The conditional treatment effect for competing risks data in observational studies is estimated. While it is described as a constant difference between the hazard functions given the covariates, we do not assume specific functional forms for the covariates. Rava, D. and Xu, R. (2021) <arXiv:2112.09535>.

Functions, data sets, analyses and examples from the book A Handbook of Statistical Analyses Using R (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2006). The first chapter of the book, which is entitled An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available.

The heterogeneous multi-task feature learning is a data integration method to conduct joint feature selection across multiple related data sets with different distributions. The algorithm can combine different types of learning tasks, including linear regression, Huber regression, adaptive Huber, and logistic regression. The modified version of Bayesian Information Criterion (BIC) is produced to measure the model performance. Package is based on Yuan Zhong, Wei Xu, and Xin Gao (2022) <https://www.fields.utoronto.ca/talk-media/1/53/65/slides.pdf>.

This package provides tools for estimating sample sizes primarily based on heritability, while also considering additional parameters such as statistical power and fold change. The package normalizes heritability values according to trait-specific heritability and classification to enhance accuracy in sample size estimation.

This package provides a shiny application, which allows you to perform single- and multi-omics analyses using your own omics datasets. After the upload of the omics datasets and a metadata file, single-omics is performed for feature selection and dataset reduction. These datasets are used for pairwise- and multi-omics analyses, where automatic tuning is done to identify correlations between the datasets - the end goal of the recommended Holomics workflow. Methods used in the package were implemented in the package mixomics by Florian Rohart,Benoît Gautier,Amrit Singh,Kim-Anh Lê Cao (2017) <doi:10.1371/journal.pcbi.1005752> and are described there in further detail.

The presence of outliers in a dataset can substantially bias the results of statistical analyses. To correct for outliers, micro edits are manually performed on all records. A set of constraints and decision rules is typically used to aid the editing process. However, straightforward decision rules might overlook anomalies arising from disruption of linear relationships. Computationally efficient methods are provided to identify historical, tail, and relational anomalies at the data-entry level (Sartore et al., 2024; <doi:10.6339/24-JDS1136>). A score statistic is developed for each anomaly type, using a distribution-free approach motivated by the Bienaymé-Chebyshev's inequality, and fuzzy logic is used to detect cellwise outliers resulting from different types of anomalies. Each data entry is individually scored and individual scores are combined into a final score to determine anomalous entries. In contrast to fuzzy logic, Bayesian bootstrap and a Bayesian test based on empirical likelihoods are also provided as studied by Sartore et al. (2024; <doi:10.3390/stats7040073>). These algorithms allow for a more nuanced approach to outlier detection, as it can identify outliers at data-entry level which are not obviously distinct from the rest of the data. --- This research was supported in part by the U.S. Department of Agriculture, National Agriculture Statistics Service. The findings and conclusions in this publication are those of the authors and should not be construed to represent any official USDA, or US Government determination or policy.

This package provides a program that conducts group variable selection for quantile and robust mean regression (Sherwood and Li, 2022). The group lasso penalty (Yuan and Lin, 2006) is used for group-wise variable selection. Both of the quantile and mean regression models are based on the Huber loss. Specifically, with the tuning parameter in the Huber loss approaching to 0, the quantile check function can be approximated by the Huber loss for the median and the tilted version of Huber loss at other quantiles. Such approximation provides computational efficiency and stability, and has also been shown to be statistical consistent.

Pure set data visualization approaches are often limited in scalability due to the combinatorial explosion of distinct set families as the number of sets under investigation increases. hierarchicalSets applies a set centric hierarchical clustering of the sets under investigation and uses this hierarchy as a basis for a range of scalable visual representations. hierarchicalSets is especially well suited for collections of sets that describe comparable comparable entities as it relies on the sets to have a meaningful relational structure.

Tests for two high-dimensional population mean vectors. The user has the option to compute the asymptotic, the permutation or the bootstrap based p-value of the test. Some references are: Chen S.X. and Qin Y.L. (2010). <doi:10.1214/09-AOS716>, Cai T.T., Liu W., and Xia Y. (2014) <doi:10.1111/rssb.12034> and Yu X., Li D., Xue L. and Li, R. (2023) <doi:10.1080/01621459.2022.2061354>.

This package implements hierarchically regularized entropy balancing proposed by Xu and Yang (2022) <doi:10.1017/pan.2022.12>. The method adjusts the covariate distributions of the control group to match those of the treatment group. hbal automatically expands the covariate space to include higher order terms and uses cross-validation to select variable penalties for the balancing conditions.

Meyer and Held (2017) <doi:10.1093/biostatistics/kxw051> present an age-structured spatio-temporal model for infectious disease counts. The approach is illustrated in a case study on norovirus gastroenteritis in Berlin, 2011-2015, by age group, city district and week, using additional contact data from the POLYMOD survey. This package contains the data and code to reproduce the results from the paper, see demo("hhh4contacts")'.

Used for predicting a genotypeâ s allelic state at a specific locus/QTL/gene. This is accomplished by using both a genotype matrix and a separate file which has categorizations about loci/QTL/genes of interest for the individuals in the genotypic matrix. A training population can be created from a panel of individuals who have been previously screened for specific loci/QTL/genes, and this previous screening could be summarized into a category. Using the categorization of individuals which have been genotyped using a genome wide marker platform, a model can be trained to predict what category (haplotype) an individual belongs in based on their genetic sequence in the region associated with the locus/QTL/gene. These trained models can then be used to predict the haplotype of a locus/QTL/gene for individuals which have been genotyped with a genome wide platform yet not genotyped for the specific locus/QTL/gene. This package is based off work done by Winn et al 2021. For more specific information on this method, refer to <doi:10.1007/s00122-022-04178-w>.

This package provides a toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA GitHub repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.

This package provides access to datasets published by Hlà daÄ státu <https://www.hlidacstatu.cz/>, a Czech watchdog, via their API.

This package provides two functions that implement the one-sided and two-sided versions of the Hodrick-Prescott filter. The one-sided version is a Kalman filter-based implementation, whereas the two- sided version uses sparse matrices for improved efficiency. References: Hodrick, R. J., and Prescott, E. C. (1997) <doi:10.2307/2953682> Mcelroy, T. (2008) <doi:10.1111/j.1368-423X.2008.00230.x> Meyer-Gohde, A. (2010) <https://ideas.repec.org/c/dge/qmrbcd/181.html> For more references, see the vignette.

This package provides functions to view files in raw binary form like in a hex editor. Additional functions to specify and read arbitrary binary formats.

Template R package with minimal setup to use Rust code in R without hacks or frameworks. Includes basic examples of importing cargo dependencies, spawning threads and passing numbers or strings from Rust to R. Cargo crates are automatically vendored in the R source package to support offline installation. The GitHub repository for this package has more details and also explains how to set up CI. This project was first presented at Erum2018 to showcase R-Rust integration <https://jeroen.github.io/erum2018/>; for a real world use-case, see the gifski package on CRAN'.

In streaming data analysis, it is crucial to detect significant shifts in the data distribution or the accuracy of predictive models over time, a phenomenon known as concept drift. The package aims to identify when concept drift occurs and provide methodologies for adapting models in non-stationary environments. It offers a range of state-of-the-art techniques for detecting concept drift and maintaining model performance. Additionally, the package provides tools for adapting models in response to these changes, ensuring continuous and accurate predictions in dynamic contexts. Methods for concept drift detection are described in Tavares (2022) <doi:10.1007/s12530-021-09415-z>.

An S4 class and several functions which utilize internally stored datasets and gauging data enable 1d water level interpolation. The S4 class (WaterLevelDataFrame) structures the computation and visualisation of 1d water level information along the German federal waterways Elbe and Rhine. hyd1d delivers 1d water level data - extracted from the FLYS database - and validated gauging data - extracted from the hydrological database WISKI7 - package-internally. For computations near real time gauging data are queried externally from the PEGELONLINE REST API <https://pegelonline.wsv.de/webservice/dokuRestapi>.

Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

In some cases you will have data in a histogram format, where you have a vector of all possible observations, and a vector of how many times each observation appeared. You could expand this into a single 1D vector, but this may not be advisable if the counts are extremely large. HistDat allows for the calculation of summary statistics without the need for expanding your data.

This package creates nomogram visualizations for penalized Cox regression models, with the support of reproducible survival model building, validation, calibration, and comparison for high-dimensional data.

Method and tool for generating hybrid time series forecasts using an error remodeling approach. These forecasting approaches utilize a recursive technique for modeling the linearity of the series using a linear method (e.g., ARIMA, Theta, etc.) and then models (forecasts) the residuals of the linear forecaster using non-linear neural networks (e.g., ANN, ARNN, etc.). The hybrid architectures comprise three steps: firstly, the linear patterns of the series are forecasted which are followed by an error re-modeling step, and finally, the forecasts from both the steps are combined to produce the final output. This method additionally provides the confidence intervals as needed. Ten different models can be implemented using this package. This package generates different types of hybrid error correction models for time series forecasting based on the algorithms by Zhang. (2003), Chakraborty et al. (2019), Chakraborty et al. (2020), Bhattacharyya et al. (2021), Chakraborty et al. (2022), and Bhattacharyya et al. (2022) <doi:10.1016/S0925-2312(01)00702-0> <doi:10.1016/j.physa.2019.121266> <doi:10.1016/j.chaos.2020.109850> <doi:10.1109/IJCNN52387.2021.9533747> <doi:10.1007/978-3-030-72834-2_29> <doi:10.1007/s11071-021-07099-3>.

Test the significance of coefficients in high dimensional generalized linear models.