Analysis of Discretely Observed Linear Birth-and-Death(-and-Immigration) Markov Chains

Provides Frequentist (EM) and Bayesian (MCMC) Methods for Inference of Birth-Death-Immigration Markov Chains.

A Modular Framework for Statistical Simulations in R

An open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments.See full documentation at < https://avi-kenny.github.io/SimEngine/>.

All Hierarchical or Graphical Models for Generalized Linear Model

Find all hierarchical models of specified generalized linear model with information criterion (AIC, BIC, or AICc) within specified cutoff of minimum value. Alternatively, find all such graphical models. Use branch and bound algorithm so we do not have to fit all models.

Get or Set UNIX Niceness

Get or set UNIX priority (niceness) of running R process.

Power Calculations for GxE and GxG Interactions for GWAS

Analytical power calculations for GxE and GxG interactions for case-control studies of candidate genes and genome-wide association studies (GWAS). This includes power calculation for four two-step screening and testing procedures. It can also calculate power for GxE and GxG without any screening.

Process Accelerometer Data for Physical Activity Measurement

It provides a function "wearingMarking" for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plot for accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. "deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail; "deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete days and removing low activity days; "markPAI" can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. It also supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions.

Meta Analysis Instrumental Variable Estimator

Meta-analysis traditionally assigns more weight to studies with lower standard errors, assuming higher precision. However, in observational research, precision must be estimated and is vulnerable to manipulation, such as p-hacking, to achieve statistical significance. This can lead to spurious precision, invalidating inverse-variance weighting and bias-correction methods like funnel plots. Common methods for addressing publication bias, including selection models, often fail or exacerbate the problem. This package introduces an instrumental variable approach to limit bias caused by spurious precision in meta-analysis. Methods are described in 'Irsova et al.' (2025) .

Project Management Tools

Tools for data importation, recoding, and inspection. There are functions to create new project folders, R code templates, create uniquely named output directories, and to quickly obtain a visual summary for each variable in a data frame. The main feature here is the systematic implementation of the "variable key" framework for data importation and recoding. We are eager to have community feedback about the variable key and the vignette about it. In version 1.7, the function 'semTable' is removed. It was deprecated since 1.67. That is provided in a separate package, 'semTable'.

Multi-Gene Descent Probabilities

Do multi-gene descent probabilities (Thompson, 1983, ) and special cases thereof (Thompson, 1986, ) including inbreeding and kinship coefficients. But does much more: probabilities of any set of genes descending from any other set of genes.

Markov Chain Monte Carlo for Potts Models

Do Markov chain Monte Carlo (MCMC) simulation of Potts models (Potts, 1952, ), which are the multi-color generalization of Ising models (so, as as special case, also simulates Ising models). Use the Swendsen-Wang algorithm (Swendsen and Wang, 1987, ) so MCMC is fast. Do maximum composite likelihood estimation of parameters (Besag, 1975, , Lindsay, 1988, ).