This package provides functions for the input/output and visualization of medical imaging data in the form of CIFTI files <https://www.nitrc.org/projects/cifti/>.

This package provides a wrapper for the EZC3D library to work with C3D motion capture data.

The cystiSim package provides an agent-based model for Taenia solium transmission and control. cystiSim was developed within the framework of CYSTINET, the European Network on taeniosis/cysticercosis, COST ACTION TD1302.

Calculating crude sequence ratio, adjusted sequence ratio and confidence intervals using data mapped to the Observational Medical Outcomes Partnership Common Data Model.

Integrative context-dependent clustering for heterogeneous biomedical datasets. Identifies local clustering structures in related datasets, and a global clusters that exist across the datasets.

Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Due to the small effect sizes of common variants, the power to detect individual risk variants is generally low. Complementary to SNP-level analysis, a variety of gene-based association tests have been proposed. However, the power of existing gene-based tests is often dependent on the underlying genetic models, and it is not known a priori which test is optimal. Here we proposed COMBined Association Test (COMBAT) to incorporate strengths from multiple existing gene-based tests, including VEGAS, GATES and simpleM. Compared to individual tests, COMBAT shows higher overall performance and robustness across a wide range of genetic models. The algorithm behind this method is described in Wang et al (2017) <doi:10.1534/genetics.117.300257>.

This package provides functions for classical test theory analysis, following methods presented by Wu et al. (2006) <doi:10.1007/978-981-10-3302-5>.

This package provides a set of utilities for matching products in different classification codes used in international trade research. It supports concordance between the Harmonized System (HS0, HS1, HS2, HS3, HS4, HS5, HS combined), the Standard International Trade Classification (SITC1, SITC2, SITC3, SITC4), the North American Industry Classification System (NAICS combined), as well as the Broad Economic Categories (BEC), the International Standard of Industrial Classification (ISIC), and the Standard Industrial Classification (SIC). It also provides code nomenclature/descriptions look-up, Rauch classification look-up (via concordance to SITC2), and trade elasticity look-up (via concordance to HS0 or SITC3 codes).

Create and manipulate study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model.

This package provides a simple way to write ".Rprofile" code in an R Markdown file and have it knit to the correct location for your operating system.

Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).

This package provides functions and data files to help CE Public-Use Microdata (PUMD) users calculate annual estimated expenditure means, standard errors, and quantiles according to the methods used by the CE with PUMD. For more information on the CE please visit <https://www.bls.gov/cex>. For further reading on CE estimate calculations please see the CE Calculation section of the U.S. Bureau of Labor Statistics (BLS) Handbook of Methods at <https://www.bls.gov/opub/hom/cex/calculation.htm>. For further information about CE PUMD please visit <https://www.bls.gov/cex/pumd.htm>.

This is a one-function package that will pass only unique values to a computationally-expensive function that returns an output of the same length as the input. In importing and working with tidy data, it is common to have index columns, often including time stamps that are far from unique. Some functions to work with these such as text conversion to other variable types (e.g. as.POSIXct()), various grep()-based functions, and often the cut() function are relatively slow when working with tens of millions of rows or more.

Computes p-values using the largest root test using an approximation to the null distribution by Johnstone (2008) <DOI:10.1214/08-AOS605>.

Utilities to make your clinical collaborations easier if not fun. It contains functions for designing studies such as Simon 2-stage and group sequential designs and for data analysis such as Jonckheere-Terpstra test and estimating survival quantiles.

CODATA internationally recommended values of the fundamental physical constants, provided as symbols for direct use within the R language. Optionally, the values with uncertainties and/or units are also provided if the errors', units and/or quantities packages are installed. The Committee on Data for Science and Technology (CODATA) is an interdisciplinary committee of the International Council for Science which periodically provides the internationally accepted set of values of the fundamental physical constants. This package contains the "2022 CODATA" version, published on May 2024: Eite Tiesinga, Peter J. Mohr, David B. Newell, and Barry N. Taylor (2024) <https://physics.nist.gov/cuu/Constants/>.

Solving the problem of project management using CPM (Critical Path Method), PERT (Program Evaluation and Review Technique) and LESS (Least Cost Estimating and Scheduling) methods. The package sets the critical path, schedule and Gantt chart. In addition, it allows to draw a graph even with marked critical activities. For more information about project management see: Taha H. A. "Operations Research. An Introduction" (2017, ISBN:978-1-292-16554-7), Rama Murthy P. "Operations Research" (2007, ISBN:978-81-224-2944-2), Yuval Cohen & Arik Sadeh (2006) "A New Approach for Constructing and Generating AOA Networks", Journal of Engineering, Computing and Architecture 1. 1-13, Konarzewska I., Jewczak M., Kucharski A. (2020, ISBN:978-83-8220-112-3), MiszczyÅ ska D., MiszczyÅ ski M. "Wybrane metody badaÅ operacyjnych" (2000, ISBN:83-907712-0-9).

The Cauchy Process can model pulsed continuous trait evolution on phylogenies. The likelihood is tractable, and is used for parameter inference and ancestral trait reconstruction. See Bastide and Didier (2023) <doi:10.1093/sysbio/syad053>.

This package performs a series of offline and/or online change-point detection algorithms for 1) univariate mean: <doi:10.1214/20-EJS1710>, <arXiv:2006.03283>; 2) univariate polynomials: <doi:10.1214/21-EJS1963>; 3) univariate and multivariate nonparametric settings: <doi:10.1214/21-EJS1809>, <doi:10.1109/TIT.2021.3130330>; 4) high-dimensional covariances: <doi:10.3150/20-BEJ1249>; 5) high-dimensional networks with and without missing values: <doi:10.1214/20-AOS1953>, <arXiv:2101.05477>, <arXiv:2110.06450>; 6) high-dimensional linear regression models: <arXiv:2010.10410>, <arXiv:2207.12453>; 7) high-dimensional vector autoregressive models: <arXiv:1909.06359>; 8) high-dimensional self exciting point processes: <arXiv:2006.03572>; 9) dependent dynamic nonparametric random dot product graphs: <arXiv:1911.07494>; 10) univariate mean against adversarial attacks: <arXiv:2105.10417>.

This package provides a collection of useful helper routines developed by students of the Center for Mathematical Research, Stankin, Moscow.

This package provides a Bayesian meta-analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. CPBayes is based on a spike and slab prior. The methodology is available from: A Majumdar, T Haldar, S Bhattacharya, JS Witte (2018) <doi:10.1371/journal.pgen.1007139>.

Wraps the CIRCE (<https://github.com/ohdsi/circe-be>) Java library allowing cohort definition expressions to be edited and converted to Markdown or SQL'.

This package provides recent kernel density estimation methods for circular data, including adaptive and higher-order techniques. The implementation is based on recent advances in bandwidth selection and circular smoothing. Key methods include adaptive bandwidth selection methods by ZámeÄ nà k et al. (2024) <doi:10.1007/s00180-023-01401-0>, complete cross-validation by Hasilová et al. (2024) <doi:10.59170/stattrans-2024-024>, Fourier-based plug-in rules by Tenreiro (2022) <doi:10.1080/10485252.2022.2057974>, and higher-order kernels by Tsuruta & Sagae (2017) <doi:10.1016/j.spl.2017.08.003>.

Reads chromatograms from binary formats into R objects. Currently supports conversion of Agilent ChemStation', Agilent MassHunter', Shimadzu LabSolutions', ThermoRaw', and Varian Workstation files as well as various text-based formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as Aston <https://github.com/bovee/aston>, Entab <https://github.com/bovee/entab>, rainbow <https://rainbow-api.readthedocs.io/>, and ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>.