Nonlinear growth models are extremely useful in gaining insight into the underlying mechanism. These models are generally mechanistic, with parameters that have biological meaning. This package allows you to fit and forecast time series data using nonlinear growth models.

It includes functions like tropical addition, tropical multiplication for vectors and matrices. In tropical algebra, the tropical sum of two numbers is their minimum and the tropical product of two numbers is their ordinary sum. For more information see also I. Simon (1988) Recognizable sets with multiplicities in the tropical semi ring: Volume 324 Lecture Notes I Computer Science, pages 107-120 <doi: 10.1007/BFb0017135>.

This package provides a lightweight and focused text annotation tool built with shiny'. Provides an interactive graphical user interface for coding text documents, managing code hierarchies, creating memos, and analyzing coding patterns. Features include code co-occurrence analysis, visualization of coding patterns, comparison of multiple coding sets, and export capabilities. Supports collaborative qualitative research through standardized annotation formats and analysis tools.

This package provides R Markdown output formats to use Tufte styles for PDF and HTML output.

Plots and analyzes time-intensity curve data, such as data from (contrast-enhanced) ultrasound. Values such as peak intensity, time to peak, area under the curve, wash in rate and wash out rate are calculated.

Simplify reporting many tables by creating tibbles of tables. With tabtibble', a tibble of tables is created with captions and automatic printing using knit_print()'.

Unsupervised text tokenizer focused on computational efficiency. Wraps the YouTokenToMe library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://aclanthology.org/P16-1162/>.

This package provides tools to deploy TensorFlow <https://www.tensorflow.org/> models across multiple services. Currently, it provides a local server for testing cloudml compatible services.

This package provides a comprehensive and user-friendly interface for accessing, manipulating, and analyzing country-level data from around the world. It allows users to retrieve detailed information on countries, including names, regions, continents, populations, currencies, calling codes, and more, all in a tidy data format. The package is designed to work seamlessly within the tidyverse ecosystem, making it easy to filter, arrange, and visualize country-level data in R.

This package provides a game inspired by Tetris'. Opens a plot window device and starts a game of tetRys in it. Steer the tetrominos with the arrow keys, press Pause to pause and Esc to end the game.

This package provides a universal non-uniform random number generator for quite arbitrary distributions with piecewise twice differentiable densities.

Torch code for computing multi-class Area Under The Minimum, <https://www.jmlr.org/papers/v24/21-0751.html>, Generalization. Useful for optimizing Area under the curve.

Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM and MM algorithms. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette("turboEM").

Multiscale multifractal analysis (MMA) (GieraÅ towski et al., 2012)<DOI:10.1103/PhysRevE.85.021915> is a time series analysis method, designed to describe scaling properties of fluctuations within the signal analyzed. The main result of this procedure is the so called Hurst surface h(q,s) , which is a dependence of the local Hurst exponent h (fluctuation scaling exponent) on the multifractal parameter q and the scale of observation s (data window width).

The modern database TileDB introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', GCS', Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Targets parameters that solve Ordinary Differential Equations (ODEs) driven by a vector of cumulative hazard functions. The package provides a method for estimating these parameters using an estimator defined by a corresponding Stochastic Differential Equation (SDE) system driven by cumulative hazard estimates. By providing cumulative hazard estimates as input, the package gives estimates of the parameter as output, along with pointwise (co)variances derived from an asymptotic expression. Examples of parameters that can be targeted in this way include the survival function, the restricted mean survival function, cumulative incidence functions, among others; see Ryalen, Stensrud, and Røysland (2018) <doi:10.1093/biomet/asy035>, and further applications in Stensrud, Røysland, and Ryalen (2019) <doi:10.1111/biom.13102> and Ryalen et al. (2021) <doi:10.1093/biostatistics/kxab009>.

This package provides bindings to a C grammar for Tree-sitter, to be used alongside the treesitter package. Tree-sitter builds concrete syntax trees for source files and can efficiently update them or generate code like producing R C API wrappers from C functions, structs and global definitions from header files.

An easy tool for plotting annotated timelines, grouped timelines, and exploratory graphics (boxplot/histogram/density plot/scatter plot/line plot). Filter, summarize date data by duration and convert to calendar units.

Calculates the number of true positives and false positives from a dataset formatted for Jackknife alternative free-response receiver operating characteristic which is used for statistical analysis which is explained in the book Chakraborty DP (2017), "Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples", Taylor-Francis <https://www.crcpress.com/9781482214840>.

Fit two-part regression models for zero-inflated data. The models and their components are represented using S4 classes and methods. Average Marginal effects and predictive margins with standard errors and confidence intervals can be calculated from two-part model objects. Belotti, F., Deb, P., Manning, W. G., & Norton, E. C. (2015) <doi:10.1177/1536867X1501500102>.

This package implements combined p-value functions for two trials along with compatible combined point and interval estimates as described in Pawel, Roos, and Held (2025) <doi:10.48550/arXiv.2503.10246>.

Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.

Utilities for text analysis.

This package provides functions for multivariate analysis with compositional data. Includes a function for doing compositional canonical correlation analysis. This analysis requires two data matrices of compositions, which can be adequately transformed and used as entries in a specialized program for canonical correlation analysis, that is able to deal with singular covariance matrices. The methodology is described in Graffelman et al. (2017) <doi:10.1101/144584>. Functions for log-ratio principal component analysis with condition number computations and log-ratio discriminant analysis have been added to the package.