This package provides bibliographic information and term-frequency text analysis tools for publications of the U.S. Geological Survey (USGS) Idaho National Laboratory (INL) Project Office. Includes datasets of publications, authors, and term frequencies, along with functions to search terms, build word clouds, and extract text and cover images from publication documents.

To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as iCAMP (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model and quantifying assembly processes based on entire-community null models ('QPEN', Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche difference and phylogenetic distance calculation, phylogenetic signal test within phylogenetic groups, midpoint root of big trees, etc. Version 1.3.x mainly improved the function for QPEN and added function icamp.cate() to summarize iCAMP results for different categories of taxa (e.g. core versus rare taxa).

Computes individual causes of death and population cause-specific mortality fractions using the InSilicoVA algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used InterVA method. This package provides general model fitting and customization for InSilicoVA algorithm and basic graphical visualization of the output.

This package provides functions to conduct a model-agnostic asymptotic hypothesis test for the identification of interaction effects in black-box machine learning models. The null hypothesis assumes that a given set of covariates does not contribute to interaction effects in the prediction model. The test statistic is based on the difference of variances of partial dependence functions (Friedman (2008) <doi:10.1214/07-AOAS148> and Welchowski (2022) <doi:10.1007/s13253-021-00479-7>) with respect to the original black-box predictions and the predictions under the null hypothesis. The hypothesis test can be applied to any black-box prediction model, and the null hypothesis of the test can be flexibly specified according to the research question of interest. Furthermore, the test is computationally fast to apply as the null distribution does not require resampling or refitting black-box prediction models.

Allows access to data from the Rio de Janeiro Public Security Institute (ISP), such as criminal statistics, data on gun seizures and femicide. The package also contains the spatial data of Pacifying Police Units (UPPs) and Integrated Public Safety Regions, Areas and Circumscriptions.

Download ifo business survey data and more time series from ifo institute <https://www.ifo.de/en/ifo-time-series>.

Estimation of joint models for multivariate longitudinal markers (with various distributions available) and survival outcomes (possibly accounting for competing risks) with Integrated Nested Laplace Approximations (INLA). The flexible and user friendly function joint() facilitates the use of the fast and reliable inference technique implemented in the INLA package for joint modeling. More details are given in the help page of the joint() function (accessible via ?joint in the R console) and the vignette associated to the joint() function (accessible via vignette("INLAjoint") in the R console).

This package implements multiple variants of the Information Bottleneck ('IB') method for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables. The package provides deterministic, agglomerative, generalised, sequential, and standard IB clustering algorithms that preserve relevant information while forming interpretable clusters. The Deterministic Information Bottleneck is described in Costa et al. (2026) <doi:10.1016/j.patcog.2026.113580>. The standard IB method originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>, the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>, the generalised IB from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>, and the sequential IB from Slonim et al. (2002) <doi:10.1145/564376.564401>. Diagnostic and plotting functions are provided to summarise, visualise, and predict from the resulting clusterings.

Assists in generating binary clustered data, estimates of Intracluster Correlation coefficient (ICC) for binary response in 16 different methods, and 5 different types of confidence intervals.

This package provides a user-friendly toolbox for doing the statistical analysis of interval-valued responses in questionnaires measuring intrinsically imprecise human attributes or features (attitudes, perceptions, opinions, feelings, etc.). In particular, this package provides S4 classes, methods, and functions in order to compute basic arithmetic and statistical operations with interval-valued data; prepare customized plots; associate each interval-valued response to its equivalent Likert-type and visual analogue scales answers through the minimum theta-distance and the mid-point criteria; analyze the reliability of respondents answers from the internal consistency point of view by means of Cronbach's alpha coefficient; and simulate interval-valued responses in this type of questionnaires. The package also incorporates some real-life data that can be used to illustrate its working with several non-trivial reproducible examples. The methodology used in this package is based in many theoretical and applied publications from SMIRE+CoDiRE (Statistical Methods with Imprecise Random Elements and Comparison of Distributions of Random Elements) Research Group (<https://bellman.ciencias.uniovi.es/smire+codire/>) from the University of Oviedo (Spain).

Improve optical character recognition by binarizing images. The package focuses primarily on local adaptive thresholding algorithms. In English, this means that it has the ability to turn a color or gray scale image into a black and white image. This is particularly useful as a preprocessing step for optical character recognition or handwritten text recognition.

This package implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.

Estimation, inference, and quantities of interest for ordered probit and ordered logit models whose outcome contains an inflated category: a single ordered category (bottom, middle, top, or any other) that mixes observations generated by the ordered process with observations generated by a distinct split-population process. Fits the zero-inflated ordered probit of Harris and Zhao (2007) <doi:10.1016/j.jeconom.2007.01.002> and its middle- and top-inflated extensions (Bagozzi and Mukherjee 2012 <doi:10.1093/pan/mps020>; Bagozzi, Hill, Moore and Mukherjee 2015 <doi:10.1177/0022002713520530>; Bagozzi, Joo and Mukherjee 2024 <doi:10.1093/fpa/orae006>), generalized to an arbitrary inflated category and to the logit link, with optional correlated errors for the probit form, plus the standard ordered probit and logit and their partial proportional-odds (non-parallel) variants on the same footing. Provides analytic, robust, and cluster-robust standard errors, survey weights and offsets, model comparison (Vuong, likelihood-ratio, information criteria), regime-specific predicted probabilities and first differences, simulation for residual diagnostics, and tidy/table-package integration. The likelihood, its gradient, and the bivariate-normal probabilities are implemented in C++.

Independent vector analysis (IVA) is a blind source separation (BSS) model where several datasets are jointly unmixed. This package provides several methods for the unmixing together with some performance measures. For details, see Anderson et al. (2011) <doi:10.1109/TSP.2011.2181836> and Lee et al. (2007) <doi:10.1016/j.sigpro.2007.01.010>.

This package provides tools for passing messages between R processes. Shiny examples are provided showing how to perform useful tasks such as: updating reactive values from within a future, progress bars for long running async tasks, and interrupting async tasks based on user input.

This package provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred. See Tong and Coombes (2012) <doi:10.1093/bioinformatics/bts561>.

Runs classical item analysis for multiple-choice test items and polytomous items (e.g., rating scales). The statistics reported in this package can be found in any measurement textbook such as Crocker and Algina (2006, ISBN:9780495395911).

This package provides a phylogenetic modelling approach for predicting species invasion risk, out of a given pool of local species where a subset is known to be invasive elsewhere. The package uses phylogenetic signal estimation and phylogenetic linear and logistic models to estimate probabilities of being invasive based on phylogeny and any set of additional predictors. A ranking method is implemented to evaluate prioritisation strategies. A manuscript describing these methods, by Shahar Dubiner and Tamar Guy-Haim, is in preparation.

Comprehensive computational routines for random data generation, Maximum Likelihood Estimation (MLE), Maximum Product of Spacings Estimation (MPSE), and MCMC Bayesian estimation under the Improved Adaptive Type-II Progressive Censoring Scheme (IAT-II PCS). Users can supply custom probability density functions (PDF), cumulative distribution functions (CDF), survival functions, parameter ranges, and progressive censoring plans for any continuous univariate lifetime distribution, or rely on built-in parametric models (e.g., Generalized Exponential). Point estimation methods include MLE via optimization algorithms (Broyden-Fletcher-Goldfarb-Shanno (BFGS), Newton-Raphson (NR), Nelder-Mead (NM), Conjugate Gradients (CG), L-BFGS-B, Simulated Annealing (SANN), and Berndt-Hall-Hall-Hausman (BHHH)) and MPSE. Bayesian inference utilizes Metropolis-Hastings within Gibbs sampling under Squared Error Loss (SEL) and LINEX Loss (LL) functions to compute point estimates and Highest Posterior Density (HPD) credible intervals. Asymptotic confidence intervals for parameters, reliability, and hazard rate functions are constructed using asymptotic normality and delta method. Methods are based on Dev and Chacko (2026, Journal of the Iranian Statistical Society, 25, 1-29), Yan, Zhang, and Dong (2021, Journal of Computational and Applied Mathematics, 381, 113022, <doi:10.1016/j.cam.2020.113022>), Ng, Kundu, and Chan (2004, Naval Research Logistics, 51, 1145-1168, <doi:10.1002/nav.20045>), Cheng and Amin (1983, Journal of the Royal Statistical Society Series B, 45, 394-403, <doi:10.1111/j.2517-6161.1983.tb01268.x>), Kundu and Gupta (1999, Australian & New Zealand Journal of Statistics, 41, 173-188, <doi:10.1111/1467-842X.00072>), and Berndt, Hall, Hall, and Hausman (1974, Annals of Economic and Social Measurement, 3, 653-665).

The inti package is part of the inkaverse project for developing different procedures and tools used in plant science and experimental designs. The mean aim of the package is to support researchers during the planning of experiments and data collection (tarpuy()), data analysis and graphics (yupana()) , and scientific writing. Learn more about the inkaverse project at <https://inkaverse.com/>.

Takes in vivo toxicokinetic concentration-time data and fits parameters of 1-compartment and 2-compartment models for each chemical. These methods are described in detail in "Informatics for Toxicokinetics" (2025).

Geostatistical interpolation has traditionally been done by manually fitting a variogram and then interpolating. Here, we introduce classes and methods that can do this interpolation automatically. Pebesma et al (2010) gives an overview of the methods behind and possible usage <doi:10.1016/j.cageo.2010.03.019>.

An R interface to the InfluxDB time series database <https://www.influxdata.com>. This package allows you to fetch and write time series data from/to an InfluxDB server. Additionally, handy wrappers for the Influx Query Language (IQL) to manage and explore a remote database are provided.

This package provides functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].