Feature selection from high dimensional data using a diploid genetic algorithm with Incomplete Dominance for genotype to phenotype mapping and Random Assortment of chromosomes approach to recombination.

Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA package). Using the framework of linear model-based differential expression comparisons ('limma package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.

This package provides tools for temporal disaggregation, including: (1) High-dimensional and low-dimensional series generation for simulation studies; (2) A toolkit for temporal disaggregation and benchmarking using low-dimensional indicator series as proposed by Dagum and Cholette (2006, ISBN:978-0-387-35439-2); (3) Novel techniques by Mosley, Gibberd, and Eckley (2022, <doi:10.1111/rssa.12952>) for disaggregating low-frequency series in the presence of high-dimensional indicator matrices.

Several functions are provided for dose-response (or concentration-response) characterization from omics data. DRomics is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). DRomics provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, DRomics also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) <DOI:10.24072/pcjournal.325> and Larras et al (2018) <DOI:10.1021/acs.est.8b04752>.

This package provides tools for exploration of R package dependencies. The main deepdep() function allows to acquire deep dependencies of any package and plot them in an elegant way. It also adds some popularity measures for the packages e.g. in the form of download count through the cranlogs package. Uses the CRAN metadata database <http://crandb.r-pkg.org> and Bioconductor metadata <https://bioconductor.org>. Other data acquire functions are: get_dependencies(), get_downloads() and get_description(). The deepdep_shiny() function runs shiny application that helps to produce a nice deepdep plot.

This package contains the support functions for the Time Series Analysis book. We present a function to calculate MSE and MAE for inputs of actual and forecast values. We also have the code for disaggregation as found in Wei and Stram (1990, <doi:10.1111/j.2517-6161.1990.tb01799.x>), and Hodgess and Wei (1996, "Temporal Disaggregation of Time Series").

This package provides a collection of utility functions.

Function to create forest plots. Functions to use posterior samples from Bayesian bivariate meta-analysis model, Bayesian hierarchical summary receiver operating characteristic (HSROC) meta-analysis model or Bayesian latent class (LC) meta-analysis model to create Summary Receiver Operating Characteristic (SROC) plots using methods described by Harbord et al (2007)<doi:10.1093/biostatistics/kxl004>.

This package provides functions to impute large gaps within time series based on Dynamic Time Warping methods. It contains all required functions to create large missing consecutive values within time series and to fill them, according to the paper Phan et al. (2017), <DOI:10.1016/j.patrec.2017.08.019>. Performance criteria are added to compare similarity between two signals (query and reference).

Dose Titration Algorithm Tuning (DTAT) is a methodologic framework allowing dose individualization to be conceived as a continuous learning process that begins in early-phase clinical trials and continues throughout drug development, on into clinical practice. This package includes code that researchers may use to reproduce or extend key results of the DTAT research programme, plus tools for trialists to design and simulate a 3+3/PC dose-finding study. Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and Norris (2017c) <doi:10.1101/240846>.

Create D3 based SVG ('Scalable Vector Graphics') graphics using a simple R API. The package aims to simplify the creation of many SVG plot types using a straightforward R API. The package relies on the r2d3 R package and the D3 JavaScript library. See <https://rstudio.github.io/r2d3/> and <https://d3js.org/> respectively.

This package provides a collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.

This package provides new types of omnibus tests which are generally much more powerful than traditional tests (including the Kolmogorov-Smirnov, Cramer-von Mises and Anderson-Darling tests),see Zhang (2002) <doi:10.1111/1467-9868.00337>.

This package provides external JAR dependencies for the DatabaseConnector package.

Numerical quadrature of functions of one variable over a finite or infinite interval with double exponential formulas.

This package provides a shiny application that enables the user to create a prototype UI, being able to drag and drop UI components before being able to save or download the equivalent R code.

Given the non-negative data and its distribution, the package estimates the rank parameter for Non-negative Matrix Factorization. The method is based on hypothesis testing, using a deconvolved bootstrap distribution to assess the significance level accurately despite the large amount of optimization error. The distribution of the non-negative data can be either Normal distributed or Poisson distributed.

Fast & memory-efficient functions to analyze and manipulate large spatial data data sets. It leverages the fast analytical capabilities of DuckDB and its spatial extension (see <https://duckdb.org/docs/stable/core_extensions/spatial/overview>) while maintaining compatibility with Râ s spatial data ecosystem to work with spatial vector data.

S4-classes for setting up a coherent framework for simulation within the distr family of packages.

This package provides a sparse Partial Least Squares implementation which uses soft-threshold estimation of the covariance matrices and therein introduces sparsity. Number of components and regularization coefficients are automatically set.

Compressed spatial vector data originally from <https://dawadocs.dataforsyningen.dk/> saved as Simple Features, SF, objects with data on population, age and gender from Statistics Denmark <https://www.dst.dk/da/>.

This package implements an efficient algorithm for solving sparse-penalized support vector machines with kernel density convolution. This package is designed for high-dimensional classification tasks, supporting lasso (L1) and elastic-net penalties for sparse feature selection and providing options for tuning kernel bandwidth and penalty weights. The dcsvm is applicable to fields such as bioinformatics, image analysis, and text classification, where high-dimensional data commonly arise. Learn more about the methodology and algorithm at Wang, Zhou, Gu, and Zou (2023) <doi:10.1109/TIT.2022.3222767>.

This package creates a data dictionary from any dataframe or tibble in your R environment. You can opt to add variable labels. You can write the object directly to Excel.

An implementation of common higher order functions with syntactic sugar for anonymous function. Provides also a link to dplyr and data.table for common transformations on data frames to work around non standard evaluation by default.