Measurement error in a covariate or the outcome of regression models is common, but is often ignored, even though measurement error can lead to substantial bias in the estimated covariate-outcome association. While several texts on measurement error correction methods are available, these methods remain seldomly applied. To improve the use of measurement error correction methodology, we developed mecor, an R package that implements measurement error correction methods for regression models with continuous outcomes. Measurement error correction requires information about the measurement error model and its parameters. This information can be obtained from four types of studies, used to estimate the parameters of the measurement error model: an internal validation study, a replicates study, a calibration study and an external validation study. In the package mecor, regression calibration methods and a maximum likelihood method are implemented to correct for measurement error in a continuous covariate in regression analyses. Additionally, methods of moments methods are implemented to correct for measurement error in the continuous outcome in regression analyses. Variance estimation of the corrected estimators is provided in closed form and using the bootstrap.
The R package lcmm provides a series of functions to estimate statistical models based on linear mixed model theory. It includes the estimation of mixed models and latent class mixed models for Gaussian longitudinal outcomes (hlme), curvilinear and ordinal univariate longitudinal outcomes (lcmm) and curvilinear multivariate outcomes (multlcmm), as well as joint latent class mixed models (Jointlcmm) for a (Gaussian or curvilinear) longitudinal outcome and a time-to-event that can be possibly left-truncated right-censored and defined in a competing setting. Maximum likelihood esimators are obtai…
Background and objective: The stepped wedge cluster randomized trial is a study design increasingly used for public health intervention evaluations. Most previous literature focuses on power calculations for this particular type of cluster randomized trials for continuous outcomes, along with an approximation to this approach for binary outcomes. Although not accurate for binary outcomes, it has been widely used. To improve the approximation for binary outcomes, two new methods for stepped wedge designs (SWDs) of binary outcomes have recently been published. However, these new methods have not…
We introduce the functions included in the R Packet distdichoR for the implementation of the distributional method for the dichotomisation of continuous outcomes. While recalling the principle of the method for the distributions for which the method has already been developed, we add a new distribution - the gamma distribution - to the range of distribution available.
The R package merlin performs flexible joint modelling of hierarchical multi-outcome data. Increasingly, multiple longitudinal biomarker measurements, possibly censored time-to-event outcomes and baseline characteristics are available. However, there is limited software that allows all of this information to be incorporated into one model. In this paper, we present merlin which allows for the estimation of models with unlimited numbers of continuous, binary, count and time-to-event outcomes, with unlimited levels of nested random effects. A wide variety of link functions, including the expecte…
The Counterfactual package implements the estimation and inference methods of Chernozhukov, Fernández-Val and Melly (2013) for counterfactual analysis. The counterfactual distributions considered are the result of changing either the marginal distribution of covariates related to the outcome variable of interest, or the conditional distribution of the outcome given the covariates. They can be applied to estimate quantile treatment effects and wage decompositions. This paper serves as an introduction to the package and displays basic functionality of the commands contained within.
Researchers are often interested in using longitudinal data to estimate the causal effects of hypothetical time-varying treatment interventions on the mean or risk of a future outcome. Standard regression/conditioning methods for confounding control generally fail to recover causal effects when time-varying confounders are themselves affected by past treatment. In such settings, estimators derived from Robins's g-formula may recover time-varying treatment effects provided sufficient covariates are measured to control confounding by unmeasured risk factors. The package gfoRmula implements in R …
We present a bayesassurance R package that computes the Bayesian assurance under various settings characterized by different assumptions and objectives. The package offers a constructive set of simulation-based functions suitable for addressing a wide range of clinical trial study design problems. We provide a detailed description of the underlying framework embedded within each of the power and assurance functions and demonstrate their usage through a series of worked-out examples. Through these examples, we hope to corroborate the advantages that come with using a two-stage generalized struc…
Meta-analysis methods are used to combine evidence from multiple studies. Meta-regression as well as model-based meta-analysis are extensions of standard pairwise meta-analysis in which information about study-level covariates and (arm-level) dosing amount or exposure may be taken into account. A Bayesian approach to inference is very attractive in this context, especially when a meta-analysis is based on few studies only or rare events. In this article, we present the R package MetaStan which implements a wide range of pairwise and model-based meta-analysis models. A generalised linear mixed …
BEND: An R Package for the Bayesian Estimation of Nonlinear Longitudinal Data
Human Resources Research Organization (HumRRO)（人力资源研究组织）；Bloomington Public Schools（布卢明顿公立学校）；Center for Research and Teaching in Economics（经济研究与教学中心）；University of Minnesota（明尼苏达大学）
Extensions in the field of joint modeling of correlated data and dynamic predictions improve the development of prognosis research. The R package frailtypack provides estimations of various joint models for longitudinal data and survival events. In particular, it fits models for recurrent events and a terminal event (frailtyPenal), models for two survival outcomes for clustered data (frailtyPenal), models for two types of recurrent events and a terminal event (multivPenal), models for a longitudinal biomarker and a terminal event (longiPenal) and models for a longitudinal biomarker, recurrent …
Time-smoothed inverse probability weighted estimation of effects of generalized time-varying treatment strategies on repeated outcomes truncated by death
Identifying compromise solutions across multiple treatment benefit-harm profiles in multivariate network meta-analysis
Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg（弗赖堡大学医学院医学生物计量与统计研究所）；Oslo Center for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo（奥斯陆大学生物统计系奥斯陆生物统计与流行病学中心）
Missing data on response variables are common in clinical studies. Corresponding to the uncertainty of missing mechanism, theoretical frameworks on controlled imputation have been developed. In practice, it is recommended to conduct a statistically valid analysis under the primary assumptions on missing data, followed by sensitivity analysis under alternative assumptions to assess the robustness of results. Due to the availability of software, controlled multiple imputation (MI) procedures, including delta-based and reference-based approaches, have become popular for analyzing continuous varia…
We propose a distributed quadratic inference function framework to jointly estimate regression parameters from multiple potentially heterogeneous data sources with correlated vector outcomes. The primary goal of this joint integrative analysis is to estimate covariate effects on all outcomes through a marginal regression model in a statistically and computationally efficient way. We develop a data integration procedure for statistical estimation and inference of regression parameters that is implemented in a fully distributed and parallelized computational scheme. To overcome computational and…
This paper explores improvements in prediction accuracy and inference capability when allowing for potential correlation in team-level random effects across multiple game-level responses from different assumed distributions. First-order and fully exponential Laplace approximations are used to fit normal-binary and Poisson-binary multivariate generalized linear mixed models with non-nested random effects structures. We have built these models into the R package mvglmmRank, which is used to explore several seasons of American college football and basketball data.
Decision trees are flexible prediction models which are constructed to quantify outcome-covariate relationships and characterize relevant population subgroups. However, the standard graphical representation of fitted decision trees highlights individual split points, and hence is suboptimal for visualizing defined subgroups. In this paper, we present a novel visual representation of decision trees which shifts the primary focus to characterizing subgroups, both in terms of their defining covariates and their outcome distribution. We implement our method in the \texttt{visTree} package, which b…
We present the R package SimInf which provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and OpenMP to divide work over multiple processors ensures high performance when simulating a sample outcome.…
Multivariate regression techniques are commonly applied to explore the associations between large numbers of outcomes and predictors. In real-world applications, the outcomes are often of mixed types, including continuous measurements, binary indicators, and counts, and the observations may also be incomplete. Building upon the recent advances in mixed-outcome modeling and sparse matrix factorization, generalized co-sparse factor regression (GOFAR) is proposed, which utilizes the flexible vector generalized linear model framework and encodes the outcome dependency through a sparse singular val…
Deep autoencoders are often extended with a supervised or adversarial loss to learn latent representations with desirable properties, such as greater predictivity of labels and outcomes or fairness with respects to a sensitive variable. Despite the ubiquity of supervised and adversarial deep latent factor models, these methods should demonstrate improvement over simpler linear approaches to be preferred in practice. This necessitates a reproducible linear analog that still adheres to an augmenting supervised or adversarial objective. We address this methodological gap by presenting methods tha…
Evolution & Ecology Research Centre, UNSW（新南威尔士大学进化与生态研究中心）；School of Mathematics and Statistics, UNSW（新南威尔士大学数学与统计学院）；Stats Central, Mark Wainwright Analytical Centre, UNSW（新南威尔士大学Mark Wainwright分析中心统计中心）；National Institute of Aquatic Resources, Danish Technical University（丹麦技术大学国家水产研究所）；Department of Mathematics & Statistics, McMaster University（麦克马斯特大学数学与统计系）；Department of Biology, McMaster University（麦克马斯特大学生物学系）；Department of Biological Sciences, Faculty of Science, The University of Alberta（阿尔伯塔大学理学院生物科学系）；Department of Biosystems Engineering, Zhejiang University（浙江大学农业生物系统工程系）；Department of Psychiatry and Neuropsychology, Maastricht University（马斯特里赫特大学精神病学与神经心理学系）
Reinforcement learning refers to a group of methods from artificial intelligence where an agent performs learning through trial and error. It differs from supervised learning, since reinforcement learning requires no explicit labels; instead, the agent interacts continuously with its environment. That is, the agent starts in a specific state and then performs an action, based on which it transitions to a new state and, depending on the outcome, receives a reward. Different strategies (e.g. Q-learning) have been proposed to maximize the overall reward, resulting in a so-called policy, which def…
tteICE: An R Package for Estimating Treatment Effects on Time-to-Event Outcomes with Intercurrent Events in Two-Arm Trials
Kobe University（神户大学）；Shanghai University of International Business and Economics（上海对外经贸大学）；Chinese Academy of Medical Sciences & Peking Union Medical College（中国医学科学院 北京协和医学院）
