mlr3misc provides frequently used helper functions and assertions used in mlr3 and its companion packages. It comes with helper functions for functional programming, for printing, to work with data.table, as well as some generally useful R6 classes. This package also supersedes the package BBmisc.

This package simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.

clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.

Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.

VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

Fit Generalized Additive Models (GAM) using mgcv with parsnip'/'tidymodels via additive <doi:10.5281/zenodo.4784245>. tidymodels is a collection of packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>). The technical details of mgcv are described in Wood (2017) <doi:10.1201/9781315370279>.

This package provides functions for interacting directly with the ALTADATA API. With this R package, developers can build applications around the ALTADATA API without having to deal with accessing and managing requests and responses. ALTADATA is a curated data marketplace for more information go to <https://www.altadata.io>.

Computation of large covariance matrices having a block structure up to a permutation of their columns and rows from a small number of samples with respect to the dimension of the matrix. The method is described in the paper Perrot-Dockès et al. (2019) <arXiv:1806.10093>.

Utility functions that allow checking the basic validity of a function argument or any other value, including generating an error and assigning a default in a single line of code. The main purpose of the package is to provide simple and easily readable argument checking to improve code robustness.

Cleaning and standardizing tabular data package, tailored specifically for curating epidemiological data. It streamlines various data cleaning tasks that are typically expected when working with datasets in epidemiology. It returns the processed data in the same format, and generates a comprehensive report detailing the outcomes of each cleaning task.

Estimation of sparse nonlinear functions in nonparametric regression using component selection and smoothing. Designed for the analysis of high-dimensional data, the models support various data types, including exponential family models and Cox proportional hazards models. The methodology is based on Lin and Zhang (2006) <doi:10.1214/009053606000000722>.

Wraps cytoscape.js as a shiny widget. cytoscape.js <https://js.cytoscape.org/> is a Javascript-based graph theory (network) library for visualization and analysis. This package supports the visualization of networks with custom visual styles and several available layouts. Demo Shiny applications are provided in the package code.

Data are essential in statistical analysis. This data package consists of four datasets for descriptive statistics, two datasets for statistical hypothesis testing, and two datasets for regression analysis. All of the datasets are based on Rattanalertnusorn, A. (2024) <https://www.researchgate.net/publication/371944275_porkaermxarlaeakarprayuktchingan_R_and_its_applications>.

Supports the process of applying a cut to Standard Data Tabulation Model (SDTM), as part of the analysis of specific points in time of the data, normally as part of investigation into clinical trials. The functions support different approaches of cutting to the different domains of SDTM normally observed.

For estimation of a variable of interest using Kalman filter by incorporating results from previous assessments, i.e. through development weighted estimates where weights are assigned inversely proportional to the variance of existing and new estimates. For reference see Ehlers et al. (2017) <doi:10.20944/preprints201710.0098.v1>.

Inspect survival data, plot Kaplan-Meier curves, assess the proportional hazards assumption, fit parametric survival models, predict and plot survival and hazards, and export the outputs to Excel'. A simple interface for fitting survival models using flexsurv::flexsurvreg(), flexsurv::flexsurvspline(), flexsurvcure::flexsurvcure(), and survival::survreg().

This package provides a native R implementation of grammatical evolution (GE). GE facilitates the discovery of programs that can achieve a desired goal. This is done by performing an evolutionary optimisation over a population of R expressions generated via a user-defined context-free grammar (CFG) and cost function.

This package provides functions to fit geostatistical data. The data can be continuous, binary or count data and the models implemented are flexible. Conjugate priors are assumed on some parameters while inference on the other parameters can be done through a full Bayesian analysis of by empirical Bayes methods.

This package provides tools for simulating from spatial modeling of individual level of infectious disease transmission when co-variates measured with error, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based model within Susceptible-Infectious-Removed (SIR) compartmental frameworks.

Easily implement the checking of WHOIS information for a particular domain. IP2WHOIS supports the query for 1113 Top-level Domains(TLDs) and 634 Country Code Top-level Domains(ccTLDs). To get started with a free API key, you may sign up at here <https://www.ip2whois.com/register>.

This package implements inequality constrained inference. This includes parameter estimation in normal (linear) models under linear equality and inequality constraints, as well as normal likelihood ratio tests involving inequality-constrained hypotheses. For inequality-constrained linear models, averaging over R-squared for different orderings of regressors is also included.

Download Internet Protocol (IP) address location and more from the ip-api application programming interface (API) <https://ip-api.com/>. The package makes it easy to get the latitude, longitude, country, region, and organisation associated to the provided IP address. The information is conveniently returned in a rectangular format.

Meta-CART integrates classification and regression trees (CART) into meta-analysis. Meta-CART is a flexible approach to identify interaction effects between moderators in meta-analysis. The method is described in Dusseldorp et al. (2014) <doi:10.1037/hea0000018> and Li et al. (2017) <doi:10.1111/bmsp.12088>.

Makes Mapbox GL JS <https://docs.mapbox.com/mapbox-gl-js/api/>, an open source JavaScript library that uses WebGL to render interactive maps, available within R via the htmlwidgets package. Visualizations can be used from the R console, in R Markdown documents and in Shiny apps.