Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

This package provides a general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019.

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

This package implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

Point-scale variogram deconvolution from irregular/regular spatial support according to Goovaerts, P., (2008) <doi: 10.1007/s11004-007-9129-1>; ordinary area-to-area (co)Kriging and area-to-point (co)Kriging.

Whitening is the first step of almost all blind source separation (BSS) methods. A fast implementation of whitening for BSS is implemented to serve as a lightweight dependency for packages providing BSS methods.

Implementation of the d/p/q/r family of functions for a continuous analog to the standard discrete beta-binomial with continuous size parameter and continuous support with x in [0, size + 1].

An interactive document on the topic of confusion matrix analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://predanalyticssessions1.shinyapps.io/ConfusionMatrixShiny/>.

This package implements the instruments for complex-valued modelling, including time series analysis and forecasting. This is based on the monograph by Svetunkov & Svetunkov (2024) <doi: 10.1007/978-3-031-62608-1>.

Solves quadratic programming problems using Richard L. Dykstra's cyclic projection algorithm. Routine allows for a combination of equality and inequality constraints. See Dykstra (1983) <doi:10.1080/01621459.1983.10477029> for details.

Geodesic distance between phylogenetic trees and associated functions. The theoretical background of distory is published in Billera et al. (2001) "Geometry of the space of phylogenetic trees." <doi:10.1006/aama.2001.0759>.

This package provides methods for estimating multi-stage optimal dynamic treatment regimes for survival outcomes with dependent censoring. Cho, H., Holloway, S. T., and Kosorok, M. R. (2022) <doi:10.1093/biomet/asac047>.

The df2yaml aims to simplify the process of converting dataframe to YAML <https://yaml.org/>. The dataframe with multiple key columns and one value column will be converted to the multi-level hierarchy.

This dataset contains population estimates of all European cities with at least 10,000 inhabitants during the period 1500-1800. These data are adapted from Jan De Vries, "European Urbanization, 1500-1800" (1984).

This package provides an interface to the Kairos Face Recognition API <https://kairos.com/face-recognition-api>. The API detects faces in images and returns estimates for demographics like gender, ethnicity and age.

Parameter estimation and prediction of Gaussian Process Classifier models as described in Bachoc et al. (2020) <doi:10.1007/S10898-020-00920-0>. Important functions : gpcm(), predict.gpcm(), update.gpcm().

Homogenize GNSS (Global Navigation Satellite System) time-series. The general model is a segmentation in the mean model including a periodic function and considering monthly variances, see Quarello (2020) <arXiv:2005.04683>.

This package provides a simple wrapper for Wikipedia data. Specifically, this package looks to fill a gap in retrieving text data in a tidy format that can be used for Natural Language Processing.

Read hierarchical fixed width files like those commonly used by many census data providers. Also allows for reading of data in chunks, and reading gzipped files without storing the full file in memory.

This package provides functions to parse strings with ISO8601 dates, times, and date-times into R-objects. Additionally, there are functions to determine the type of ISO8601 string and to standardise ISO8601 strings.

Data sets for Chirok Han (2024, ISBN:979-11-303-1964-3, "Lectures on Econometrics"). Students, teachers, and self-learners will find the data sets essential for replicating the results in the book.

An interactive document on the topic of naive Bayes classification analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://kartikeyab.shinyapps.io/NBShiny/>.

Various visual and numerical diagnosis methods for the nonlinear mixed effect model, including visual predictive checks, numerical predictive checks, and coverage plots (Karlsson and Holford, 2008, <https://www.page-meeting.org/?abstract=1434>).

Perform a Bayesian estimation of the ordinal exploratory Higher-order General Diagnostic Model (OHOEGDM) for Polytomous Data described by Culpepper, S. A. and Balamuta, J. J. (2021) <doi:10.1080/00273171.2021.1985949>.