This package provides a novel feature-wise normalization method based on a zero-inflated negative binomial model. This method assumes that the effects of sequencing depth vary for each taxon on their mean and also incorporates a rational link of zero probability and taxon dispersion as a function of sequencing depth. Ziyue Wang, Dillon Lloyd, Shanshan Zhao, Alison Motsinger-Reif (2023) <doi:10.1101/2023.10.31.563648>.

This package provides tools for estimating and inferring two-way partial area under receiver operating characteristic curves (two-way pAUC), partial area under receiver operating characteristic curves (pAUC), and partial area under ordinal dominance curves (pODC). Methods includes Mann-Whitney statistic and Jackknife, etc.

This package implements models of leaf temperature using energy balance. It uses units to ensure that parameters are properly specified and transformed before calculations. It allows separate lower and upper surface conductances to heat and water vapour, so sensible and latent heat loss are calculated for each surface separately as in Foster and Smith (1986) <doi:10.1111/j.1365-3040.1986.tb02108.x>. It's straightforward to model leaf temperature over environmental gradients such as light, air temperature, humidity, and wind. It can also model leaf temperature over trait gradients such as leaf size or stomatal conductance. Other references are Monteith and Unsworth (2013, ISBN:9780123869104), Nobel (2009, ISBN:9780123741431), and Okajima et al. (2012) <doi:10.1007/s11284-011-0905-5>.

This package provides a shared tsibble data easily communicates between htmlwidgets on both client and server sides, powered by crosstalk'. A shiny module is provided to visually explore periodic/aperiodic temporal patterns.

This package provides functions for performing time domain signal coding as used in Chesmore (2001) <doi:10.1016/S0003-682X(01)00009-3>, and related tasks. This package creates the standard S-matrix and A-matrix (with variable lag), has tools to convert coding matrices into distributed matrices, provides published codebooks and allows for extraction of code sequences.

Temperature measurement data, equations and methods for thermocouples, wire RTD, thermistors, IC thermometers, bimetallic strips and the ITS-90.

U.S. Department of the Treasury, Alcohol and Tobacco Tax and Trade Bureau (TTB) collects data and reports on monthly beer industry production and operations. This data package includes a collection of 10 years (2006 - 2015) worth of data on materials used at U.S. breweries in pounds reported by the Brewer's Report of Operations and the Quarterly Brewer's Report of Operations forms, ready for data analysis. This package also includes historical tax rates on distilled spirits, wine, beer, champagne, and tobacco products as individual data sets.

Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <doi:10.2140/astat.2023.14.37>, Barnhill et al. (2023) <doi:10.48550/arXiv.2303.02539>, Barnhill and Yoshida (2023) <doi:10.3390/math11153433>, Aliatimis et al. (2023) <doi:10.1007/s11538-024-01327-8>, Yoshida et al. (2022) <doi:10.1109/TCBB.2024.3420815>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.

Bindings for the Tabula <https://tabula.technology/> Java library, which can extract tables from PDF files. This tool can reduce time and effort in data extraction processes in fields like investigative journalism. It allows for automatic and manual table extraction, the latter facilitated through a Shiny interface, enabling manual areas selection\ with a computer mouse for data retrieval.

This package provides tools for denoising noisy signal and images via Total Variation Regularization. Reducing the total variation of the given signal is known to remove spurious detail while preserving essential structural details. For the seminal work on the topic, see Rudin et al (1992) <doi:10.1016/0167-2789(92)90242-F>.

High-resolution movement-sensor tags typically include accelerometers to measure body posture and sudden movements or changes in speed, magnetometers to measure direction of travel, and pressure sensors to measure dive depth in aquatic or marine animals. The sensors in these tags usually sample many times per second. Some tags include sensors for speed, turning rate (gyroscopes), and sound. This package provides software tools to facilitate calibration, processing, and analysis of such data. Tools are provided for: data import/export; calibration (from raw data to calibrated data in scientific units); visualization (for example, multi-panel time-series plots); data processing (such as event detection, calculation of derived metrics like jerk and dynamic acceleration, dive detection, and dive parameter calculation); and statistical analysis (for example, track reconstruction, a rotation test, and Mahalanobis distance analysis).

Easy visualization, wrangling, and feature engineering of time series data for forecasting and machine learning prediction. Consolidates and extends time series functionality from packages including dplyr', stats', xts', forecast', slider', padr', recipes', and rsample'.

This package provides a variety of tools for assessing dose response curves, with an emphasis on toxicity test data. The main feature of this package are modular functions which can be combined through the namesake pipeline, runtoxdrc', to automate the analysis for large and complex datasets. This includes optional data preprocessing steps, like outlier detection, solvent effects, blank correction, averaging technical replicates, and much more. Additionally, this pipeline is adaptable to any long form dataset, and does not require specific column or group naming to work.

Assists in the TOPSIS analysis process, designed to return at the end of the answer of the TOPSIS multicriteria analysis, a ranking table with the best option as the analysis proposes. TOPSIS is basically a technique developed by Hwang and Yoon in 1981, starting from the point that the best alternative should be closest to the positive ideal solution and farthest from the negative one, based on several criteria to result in the best benefit. (LIU, H. et al., 2019) <doi:10.1016/j.agwat.2019.105787>.

The aim of the R package treebalance is to provide functions for the computation of a large variety of (im)balance indices for rooted trees. The package accompanies the book Tree balance indices: a comprehensive survey by M. Fischer, L. Herbst, S. Kersting, L. Kuehn and K. Wicke (2023) <ISBN: 978-3-031-39799-8>, <doi:10.1007/978-3-031-39800-1>, which gives a precise definition for the terms balance index and imbalance index (Chapter 4) and provides an overview of the terminology in this manual (Chapter 2). For further information on (im)balance indices, see also Fischer et al. (2021) <https://treebalance.wordpress.com>. Considering both established and new (im)balance indices, treebalance provides (among others) functions for calculating the following 18 established indices and index families: the average leaf depth, the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected, quadratic and equal weights Colless index, the family of Colless-like indices, the family of I-based indices, the Rogers J index, the Furnas rank, the rooted quartet index, the s-shape statistic, the Sackin index, the symmetry nodes index, the total cophenetic index and the variance of leaf depths. Additionally, we include 9 tree shape statistics that satisfy the definition of an (im)balance index but have not been thoroughly analyzed in terms of tree balance in the literature yet. These are: the total internal path length, the total path length, the average vertex depth, the maximum width, the modified maximum difference in widths, the maximum depth, the maximum width over maximum depth, the stairs1 and the stairs2 index. As input, most functions of treebalance require a rooted (phylogenetic) tree in phylo format (as introduced in ape 1.9 in November 2006). phylo is used to store (phylogenetic) trees with no vertices of out-degree one. For further information on the format we kindly refer the reader to E. Paradis (2012) <http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.

Computes treatment patterns within a given cohort using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). As described in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.

This package provides ggplot2 geoms for drawing treemaps.

Plots ternary diagrams (simplex plots / Gibbs triangles) and Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the standard graphics functions. Allows custom annotation, interpolating, contouring and scaling of plotting region. Includes a Shiny user interface for point-and-click ternary plotting. An alternative to ggtern', which uses the ggplot2 family of plotting functions.

Collaborative writing and editing of R Markdown (or Sweave) documents. The local .Rmd (or .Rnw) is uploaded as a plain-text file to Google Drive. By taking advantage of the easily readable Markdown (or LaTeX) syntax and the well-known online interface offered by Google Docs, collaborators can easily contribute to the writing and editing process. After integrating all authorsâ contributions, the final document can be downloaded and rendered locally.

The Twilio web service provides an API for computer programs to interact with telephony. The included functions wrap the SMS and MMS portions of Twilio's API, allowing users to send and receive text messages from R. See <https://www.twilio.com/docs/> for more information.

Convert T Cell Receptor (TCR) gene names between the 10X Genomics, Adaptive Biotechnologies, and ImMunoGeneTics (IMGT) nomenclatures.

An R wrapper for the Spotify Web API <https://developer.spotify.com/web-api/>.

Uses thresholded partial least squares algorithm to create a regression or classification model. For more information, see Lee, Bradlow, and Kable <doi:10.1016/j.crmeth.2022.100227>.

Easily carry out latent profile analysis ("LPA"), determine the correct number of classes based on best practices, and tabulate and plot the results. Provides functionality to estimate commonly-specified models with free means, variances, and covariances for each profile. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Models can be estimated using the free open source R packages Mclust and OpenMx', or using the commercial program MPlus', via the MplusAutomation package.