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.

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.

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) .

Multiples Comparisons Procedures

Performs the execution of the main procedures of multiple comparisons in the literature, Scott-Knott (1974) < http://www.jstor.org/stable/2529204>, Batista (2016) < http://repositorio.ufla.br/jspui/handle/1/11466>, including graphic representations and export to different extensions of its results. An additional part of the package is the presence of the performance evaluation of the tests (Type I error per experiment and the power). This will assist the user in making the decision for the chosen test.

Causal Inference and Prediction in Cohort-Based Analyses

Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.

Incorporate Expert Opinion with Parametric Survival Models

Enables users to incorporate expert opinion with parametric survival analysis using a Bayesian or frequentist approach. Expert Opinion can be provided on the survival probabilities at certain time-point(s) or for the difference in mean survival between two treatment arms.Please reference its use as Cooney, P., White, A. (2023) .

Estimate Quantiles Curves

Non-parametric methods as local normal regression, polynomial local regression and penalized cubic B-splines regression are used to estimate quantiles curves. See Fan and Gijbels (1996) and Perperoglou et al.(2019) .