This package provides a comprehensive interface for Google Gemini API, enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R. This package facilitates seamless integration with Google Gemini, allowing for advanced language processing, text generation, and other AI-driven capabilities within the R environment. For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.

This package provides a Gaussian or Student's t copula-based procedure for generating samples from discrete random variables with prescribed correlation matrix and marginal distributions.

Fits gastric emptying time series from MRI or scintigraphic measurements using nonlinear mixed-model population fits with nlme and Bayesian methods with Stan; computes derived parameters such as t50 and AUC.

The algorithm of semi-supervised learning is based on finite Gaussian mixture models and includes a mechanism for handling missing data. It aims to fit a g-class Gaussian mixture model using maximum likelihood. The algorithm treats the labels of unclassified features as missing data, building on the framework introduced by Rubin (1976) <doi:10.2307/2335739> for missing data analysis. By taking into account the dependencies in the missing pattern, the algorithm provides more information for determining the optimal classifier, as specified by Bayes rule.

This package provides methods for model selection, estimation, inference, and simulation for the multilevel factor model, based on the principal component estimation and generalised canonical correlation approach. Details can be found in "Generalised Canonical Correlation Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.

This package provides methods for searching through genealogical data and displaying the results. Plotting algorithms assist with data exploration and publication-quality image generation. Includes interactive genealogy visualization tools. Provides parsing and calculation methods for variables in descendant branches of interest. Uses the Grammar of Graphics.

Set of functions to create datasets using a correlation matrix.

This package implements a one-sector Armington-CES gravity model with general equilibrium (GE) effects. This model is designed to analyze international and domestic trade by capturing the impacts of trade costs and policy changes within a general equilibrium framework. Additionally, it includes a local parameter to run simulations on productivity. The package provides functions for calibration, simulation, and analysis of the model.

Helper functions provide an accurate imputation algorithm for reconstructing the missing segment in a multi-variate data streams. Inspired by single-shot learning, it reconstructs the missing segment by identifying the first similar segment in the stream. Nevertheless, there should be one column of data available, i.e. a constraint column. The values of columns can be characters (A, B, C, etc.). The result of the imputed dataset will be returned a .csv file. For more details see Reza Rawassizadeh (2019) <doi:10.1109/TKDE.2019.2914653>.

This package provides methods and tools for the analysis of Genome Wide Identity-by-Descent ('gwid') mapping data, focusing on testing whether there is a higher occurrence of Identity-By-Descent (IBD) segments around potential causal variants in cases compared to controls, which is crucial for identifying rare variants. To enhance its analytical power, gwid incorporates a Sliding Window Approach, allowing for the detection and analysis of signals from multiple Single Nucleotide Polymorphisms (SNPs).

Allows users to generate a gendered language score according to the gendered language dictionary in Roberts and Utych (2019) <doi:10.1177/1065912919874883>.

Genie is a robust hierarchical clustering algorithm (Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>). genieclust is its faster, more capable implementation (Gagolewski, 2021 <DOI:10.1016/j.softx.2021.100722>). It enables clustering with respect to mutual reachability distances, allowing it to act as an alternative to HDBSCAN* that can identify any number of clusters or their entire hierarchy. When combined with the deadwood package, it can act as an outlier detector. Additional package features include the Gini and Bonferroni inequality indices, external cluster validity measures (e.g., the normalised clustering accuracy, the adjusted Rand index, the Fowlkes-Mallows index, and normalised mutual information), and internal cluster validity indices (e.g., the Calinski-Harabasz, Davies-Bouldin, Ball-Hall, Silhouette, and generalised Dunn indices). The Python version of genieclust is available via PyPI'.

Density, distribution function, quantile function, and random generation for the generalized Beta and Beta prime distributions. The family of generalized Beta distributions is conjugate for the Bayesian binomial model, and the generalized Beta prime distribution is the posterior distribution of the relative risk in the Bayesian two Poisson samples model when a Gamma prior is assigned to the Poisson rate of the reference group and a Beta prime prior is assigned to the relative risk. References: Laurent (2012) <doi:10.1214/11-BJPS139>, Hamza & Vallois (2016) <doi:10.1016/j.spl.2016.03.014>, Chen & Novick (1984) <doi:10.3102/10769986009002163>.

Simple and user-friendly wrappers to the saemix package for performing linear and non-linear mixed-effects regression modeling for growth data to account for clustering or longitudinal analysis via repeated measurements. The package allows users to fit a variety of growth models, including linear, exponential, logistic, and Gompertz functions. For non-linear models, starting values are automatically calculated using initial least-squares estimates. The package includes functions for summarizing models, visualizing data and results, calculating doubling time and other key statistics, and generating model diagnostic plots and residual summary statistics. It also provides functions for generating publication-ready summary tables for reports. Additionally, users can fit linear and non-linear least-squares regression models if clustering is not applicable. The mixed-effects modeling methods in this package are based on Comets, Lavenu, and Lavielle (2017) <doi:10.18637/jss.v080.i03> as implemented in the saemix package. Please contact us at models@dfci.harvard.edu with any questions.

Estimation and analysis of group-based multivariate trajectory models (Nagin, 2018 <doi:10.1177/0962280216673085>; Magrini, 2022 <doi:10.1007/s10182-022-00437-9>). The package implements an Expectation-Maximization (EM) algorithm allowing unbalanced panel and missing values, and provides several functionalities for prediction and graphical representation.

Convert Ensembl gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including Entrez', HGNC', and UniProt'.

This package provides a wrapper of different standard estimation methods for gravity models. This package provides estimation methods for log-log models and multiplicative models.

Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.

You can use this function to easily draw a combined histogram and restricted cubic spline. The function draws the graph through ggplot2'. RCS fitting requires the use of the rcs() function of the rms package. Can fit cox regression, logistic regression. This method was described by Per Kragh (2003) <doi:10.1002/sim.1497>.

This package implements maximum likelihood estimation for Gaussian processes, supporting both isotropic and separable models with predictive capabilities. Includes penalized likelihood estimation following Li and Sudjianto (2005, <doi:10.1198/004017004000000671>), with cross-validation guided by decorrelated prediction error (DPE) metric. DPE metric, motivated by Mahalanobis distance, serves as evaluation criteria that accounts for predictive uncertainty in tuning parameter selection (Mutoh, Booth, and Stallrich, 2025, <doi:10.48550/arXiv.2511.18111>). Designed specifically for small datasets.

Preview what a ggplot2 plot would look like if you save it to a file. Attach picture dimensions as a canvas() element and get an instant preview. These dimensions will then be used when you save the plot.

Execute Latent Class Analysis (LCA) and Latent Class Regression (LCR) by using Generalized Structured Component Analysis (GSCA). This is explained in Ryoo, Park, and Kim (2019) <doi:10.1007/s41237-019-00084-6>. It estimates the parameters of latent class prevalence and item response probability in LCA with a single line comment. It also provides graphs of item response probabilities. In addition, the package enables to estimate the relationship between the prevalence and covariates.

Fit Generalized Linear Models to continuous and count outcomes, as well as estimate the prevalence of misrepresentation of an important binary predictor. Misrepresentation typically arises when there is an incentive for the binary factor to be misclassified in one direction (e.g., in insurance settings where policy holders may purposely deny a risk status in order to lower the insurance premium). This is accomplished by treating a subset of the response variable as resulting from a mixture distribution. Model parameters are estimated via the Expectation Maximization algorithm and standard errors of the estimates are obtained from closed forms of the Observed Fisher Information. For an introduction to the models and the misrepresentation framework, see Xia et. al., (2023) <https://variancejournal.org/article/73151-maximum-likelihood-approaches-to-misrepresentation-models-in-glm-ratemaking-model-comparisons>.

This package provides a memory-efficient implementation for integrating gene expression data from single-cell RNA sequencing experiments. Uses a C++ backend with thin R wrappers to enable analysis of large-scale single-cell datasets. The package supports multiple data modalities including count matrices, paired data (splicing, RNA velocity, CITE-seq), and binary indicators. It implements a latent variable model with block coordinate descent optimization for dimensionality reduction and batch effect correction. Core algorithms are described in Madrigal et al. (2024) <doi:10.1038/s41467-024-50963-0>.