilateral index number methods such as GEKS, GEKS-Tornqvist (or CCDI), Geary-Khamis and the weighted time product dummy (for details on these methods see Diewert and Fox (2020) <doi:10.1080/07350015.2020.1816176>). It also supports updating of multilateral indexes using several splicing methods.

It provides a general framework to analyse dependence between point processes in time. It includes parametric and non-parametric tests to study independence, and functions for generating and analysing different types of dependence.

This package provides functions to import and handle infrared spectra (import from .csv and Thermo Galactic's .spc', baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, atmospheric correction, tidyverse methods, plotting).

This package provides facilities of general to specific model selection for exogenous regressors in 2SLS models. Furthermore, indicator saturation methods can be used to detect outliers and structural breaks in the sample.

Expands iNEXT to include the estimation of sample completeness and evenness. The package provides simple functions to perform the following four-step biodiversity analysis: STEP 1: Assessment of sample completeness profiles. STEP 2a: Analysis of size-based rarefaction and extrapolation sampling curves to determine whether the asymptotic diversity can be accurately estimated. STEP 2b: Comparison of the observed and the estimated asymptotic diversity profiles. STEP 3: Analysis of non-asymptotic coverage-based rarefaction and extrapolation sampling curves. STEP 4: Assessment of evenness profiles. The analyses in STEPs 2a, 2b and STEP 3 are mainly based on the previous iNEXT package. Refer to the iNEXT package for details. This package is mainly focusing on the computation for STEPs 1 and 4. See Chao et al. (2020) <doi:10.1111/1440-1703.12102> for statistical background.

This package provides a runtime type system, allowing users to define and implement interfaces, enums, typed data.frame/data.table, as well as typed functions. This package enables stricter type checking and validation, improving code structure, robustness and reliability.

This package implements an S7 class for estimates based on influence functions, with forward mode automatic differentiation defined for standard arithmetic operations.

Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).

This package provides a personalized dynamic latent factor model (Zhang et al. (2024) <doi:10.1093/biomet/asae015>) for irregular multi-resolution time series data, to interpolate unsampled measurements from low-resolution time series.