Soundscape Background Noise, Power, and Saturation

Accessible and flexible implementation of three ecoacoustic indices that are less commonly available in existing R frameworks: Background Noise, Soundscape Power and Soundscape Saturation. The functions were design to accommodate a variety of sampling designs. Users can tailor calculations by specifying spectrogram time bin size, amplitude thresholds and normality tests. By simplifying computation and standardizing reproducible methods, the package aims to support ecoacoustics studies. For more details about the indices read Towsey (2014) and Burivalova (2017) .

Classify Occurrences by Confidence Levels in the Species ID

Classify occurrence records based on confidence levels of species identification. In addition, implement tools to filter occurrences inside grid cells and to manually check for possibles errors with an interactive shiny application.

A Set of Methods for Longitudinal Data Objects

A very simple implementation of a class for longitudinal data.

Externally Studentized Midrange Distribution

Computes the studentized midrange distribution (pdf, cdf and quantile) and generates random numbers.

Rank-Based Test to Evaluate a Surrogate Marker

Uses a novel rank-based nonparametric approach to evaluate a surrogate marker in a small sample size setting. Details are described in Parast et al (2024) and Hughes A et al (2025) . A tutorial for this package can be found at < https://www.laylaparast.com/surrogaterank> and a Shiny App implementing the package can be found at < https://parastlab.shinyapps.io/SurrogateRankApp/>.

Estimate Entry Models

Tools for measuring empirically the effects of entry in concentrated markets, based in Bresnahan and Reiss (1991) < https://www.jstor.org/stable/2937655>.

'Shiny' Application for Whole Genome Duplication Analysis

Provides a comprehensive 'Shiny' application for analyzing Whole Genome Duplication ('WGD') events. This package provides a user-friendly 'Shiny' web application for non-experienced researchers to prepare input data and execute command lines for several well-known 'WGD' analysis tools, including 'wgd', 'ksrates', 'i-ADHoRe', 'OrthoFinder', and 'Whale'. This package also provides the source code for experienced researchers to adjust and install the package to their own server. Key Features 1) Input Data Preparation This package allows users to conveniently upload and format their data, making it compatible with various 'WGD' analysis tools. 2) Command Line Generation This package automatically generates the necessary command lines for selected 'WGD' analysis tools, reducing manual errors and saving time. 3) Visualization This package offers interactive visualizations to explore and interpret 'WGD' results, facilitating in-depth 'WGD' analysis. 4) Comparative Genomics Users can study and compare 'WGD' events across different species, aiding in evolutionary and comparative genomics studies. 5) User-Friendly Interface This 'Shiny' web application provides an intuitive and accessible interface, making 'WGD' analysis accessible to researchers and 'bioinformaticians' of all levels.

Estimating Speakers of Texts

Estimates the authors or speakers of texts. Methods developed in Huang, Perry, and Spirling (2020) . The model is built on a Bayesian framework in which the distinctiveness of each speaker is defined by how different, on average, the speaker's terms are to everyone else in the corpus of texts. An optional cross-validation method is implemented to select the subset of terms that generate the most accurate speaker predictions. Once a set of terms is selected, the model can be estimated. Speaker distinctiveness and term influence can be recovered from parameters in the model using package functions. Once fitted, the model can be used to predict authorship of new texts.

Analyze Data from Stepped Wedge Cluster Randomized Trials

Provide various functions and tools to help fit models for estimating treatment effects in stepped wedge cluster randomized trials. Implements methods described in Kenny, Voldal, Xia, and Heagerty (2022) "Analysis of stepped wedge cluster randomized trials in the presence of a time-varying treatment effect", .

Estimating Speaker Style Distinctiveness

Estimates distinctiveness in speakers' (authors') style. Fits models that can be used for predicting speakers of new texts. Methods developed in Huang et al (2020) .