Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.

Uses C++ via the Rcpp package to parse modern Excel files ('.xlsx'). Memory usage is kept minimal by decompressing only parts of the file at a time, while employing multiple threads to achieve significant runtime reduction. Uses <https://github.com/richgel999/miniz> and <https://github.com/lemire/fast_double_parser>.

Download data from StatsWales into R. Removes the need for the user to write their own loops when parsing data from the StatsWales API. Provides functions for datasets (<http://open.statswales.gov.wales/en-gb/dataset>) and metadata (<http://open.statswales.gov.wales/en-gb/discover/metadata>) endpoints.

There are several functions to implement the method for analysis in a randomized clinical trial with strata with following key features. A stratified Mann-Whitney estimator addresses the comparison between two randomized groups for a strictly ordinal response variable. The multivariate vector of such stratified Mann-Whitney estimators for multivariate response variables can be considered for one or more response variables such as in repeated measurements and these can have missing completely at random (MCAR) data. Non-parametric covariance adjustment is also considered with the minimal assumption of randomization. The p-value for hypothesis test and confidence interval are provided.

This package provides a framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.

This package provides computational tools for estimating inverse regions and constructing the corresponding simultaneous outer and inner confidence regions. Acceptable input includes both one-dimensional and two-dimensional data for linear, logistic, functional, and spatial generalized least squares regression models. Functions are also available for constructing simultaneous confidence bands (SCBs) for these models. The definition of simultaneous confidence regions (SCRs) follows Sommerfeld et al. (2018) <doi:10.1080/01621459.2017.1341838>. Methods for estimating inverse regions, SCRs, and the nonparametric bootstrap are based on Ren et al. (2024) <doi:10.1093/jrsssc/qlae027>. Methods for constructing SCBs are described in Crainiceanu et al. (2024) <doi:10.1201/9781003278726> and Telschow et al. (2022) <doi:10.1016/j.jspi.2021.05.008>.

This package provides a collection of sample datasets on various fields such as automotive performance and safety data to historical demographics and socioeconomic indicators, as well as recreational data. It serves as a resource for researchers and analysts seeking to perform analyses and derive insights from classic data sets in R.

Univariate time series forecasting with STL decomposition based auto regressive integrated moving average (ARIMA) hybrid model. For method details see Xiong T, Li C, Bao Y (2018). <doi:10.1016/j.neucom.2017.11.053>.

Computes clustering by fitting Gaussian mixture models (GMM) via stochastic approximation following the methods of Nguyen and Jones (2018) <doi:10.1201/9780429446177>. It also provides some test data generation and plotting functionality to assist with this process.

This package provides drop-in replacements for functions from the stringr package, with the same user interface. These functions have no external dependencies and can be copied directly into your package code using the staticimports package.

This package provides you with easy, programmatic access to SRDP data.

This package provides a rudimentary sequencer to define, manipulate and mix sound samples. The underlying motivation is to sonify data, as demonstrated in the blog <https://globxblog.github.io/>, the presentation by Renard and Le Bescond (2022, <https://hal.science/hal-03710340v1>) or the poster by Renard et al. (2023, <https://hal.inrae.fr/hal-04388845v1>).

Simple classic graph algorithms for simple graph classes. Graphs may possess vertex and edge attributes. simplegraph has no dependencies and it is written entirely in R, so it is easy to install.

This package provides a novel semi-supervised machine learning algorithm to predict phenotype event times using Electronic Health Record (EHR) data.

Collection (syllogi in greek) of real and fictitious data sets for teaching purposes. The datasets were manually entered by the author from the respective references as listed in the individual dataset documentation. The fictions datasets are the creation of the author, that he has found useful for teaching statistics.

Visualizes sulcal morphometry data derived from BrainVisa <https://brainvisa.info/> including width, depth, surface area, and length. The package enables mapping of statistical group results or subject-level values onto cortical surface maps, with options to focus on all sulci or only selected regions of interest. Users can display all four measures simultaneously or restrict plots to chosen measures, creating composite, publication-quality brain visualizations in R to support the analysis and interpretation of sulcal morphology.

Data sets and functions to support the books "Statistics: Data analysis and modelling" by Speekenbrink, M. (2021) <https://mspeekenbrink.github.io/sdam-book/> and "An R companion to Statistics: data analysis and modelling" by Speekenbrink, M. (2021) <https://mspeekenbrink.github.io/sdam-r-companion/>. All datasets analysed in these books are provided in this package. In addition, the package provides functions to compute sample statistics (variance, standard deviation, mode), create raincloud and enhanced Q-Q plots, and expand Anova results into omnibus tests and tests of individual contrasts.

In a clinical trial with repeated measures designs, outcomes are often taken from subjects at fixed time-points. The focus of the trial may be to compare the mean outcome in two or more groups at some pre-specified time after enrollment. In the presence of missing data auxiliary assumptions are necessary to perform such comparisons. One commonly employed assumption is the missing at random assumption (MAR). The samon package allows the user to perform a (parameterized) sensitivity analysis of this assumption. In particular it can be used to examine the sensitivity of tests in the difference in outcomes to violations of the MAR assumption. The sensitivity analysis can be performed under two scenarios, a) where the data exhibit a monotone missing data pattern (see the samon() function), and, b) where in addition to a monotone missing data pattern the data exhibit intermittent missing values (see the samonIM() function).

Provide a workflow to jointly embed chromatin accessibility peaks and expressed genes into a shared low-dimensional space using paired single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq) data. It integrates regulatory relationships among peak-peak interactions (via Cicero'), peak-gene interactions (via Lasso, random forest, and XGBoost), and gene-gene interactions (via principal component regression). With the input of paired scATAC-seq and scRNA-seq data matrices, it assigns a low-dimensional feature vector to each gene and peak. Additionally, it supports the reconstruction of gene-gene network with low-dimensional projections (via epsilon-NN) and then the comparison of the networks of two conditions through manifold alignment implemented in scTenifoldNet'. See <doi:10.1093/bioinformatics/btaf483> for more details.

An open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments.See full documentation at <https://avi-kenny.github.io/SimEngine/>.

Balancing computational and statistical efficiency, subsampling techniques offer a practical solution for handling large-scale data analysis. Subsampling methods enhance statistical modeling for massive datasets by efficiently drawing representative subsamples from full dataset based on tailored sampling probabilities. These probabilities are optimized for specific goals, such as minimizing the variance of coefficient estimates or reducing prediction error.

This package provides a general framework to perform statistical inference of each gene pair and global inference of whole-scale gene pairs in gene networks using the well known Gaussian graphical model (GGM) in a time-efficient manner. We focus on the high-dimensional settings where p (the number of genes) is allowed to be far larger than n (the number of subjects). Four main approaches are supported in this package: (1) the bivariate nodewise scaled Lasso (Ren et al (2015) <doi:10.1214/14-AOS1286>) (2) the de-sparsified nodewise scaled Lasso (Jankova and van de Geer (2017) <doi:10.1007/s11749-016-0503-5>) (3) the de-sparsified graphical Lasso (Jankova and van de Geer (2015) <doi:10.1214/15-EJS1031>) (4) the GGM estimation with false discovery rate control (FDR) using scaled Lasso or Lasso (Liu (2013) <doi:10.1214/13-AOS1169>). Windows users should install Rtools before the installation of this package.

This package provides a collection of functions that creates graphs with error bars for data collected from one-way or higher factorial designs.

Visual representations of model fit or predictive success in the form of "separation plots." See Greenhill, Brian, Michael D. Ward, and Audrey Sacks. "The separation plot: A new visual method for evaluating the fit of binary models." American Journal of Political Science 55.4 (2011): 991-1002.