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Reliably Return the Source and Call Location of a Command
Robust and reliable functions to return informative outputs to console with the run or source location of a command. This can be from the 'RScript'/R terminal commands or 'RStudio' console, source editor, 'Rmarkdown' document and a Shiny application.
Text Processing Tools for Turkish E-Commerce Data
Provides several datasets useful for processing and analysis of text in Turkish from an online shopping platform.
Power Analyses for Interaction Effects in Cross-Sectional Regressions
Power analysis for regression models which test the interaction of
two or three independent variables on a single dependent variable. Includes options
for correlated interacting variables and specifying variable reliability.
Two-way interactions can include continuous, binary, or ordinal variables.
Power analyses can be done either analytically or via simulation. Includes
tools for simulating single data sets and visualizing power analysis results.
The primary functions are power_interaction_r2() and power_interaction() for two-way
interactions, and power_interaction_3way_r2() for three-way interactions.
Please cite as: Baranger DAA, Finsaas MC, Goldstein BL, Vize CE, Lynam DR,
Olino TM (2023). "Tutorial: Power analyses for interaction effects in
cross-sectional regressions."
Nonparametric Models for Longitudinal Data
Support the book: Wu CO and Tian X (2018). Nonparametric Models for Longitudinal Data. Chapman & Hall/CRC (to appear); and provide fit for using global and local smoothing methods for the conditional-mean and conditional-distribution based models with longitudinal Data.
Lexicons for Text Analysis
A collection of lexical hash tables, dictionaries, and word lists.
Trajectories and Phylogenies Simulator
Generates stochastic time series and genealogies associated with a population dynamics model. Times series are simulated using the Gillespie exact and approximate algorithms and a new algorithm we introduce that uses both approaches to optimize the time execution of the simulations. Genealogies are simulated from a trajectory using a backwards-in-time based approach. Methods are described in Danesh G et al (2022)
Random Survival Forest for Recurrent Events
Analyze recurrent events with right-censored data and the potential presence of a terminal event (that prevents further occurrences, like death). 'recofest' extends the random survival forest algorithm, adapting splitting rules and node estimators to handle complexities of recurrent events. The methodology is fully described in Murris, J., Bouaziz, O., Jakubczak, M., Katsahian, S., & Lavenu, A. (2024) (< https://hal.science/hal-04612431v1/document>).
Tools for Modelling of Animal Flight Performance
Allows estimation and modelling of flight costs in animal (vertebrate) flight,
implementing the aerodynamic power model described in Klein Heerenbrink et al.
(2015)
Scale Mixture of Normal Distribution in Linear Mixed-Effects Model
Bayesian analysis of censored linear mixed-effects models that replace Gaussian assumptions with a flexible class of distributions, such as the scale mixture of normal family distributions, considering a damped exponential correlation structure which was employed to account for within-subject autocorrelation among irregularly observed measures. For more details, see Kelin Zhong, Fernanda L. Schumacher, Luis M. Castro, Victor H. Lachos (2025)
Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation
Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021)