Token-Oriented Object Notation (TOON) is a compact, human-readable serialization format designed for passing structured data to Large Language Models with significantly reduced token usage. It's intended for LLM input as a lossless, drop-in representation of JSON data.

Includes functions for mapping named lists to function arguments, random strings, pasting and combining rows together across columns, etc.

Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

The trigger strategy is a general framework for a multistage statistical design with multiple hypotheses, allowing an adaptive selection of interim analyses. The selection of interim stages can be associated with some prespecified endpoints which serve as the trigger. This selection allows us to refine the critical boundaries in hypotheses testing procedures, and potentially increase the statistical power. This package includes several trial designs using the trigger strategy. See Gou, J. (2023), "Trigger strategy in repeated tests on multiple hypotheses", Statistics in Biopharmaceutical Research, 15(1), 133-140, and Gou, J. (2022), "Sample size optimization and initial allocation of the significance levels in group sequential trials with multiple endpoints", Biometrical Journal, 64(2), 301-311.

An R re-implementation of the treeinterpreter package on PyPI <https://pypi.org/project/treeinterpreter/>. Each prediction can be decomposed as prediction = bias + feature_1_contribution + ... + feature_n_contribution'. This decomposition is then used to calculate the Mean Decrease Impurity (MDI) and Mean Decrease Impurity using out-of-bag samples (MDI-oob) feature importance measures based on the work of Li et al. (2019) <doi:10.48550/arXiv.1906.10845>.

This package provides an interactive interface to the tfrmt package. Users can import, modify, and export tables and templates with little to no code.

This package provides a collection of functions for data analysis with two-by-two contingency tables. The package provides tools to compute measures of effect (odds ratio, risk ratio, and risk difference), calculate impact numbers and attributable fractions, and perform hypothesis testing. Statistical analysis methods are oriented towards epidemiological investigation of relationships between exposures and outcomes.

This package contains functions to standardize tracheid profiles using the traditional method (Vaganov) and a new method to standardize tracheidograms based on the relative position of tracheids within tree rings.

Simplifies access to Tunisian government open data from <https://data.gov.tn/fr/>. Queries datasets by theme, author, or keywords, retrieves metadata, and gets structured results ready for analysis; all through the official CKAN API.

Regression models for temporal process responses with time-varying coefficient.

An extension to the R tidy data environment for automated machine learning. The package allows fitting and cross validation of linear regression and classification algorithms on grouped data.

In order to easily integrate geoRSS data into analysis, tidygeoRSS parses geo feeds and returns tidy simple features data frames.

Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.

An implementation of turtle graphics <http://en.wikipedia.org/wiki/Turtle_graphics>. Turtle graphics comes from Papert's language Logo and has been used to teach concepts of computer programming.

Measure text's sentiment with dictionaries and simple rules covering negations and modifiers. User-supplied dictionaries are supported, including Unicode emojis and multi-word tokens, so this package can also be used to study constructs beyond sentiment.

Analyse data from longitudinal studies to characterise changes in values of semi-quantitative outcome variables within individual subjects, using high performance C++ code to enable rapid processing of large datasets. A flexible methodology is available for codifying these state transitions.

Enhances koRpus text object classes and methods to also support large corpora. Hierarchical ordering of corpus texts into arbitrary categories will be preserved. Provided classes and methods also improve the ability of using the koRpus package together with the tm package. To ask for help, report bugs, suggest feature improvements, or discuss the global development of the package, please subscribe to the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).

We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database. We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.

This package provides a reliable and validated tool that calculates unit test coverage for R packages with standard testing frameworks and non-standard testing frameworks.

Testing for trajectory presence and heterogeneity on multivariate data. Two statistical methods (Tenha & Song 2022) <doi:10.1371/journal.pcbi.1009829> are implemented. The tree dimension test quantifies the statistical evidence for trajectory presence. The subset specificity measure summarizes pattern heterogeneity using the minimum subtree cover. There is no user tunable parameters for either method. Examples are included to illustrate how to use the methods on single-cell data for studying gene and pathway expression dynamics and pathway expression specificity.

Simple trustworthy utility functions to use TauDEM (Terrain Analysis Using Digital Elevation Models <https://hydrology.usu.edu/taudem/taudem5/>) command-line interface. This package provides a guide to installation of TauDEM and its dependencies GDAL (Geopatial Data Abstraction Library) and MPI (Message Passing Interface) for different operating systems. Moreover, it checks that TauDEM and its dependencies are correctly installed and included to the PATH, and it provides wrapper commands for calling TauDEM methods from R.

Feasible Multivariate Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models including Dynamic Conditional Correlation (DCC), Copula GARCH and Generalized Orthogonal GARCH with Generalized Hyperbolic distribution. A review of some of these models can be found in Boudt, Galanos, Payseur and Zivot (2019) <doi:10.1016/bs.host.2019.01.001>.

Pest monitoring is crucial, especially during the early season, to understand the distribution and the proliferation of the target pest. Raw count data from pest monitoring/traps can be coupled with environmental variables such as temperature, growing degree-day ('GDD') etc. to get useful insights about the pest phenology. This package pulls temperature data from the California Irrigation Management Information System ('CIMIS', <https://cimis.water.ca.gov>), the Daymet application programming interface ('API', <https://daymet.ornl.gov>), or Open Meteo ('API', <https://open-meteo.com/>) sequentially for a user-specified time period and calculates cumulative growing degree-days. Users provide pest development thresholds (lower and upper temperatures), pest of concern, and the geographic coordinates of the trap location to track emergence and phenology.

Topological data analysis methods based on graph-theoretic approaches for discovering topological structures in data. Constructs topological spaces from graphs following Nada et al. (2018) <doi:10.1002/mma.4726>, with visibility graph construction for time series following Lacasa et al. (2008) <doi:10.1073/pnas.0709247105>. Supports directed visibility graphs for bitopological analysis of temporal irreversibility (Kelly, 1963), and Alexandrov topology construction from reachability preorders.