This package provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.

Classical methods for combining summary data from genome-wide association studies (GWAS) only use marginal genetic effects and power can be compromised in the presence of heterogeneity. subgxe is a R package that implements p-value assisted subset testing for association (pASTA), a method developed by Yu et al. (2019) <doi:10.1159/000496867>. pASTA generalizes association analysis based on subsets by incorporating gene-environment interactions into the testing procedure.

This package provides a set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series. U. Mori, A. Mendiburu and J.A. Lozano (2016), <doi:10.32614/RJ-2016-058>.

Multivariate regression methodologies including classical reduced-rank regression (RRR) studied by Anderson (1951) <doi:10.1214/aoms/1177729580> and Reinsel and Velu (1998) <doi:10.1007/978-1-4757-2853-8>, reduced-rank regression via adaptive nuclear norm penalization proposed by Chen et al. (2013) <doi:10.1093/biomet/ast036> and Mukherjee et al. (2015) <doi:10.1093/biomet/asx080>, robust reduced-rank regression (R4) proposed by She and Chen (2017) <doi:10.1093/biomet/asx032>, generalized/mixed-response reduced-rank regression (mRRR) proposed by Luo et al. (2018) <doi:10.1016/j.jmva.2018.04.011>, row-sparse reduced-rank regression (SRRR) proposed by Chen and Huang (2012) <doi:10.1080/01621459.2012.734178>, reduced-rank regression with a sparse singular value decomposition (RSSVD) proposed by Chen et al. (2012) <doi:10.1111/j.1467-9868.2011.01002.x> and sparse and orthogonal factor regression (SOFAR) proposed by Uematsu et al. (2019) <doi:10.1109/TIT.2019.2909889>.

BSeq-sc is a bioinformatics analysis pipeline that leverages single-cell sequencing data to estimate cell type proportion and cell type-specific gene expression differences from RNA-seq data from bulk tissue samples. This is a companion package to the publication "A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure." Baron et al. Cell Systems (2016) https://www.ncbi.nlm.nih.gov/pubmed/27667365.

This package provides an implementation of sparse linear discriminant analysis, which is a supervised classification method for multiple classes. Various novel optimization approaches to this problem are implemented including alternating direction method of multipliers (ADMM), proximal gradient (PG) and accelerated proximal gradient (APG). Functions for performing cross validation are also supplied along with basic prediction and plotting functions. Sparse zero variance discriminant (SZVD) analysis is also included in the package.

This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.

This a package containing diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class sf, Spatial, and nb. It also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some of the datasets are designed to illustrate specific analysis techniques. cycle_hire() and cycle_hire_osm(), for example, are designed to illustrate point pattern analysis techniques.

This package implements anomaly detection as binary classification for cross-sectional data. Uses maximum likelihood estimates and normal probability functions to classify observations as anomalous. The method is presented in the following lecture from the Machine Learning course by Andrew Ng: <https://www.coursera.org/learn/machine-learning/lecture/C8IJp/algorithm/>, and is also described in: Aleksandar Lazarevic, Levent Ertoz, Vipin Kumar, Aysel Ozgur, Jaideep Srivastava (2003) <doi:10.1137/1.9781611972733.3>.

Impute the survival times for censored observations based on their conditional survival distributions derived from the Kaplan-Meier estimator. CondiS can replace the censored observations with the best approximations from the statistical model, allowing for direct application of machine learning-based methods. When covariates are available, CondiS is extended by incorporating the covariate information through machine learning-based regression modeling ('CondiS_X'), which can further improve the imputed survival time.

Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA package). Using the framework of linear model-based differential expression comparisons ('limma package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.

This package implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

This package contains logic for computing sparse principal components via the EESPCA method, which is based on an approximation of the eigenvector/eigenvalue identity. Includes logic to support execution of the TPower and rifle sparse PCA methods, as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle via cross-validation to minimize the out-of-sample reconstruction error. H. Robert Frost (2021) <doi:10.1080/10618600.2021.1987254>.

Computes the sample probability value (p-value) for the estimated coefficient from a standard genome-wide univariate regression. It computes the exact finite-sample p-value under the assumption that the measured phenotype (the dependent variable in the regression) has a known Bernoulli-normal mixture distribution. Finite-sample genome-wide regression p-values (Gwrpv) with a non-normally distributed phenotype (Gregory Connor and Michael O'Neill, bioRxiv 204727 <doi:10.1101/204727>).

This package provides tools for the development of packages related to General Transit Feed Specification (GTFS) files. Establishes a standard for representing GTFS feeds using R data types. Provides fast and flexible functions to read and write GTFS feeds while sticking to this standard. Defines a basic gtfs class which is meant to be extended by packages that depend on it. And offers utility functions that support checking the structure of GTFS objects.

Implement a coherent and flexible protocol for animal color tagging. GenTag provides a simple computational routine with low CPU usage to create color sequences for animal tag. First, a single-color tag sequence is created from an algorithm selected by the user, followed by verification of the combination uniqueness. Three methods to produce color tag sequences are provided. Users can modify the main function core to allow a wide range of applications.

Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) /doi10.1002/sim.7350 and the models with missing event types as described in Park, Bakoyannis, Zhang, & Yiannoutsos (2021) \doi10.1093/biostatistics/kxaa052. The proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.

This package provides tools to create an interactive web-based visualization of a topic model that has been fit to a corpus of text data using Latent Dirichlet Allocation (LDA). Given the estimated parameters of the topic model, it computes various summary statistics as input to an interactive visualization built with D3.js that is accessed via a browser. The goal is to help users interpret the topics in their LDA topic model.

This package provides functions implementing multivariate state space models for purposes of time series analysis and forecasting. The focus of the package is on multivariate models, such as Vector Exponential Smoothing, Vector ETS (Error-Trend-Seasonal model) etc. It currently includes Vector Exponential Smoothing (VES, de Silva et al., 2010, <doi:10.1177/1471082X0901000401>), Vector ETS (Svetunkov et al., 2023, <doi:10.1016/j.ejor.2022.04.040>) and simulation function for VES.

This package provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation. * The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.

This package provides statistical methods for network meta-analysis of 1â 5 diagnostic tests to simultaneously compare multiple tests within a missing data framework, including: - Bayesian hierarchical model for network meta-analysis of multiple diagnostic tests (Ma, Lian, Chu, Ibrahim, and Chen (2018) <doi:10.1093/biostatistics/kxx025>) - Bayesian Hierarchical Summary Receiver Operating Characteristic Model for Network Meta-Analysis of Diagnostic Tests (Lian, Hodges, and Chu (2019) <doi:10.1080/01621459.2018.1476239>).

This package provides a framework for estimating difference-in-differences with unpoolable data, based on Karim, Webb, Austin, and Strumpf (2024) <doi:10.48550/arXiv.2403.15910>. Supports common or staggered adoption, multiple groups, and the inclusion of covariates. Also computes p-values for the aggregate average treatment effect on the treated via the randomization inference procedure described in MacKinnon and Webb (2020) <doi:10.1016/j.jeconom.2020.04.024>.

This package provides bindings to ImageMagick, a comprehensive image processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio, images are automatically previewed when printed to the console, resulting in an interactive editing environment.

This package represents a collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.