Perform censored quantile regression of Huang (2010) <doi:10.1214/09-AOS771>, and restore monotonicity respecting via adaptive interpolation for dynamic regression of Huang (2017) <doi:10.1080/01621459.2016.1149070>. The monotonicity-respecting restoration applies to general dynamic regression models including (uncensored or censored) quantile regression model, additive hazards model, and dynamic survival models of Peng and Huang (2007) <doi:10.1093/biomet/asm058>, among others.

In metabolic flux experiments tracer molecules (often glucose containing labelled carbon) are incorporated in compounds measured using mass spectrometry. The mass isotopologue distributions of these compounds needs to be corrected for natural abundance of labelled carbon and other effects, which are specific on the compound and ionization technique applied. This package provides functions to correct such effects in gas chromatography atmospheric pressure chemical ionization mass spectrometry analyses.

This package provides a simple interface for multivariate correlation analysis that unifies various classical statistical procedures including t-tests, tests in univariate and multivariate linear models, parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score tests of particular hypotheses in generalized linear models, canonical correlation analysis and linear discriminant analysis.

Decorrelates a set of summary statistics (i.e., Z-scores or P-values per SNP) via Decorrelation by Orthogonal Transformation (DOT) approach and performs gene-set analyses by combining transformed statistic values; operations are performed with algorithms that rely only on the association summary results and the linkage disequilibrium (LD). For more details on DOT and its power, see Olga (2020) <doi:10.1371/journal.pcbi.1007819>.

Replication methods to compute some basic statistic operations (means, standard deviations, frequency tables, percentiles, mean comparisons using weighted effect coding, generalized linear models, and linear multilevel models) in complex survey designs comprising multiple imputed or nested imputed variables and/or a clustered sampling structure which both deserve special procedures at least in estimating standard errors. See the package documentation for a more detailed description along with references.

Lightweight utilities to estimate autoregressive (AR) and autoregressive moving average (ARMA) noise models from residuals and apply matched generalized least squares to whiten functional magnetic resonance imaging (fMRI) design and data matrices. The ARMA estimator follows a classic 1982 approach <doi:10.1093/biomet/69.1.81>, and a restricted AR family mirrors workflows described by Cox (2012) <doi:10.1016/j.neuroimage.2011.08.056>.

Fair machine learning regression models which take sensitive attributes into account in model estimation. Currently implementing Komiyama et al. (2018) <http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf>, Zafar et al. (2019) <https://www.jmlr.org/papers/volume20/18-262/18-262.pdf> and my own approach from Scutari, Panero and Proissl (2022) <doi:10.1007/s11222-022-10143-w> that uses ridge regression to enforce fairness.

Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (<https://www.nature.com/articles/nmeth.2848>). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.

Launches a shiny based application for Nuclear Magnetic Resonance (NMR)data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of STOCSY method could be found at Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>.

Compute effect sizes and their sampling variances from factorial experimental designs. The package supports calculation of simple effects, overall effects, and interaction effects for use in factorial meta-analyses. See Gurevitch et al. (2000) <doi:10.1086/303337>, Morris et al. (2007) <doi:10.1890/06-0442>, Lajeunesse (2011) <doi:10.1890/11-0423.1> and Macartney et al. (2022) <doi:10.1016/j.neubiorev.2022.104554>.

This package provides a collection of statistical tests for the detection of differential item functioning (DIF) in multistage tests. Methods entail logistic regression, an adaptation of the simultaneous item bias test (SIBTEST), and various score-based tests. The presented tests provide itemwise test for DIF along categorical, ordinal or metric covariates. Methods for uniform and non-uniform DIF effects are available depending on which method is used.

This package provides a new method to implement clustering from multiple modality data of certain samples, the function M2SMjF() jointly factorizes multiple similarity matrices into a shared sub-matrix and several modality private sub-matrices, which is further used for clustering. Along with this method, we also provide function to calculate the similarity matrix and function to evaluate the best cluster number from the original data.

This package performs nonparametric analysis of longitudinal data in factorial experiments. Longitudinal data are those which are collected from the same subjects over time, and they frequently arise in biological sciences. Nonparametric methods do not require distributional assumptions, and are applicable to a variety of data types (continuous, discrete, purely ordinal, and dichotomous). Such methods are also robust with respect to outliers and for small sample sizes.

Estimates DNA target concentration by classifying digital PCR (polymerase chain reaction) droplets as positive, negative, or rain, using Expectation-Maximization Clustering. The fitting is accomplished using the EMMIXskew R package (v. 1.0.3) by Kui Wang, Angus Ng, and Geoff McLachlan (2018) as based on their paper "Multivariate Skew t Mixture Models: Applications to Fluorescence-Activated Cell Sorting Data" <doi:10.1109/DICTA.2009.88>.

Identifies what optimal subset of a desired number of items should be retained in a short version of a psychometric instrument to assess the â broadestâ proportion of the construct-level content of the set of items included in the original version of the said psychometric instrument. Expects a symmetric adjacency matrix as input (undirected weighted network model). Supports brute force and simulated annealing combinatorial search algorithms.

An R API providing access to a relational database with macroeconomic time series data for South Africa, obtained from the South African Reserve Bank (SARB) and Statistics South Africa (STATSSA), and updated on a weekly basis via the EconData <https://www.econdata.co.za/> platform and automated scraping of the SARB and STATSSA websites. The database is maintained at the Department of Economics at Stellenbosch University.

Estimation of group-based trajectory models, including finite mixture models for longitudinal data, supporting censored normal, zero-inflated Poisson, logit, and beta distributions, using expectation-maximization and quasi-Newton methods, with tools for model selection, diagnostics, and visualization of latent trajectory groups, <doi:10.4159/9780674041318>, Nagin, D. (2005). Group-Based Modeling of Development. Cambridge, MA: Harvard University Press. and Noel (2022), <https://orbilu.uni.lu/>, thesis.

This package provides low-level access to GDAL functionality. GDAL is the Geospatial Data Abstraction Library a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable developing further tools.

This package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. AbseqR empowers the users of abseqPy with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.

This package includes functions and reference data to generate and manipulate log-ratios (also known as log size index (LSI) values) from measurements obtained on zooarchaeological material. Log ratios are used to compare the relative (rather than the absolute) dimensions of animals from archaeological contexts. The zoolog package is also able to seamlessly integrate data and references with heterogeneous nomenclature, which is internally managed by a zoolog thesaurus.

Perform seasonal adjustment and forecasting of weekly data. The package provides a user-friendly interface for computing seasonally adjusted estimates and forecasts of weekly time series and includes functions for the construction of country-specific prior adjustment variables, as well as diagnostic tools to assess the quality of the adjustments. The methodology is described in more detail in Ginker (2024) <doi:10.13140/RG.2.2.12221.44000>.

Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) <DOI:10.1186/s12859-017-1863-x> and the package vignette.

Conditional distance correlation <doi:10.1080/01621459.2014.993081> is a novel conditional dependence measurement of two multivariate random variables given a confounding variable. This package provides conditional distance correlation, performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data <https://www3.stat.sinica.edu.tw/statistica/J28N1/J28N114/J28N114.html>, and conducts conditional distance covariance test for conditional independence assumption of two multivariate variable.