This package provides simplified methods for managing classic Rubik's cubes and many other modifications of it (such as NxNxN size cubes, void cubes and 8-coloured cubes - so called octa cubes). Includes functions of handling special syntax for managing such cubes; and different approach to plotting 3D cubes without using external libraries (for example OpenGL').
Cross validate large genetic data while specifying clinical variables that should always be in the model using the function cv(). An ROC plot from the cross validation data with AUC can be obtained using rocplot(), which also can be used to compare different models. Framework was built to handle genetic data, but works for any data.
Perform optimal transport on somatic point mutations and kernel regression hypothesis testing by integrating pathway level similarities at the gene level (Little et al. (2023) <doi:10.1111/biom.13769>). The software implements balanced and unbalanced optimal transport and omnibus tests with C++ across a set of tumor samples and allows for multi-threading to decrease computational runtime.
This package provides tools for grading the coding style and documentation of R scripts. This is the R component of Roger the Omni Grader, an automated grading system for computer programming projects based on Unix shell scripts; see <https://gitlab.com/roger-project>. The package also provides an R interface to the shell scripts. Inspired by the lintr package.
Decimal rounding is non-trivial in binary arithmetic. ISO standard round to even is more rare than typically assumed as most decimal fractions are not exactly representable in binary. Our roundX() versions explore differences between current and potential future versions of round() in R. Further, provides (some partly related) C99 math lib functions not in base R.
This package provides an R6 class and several utility methods to facilitate the implementation of models based on ordinary differential equations. The heart of the package is a code generator that creates compiled Fortran (or R') code which can be passed to a numerical solver. There is direct support for solvers contained in packages deSolve and rootSolve'.
An interface to the API for arXiv', a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics.
Autoregressive-based decomposition of a time series based on the approach in West (1997). Particular cases include the extraction of trend and seasonal components.
Compute the R-squared measure under the accelerated failure time (AFT) models proposed in Chan et. al. (2018) <doi:10.1080/03610918.2016.1177072>.
Beta-binomial Mixture Model is used to infer the pattern from count data. It can be used for clustering of RNA methylation sequencing data.
Basic functions for plotting 2D and 3D views of a sphere, by default the Earth with its major coastline, and additional lines and points.
For plant physiologists, converts conductance (e.g. stomatal conductance) to different units: m/s, mol/m^2/s, and umol/m^2/s/Pa.
This package provides a zero-inflated quasi-Poisson factor model to display similarity between samples visually in a low (2 or 3) dimensional space.
Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.
Web scraping the <https://www.dallasfed.org> for up-to-date data on international house prices and exuberance indicators. Download data in tidy format.
Quickly generate lorem ipsum placeholder text. Easy to integrate in RMarkdown documents. Includes an RStudio addin to insert lorem ipsum into the current document.
Handling, processing, and analyzing geographic data on species distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.
Summarize multiple biomarker responses of aquatic organisms to contaminants using Cliffâ s delta, as described in Pham & Sokolova (2023) <doi:10.1002/ieam.4676>.
Calculates k-best solutions and costs for an assignment problem following the method outlined in Murty (1968) <doi:10.1287/opre.16.3.682>.
An S4 update of the mefa package using sparse matrices for enhanced efficiency. Sparse array-like objects are supported via lists of sparse matrices.
This package provides a method to impute the missingness in categorical data. Details see the paper <doi:10.4310/SII.2020.v13.n1.a2>.
Estimates the multi-level vector autoregression model on time-series data. Three network structures are obtained: temporal networks, contemporaneous networks and between-subjects networks.
This package provides functions to estimate start and duration of moult from moult data, based on models developed in Underhill and Zucchini (1988, 1990).
This package provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).