Methods for Evaluating Principal Surrogates of Treatment Response

Contains the core methods for the evaluation of principal surrogates in a single clinical trial. Provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation summary methods are provided, including print, summary, plot, and testing.

Diagnostics for Confounding of Time-Varying and Other Joint Exposures

Implements three covariate-balance diagnostics for time-varying confounding and selection-bias in complex longitudinal data, as described in Jackson (2016) and Jackson (2019) . Diagnostic 1 assesses measured confounding/selection-bias, diagnostic 2 assesses exposure-covariate feedback, and diagnostic 3 assesses residual confounding/selection-bias after inverse probability weighting or propensity score stratification. All diagnostics appropriately account for exposure history, can be adapted to assess a particular depth of covariate history, and can be implemented in right-censored data. Balance assessments can be obtained for all times, selected-times, or averaged across person-time. The balance measures are reported as tables or plots. These diagnostics can be applied to the study of multivariate exposures including time-varying exposures, direct effects, interaction, and censoring.

Access Meetup Data

Provides programmatic access to the 'Meetup' 'GraphQL' API (< https://www.meetup.com/graphql/>), enabling users to retrieve information about groups, events, and members from 'Meetup' (< https://www.meetup.com/>). Supports authentication via 'OAuth2' and includes functions for common queries and data manipulation tasks.

Causal Inference Modeling for Estimation of Causal Effects

Provides an array of statistical models common in causal inference such as standardization, IP weighting, propensity matching, outcome regression, and doubly-robust estimators. Estimates of the average treatment effects from each model are given with the standard error and a 95% Wald confidence interval (Hernan, Robins (2020) < https://miguelhernan.org/whatifbook/>).

A Package for Processing Lexical Response Data

Lexical response data is a package that can be used for processing cued-recall, free-recall, and sentence responses from memory experiments.

Kernel Balancing

Provides a weighting approach that employs kernels to make one group have a similar distribution to another group on covariates. This method matches not only means or marginal distributions but also higher-order transformations implied by the choice of kernel. 'kbal' is applicable to both treatment effect estimation and survey reweighting problems. Based on Hazlett, C. (2020) "Kernel Balancing: A flexible non-parametric weighting procedure for estimating causal effects." Statistica Sinica. < https://www.researchgate.net/publication/299013953_Kernel_Balancing_A_flexible_non-parametric_weighting_procedure_for_estimating_causal_effects>.

Inference for Functions of Multinomial Parameters

We consider the problem where we observe k vectors (possibly of different lengths), each representing an independent multinomial random vector. For a given function that takes in the concatenated vector of multinomial probabilities and outputs a real number, this is a Monte Carlo estimation procedure of an exact p-value and confidence interval. The resulting inference is valid even in small samples, when the parameter is on the boundary, and when the function is not differentiable at the parameter value, all situations where asymptotic methods and the bootstrap would fail. For more details see Sachs, Fay, and Gabriel (2025) .

Regression Standardization for Causal Inference

Contains more modern tools for causal inference using regression standardization. Four general classes of models are implemented; generalized linear models, conditional generalized estimating equation models, Cox proportional hazards models, and shared frailty gamma-Weibull models. Methodological details are described in Sjölander, A. (2016) . Also includes functionality for doubly robust estimation for generalized linear models in some special cases, and the ability to implement custom models.

An Interface to Specify Causal Graphs and Compute Bounds on Causal Effects

When causal quantities are not identifiable from the observed data, it still may be possible to bound these quantities using the observed data. We outline a class of problems for which the derivation of tight bounds is always a linear programming problem and can therefore, at least theoretically, be solved using a symbolic linear optimizer. We extend and generalize the approach of Balke and Pearl (1994) and we provide a user friendly graphical interface for setting up such problems via directed acyclic graphs (DAG), which only allow for problems within this class to be depicted. The user can then define linear constraints to further refine their assumptions to meet their specific problem, and then specify a causal query using a text interface. The program converts this user defined DAG, query, and constraints, and returns tight bounds. The bounds can be converted to R functions to evaluate them for specific datasets, and to latex code for publication. The methods and proofs of tightness and validity of the bounds are described in a paper by Sachs, Jonzon, Gabriel, and Sjölander (2022) .

Calculate Outbreak Probabilities for a Branching Process Model

Quantify outbreak risk posed by individual importers of a transmissible pathogen. Input parameters of negative binomial offspring distributions for the number of transmissions from each infected individual and initial number of infected. Calculate probabilities of final outbreak size and generations of transmission, as described in Toth et al. (2015) and Toth et al. (2016) .