The BAGofT assesses the goodness-of-fit of binary classifiers. Details can be found in Zhang, Ding and Yang (2021) <arXiv:1911.03063v2>.

Perform bulk and cell type-specific expression quantitative trail loci mapping with our novel method (Little et al. (2023) <doi:10.1038/s41467-023-38795-w>).

Helpful functions for the cleaning and manipulation of surveillance data, especially with regards to the creation and validation of panel data from individual level surveillance data.

Estimation of number and location of change points in mean-shift (piecewise constant) models. Particularly useful (but not confined) to model genomic sequences of continuous measurements.

This package provides functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.

Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.

This package provides functions for financial analysis and financial modeling, including batch graphs generation, beta calculation, descriptive statistics, annuity calculation, bond pricing and financial data download.

Package for haplotype-based genotype simulations. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set.

Assists in generating binary clustered data, estimates of Intracluster Correlation coefficient (ICC) for binary response in 16 different methods, and 5 different types of confidence intervals.

This package provides methods for fitting log-link GLMs and GAMs to binomial data, including EM-type algorithms with more stable convergence properties than standard methods.

Find dark genes. These genes are often disregarded due to no detected mutation or differential expression, but are important in coordinating the functionality in cancer networks.

This package provides methods of selecting one from many numeric predictors for a regression model, to ensure that the additional predictor has the maximum effect size.

This package provides functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.

Features unstructured, structured and reverse geocoding using the photon geocoding API <https://photon.komoot.io/>. Facilitates the setup of local photon instances to enable offline geocoding.

Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.

Uses statistical network modeling to understand the co-expression relationships among genes and to construct sparse gene co-expression networks from single-cell gene expression data.

Develops a framework for fisheries stock assessment simulation testing with Stock Synthesis (SS) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.

Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling. Schultze (2017) <doi:10.17169/refubium-622>.

Converts the floor speeches of Uruguayan legislators, extracted from the parliamentary minutes, to tidy data.frame where each observation is the intervention of a single legislator.

Create HTML tables of descriptive statistics, as one would expect to see as the first table (i.e. "Table 1") in a medical/epidemiological journal article.

This package provides functions for statistical analysis, prediction and control of time series based mainly on Akaike and Nakagawa (1988) <ISBN 978-90-277-2786-2>.

The companion package that provides all the datasets used in the book "Data Integration, Manipulation and Visualization of Phylogenetic Trees" by Guangchuang Yu (2022, ISBN:9781032233574).

Calculates the volume under the ROC surface and its (co)variance for ordered multi-class ROC analysis as well as certain bivariate ordinal measures of association.

Error variance estimation in ultrahigh dimensional datasets with four different methods, viz. Refitted cross validation, k-fold refitted cross validation, Bootstrap-refitted cross validation, Ensemble method.