DynTxRegime - Methods for Estimating Optimal Dynamic Treatment Regimes

Methods to estimate dynamic treatment regimes using Interactive Q-Learning, Q-Learning, weighted learning, and value-search methods based on Augmented Inverse Probability Weighted Estimators and Inverse Probability Weighted Estimators. Dynamic Treatment Regimes: Statistical Methods for Precision Medicine, Tsiatis, A. A., Davidian, M. D., Holloway, S. T., and Laber, E. B., Chapman & Hall/CRC Press, 2020, ISBN:978-1-4987-6977-8.

Last updated 1 years ago

3.42 score 2 stars 2 packages 109 scripts 487 downloads

modelObj - A Model Object Framework for Regression Analysis

A utility library to facilitate the generalization of statistical methods built on a regression framework. Package developers can use 'modelObj' methods to initiate a regression analysis without concern for the details of the regression model and the method to be used to obtain parameter estimates. The specifics of the regression step are left to the user to define when calling the function. The user of a function developed within the 'modelObj' framework creates as input a 'modelObj' that contains the model and the R methods to be used to obtain parameter estimates and to obtain predictions. In this way, a user can easily go from linear to non-linear models within the same package.

Last updated 2 years ago

3.30 score 3 packages 22 scripts 378 downloads

DOVE - Durability of Vaccine Efficacy

Implements maximum likelihood methods for evaluating the durability of vaccine efficacy in a randomized, placebo-controlled clinical trial with staggered enrollment of participants and potential crossover of placebo recipients before the end of the trial. Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021) <doi:10.1093/cid/ciab226> and Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021) <doi:10.1093/cid/ciab630>.

Last updated 12 months ago

3.00 score 295 downloads

POSTm - Phylogeny-Guided OTU-Specific Association Test for Microbiome Data

Implements the Phylogeny-Guided Microbiome OTU-Specific Association Test method, which boosts the testing power by adaptively borrowing information from phylogenetically close OTUs (operational taxonomic units) of the target OTU. This method is built on a kernel machine regression framework and allows for flexible modeling of complex microbiome effects, adjustments for covariates, and can accommodate both continuous and binary outcomes.

Last updated 7 months ago

2.30 score 2 scripts 209 downloads

iDOVE - Durability of Vaccine Efficacy Against SARS-CoV-2 Infection

Implements a nonparametric maximum likelihood method for assessing potentially time-varying vaccine efficacy (VE) against SARS-CoV-2 infection under staggered enrollment and time-varying community transmission, allowing crossover of placebo volunteers to the vaccine arm. Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021) <doi:10.1093/cid/ciab630>.

Last updated 12 months ago

2.00 score 223 downloads

contTimeCausal - Continuous Time Causal Models

Implements the semiparametric efficient estimators of continuous-time causal models for time-varying treatments and confounders in the presence of dependent censoring (including structural failure time model and Cox proportional hazards marginal structural model). S. Yang, K. Pieper, and F. Cools (2019) <doi:10.1111/biom.12845>.

Last updated 2 years ago

2.00 score 1 scripts 218 downloads

GGMridge - Gaussian Graphical Models Using Ridge Penalty Followed by Thresholding and Reestimation

Estimation of partial correlation matrix using ridge penalty followed by thresholding and reestimation. Under multivariate Gaussian assumption, the matrix constitutes an Gaussian graphical model (GGM).

Last updated 1 years ago

1.89 score 2 packages 13 scripts 230 downloads

DTRreg - DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)

Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv). Extension to continuous treatment variables. Wallace et al. (2017) <DOI:10.18637/jss.v080.i02>; Simoneau et al. (2020) <DOI:10.1080/00949655.2020.1793341>.

Last updated 8 months ago

1.78 score 1 stars 6 scripts 356 downloads

baclava - Bayesian Analysis of Cancer Latency with Auxiliary Variable Augmentation

A novel data-augmentation Markov chain Monte Carlo sampling algorithm to fit a progressive compartmental model of disease in a Bayesian framework Morsomme, R.N., Holloway, S.T., Ryser, M.D. and Xu J. (2024) <doi:10.48550/arXiv.2408.14625>.

Last updated 2 months ago

1.00 score 275 downloads

tLagPropOdds - Proportional Odds Model with Censored, Time-Lagged Categorical Outcome

Implements a semiparametric estimator for the odds ratio model with censored, time-lagged, ordered categorical outcome in a randomized clinical trial that incorporates baseline and time-dependent information. Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.

Last updated 12 months ago

1.00 score 244 downloads

roboBayes - Robust Online Bayesian Monitoring

An implementation of Bayesian online changepoint detection (Adams and MacKay (2007) <arXiv:0710.3742>) with an option for probability based outlier detection and removal (Wendelberger et. al. (2021) <arXiv:2112.12899>). Building on the independent multivariate constant mean model implemented in the 'R' package 'ocp', this package models multivariate data as multivariate normal about a linear trend, defined by user input covariates, with an unstructured error covariance. Changepoints are identified based on a probability threshold for windows of points.

Last updated 12 months ago

1.00 score 135 downloads

VEwaningVariant - Vaccine Efficacy Over Time - Variant Aware

Implements methods for inference on potential waning of vaccine efficacy and for estimation of vaccine efficacy at a user-specified time after vaccination based on data from a randomized, double-blind, placebo-controlled vaccine trial in which participants may be unblinded and placebo subjects may be crossed over to the study vaccine. The methods also for variant stratification and allow adjustment for possible confounding via inverse probability weighting through specification of models for the trial entry process, unblinding mechanisms, and the probability an unblinded placebo participant accepts study vaccine.

Last updated 12 months ago

1.00 score 181 downloads

VEwaning - Vaccine Efficacy Over Time

Implements methods for inference on potential waning of vaccine efficacy and for estimation of vaccine efficacy at a user-specified time after vaccination based on data from a randomized, double-blind, placebo-controlled vaccine trial in which participants may be unblinded and placebo subjects may be crossed over to the study vaccine. The methods also allow adjustment for possible confounding via inverse probability weighting through specification of models for the trial entry process, unblinding mechanisms, and the probability an unblinded placebo participant accepts study vaccine: Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2102.13103> .

Last updated 12 months ago

1.00 score 187 downloads

SurvLong - Analysis of Proportional Hazards Model with Sparse Longitudinal Covariates

Provides kernel weighting methods for estimation of proportional hazards models with intermittently observed longitudinal covariates. Cao H., Churpek M. M., Zeng D., and Fine J. P. (2015) <doi:10.1080/01621459.2014.957289>.

Last updated 12 months ago

1.00 score 1 stars 5 scripts 345 downloads

OTRselect - Variable Selection for Optimal Treatment Decision

A penalized regression framework that can simultaneously estimate the optimal treatment strategy and identify important variables. Appropriate for either censored or uncensored continuous response.

Last updated 1 years ago

1.00 score 1 stars 3 scripts 196 downloads

JMdesign - Joint Modeling of Longitudinal and Survival Data - Power Calculation

Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix, Sigma_theta, is unknown.

Last updated 1 years ago

1.00 score 3 scripts 391 downloads

AsynchLong - Regression Analysis of Sparse Asynchronous Longitudinal Data

Estimation of regression models for sparse asynchronous longitudinal observations, where time-dependent response and covariates are mismatched and observed intermittently within subjects. Kernel weighted estimating equations are used for generalized linear models with either time-invariant or time-dependent coefficients. Cao, H., Li, J., and Fine, J. P. (2016) <doi:10.1214/16-EJS1141>. Cao, H., Zeng, D., and Fine, J. P. (2015) <doi:10.1111/rssb.12086>.

Last updated 1 years ago

1.00 score 10 scripts 412 downloads

POINT - Protein Structure Guided Local Test

Provides an implementation of a rare variant association test that utilizes protein tertiary structure to increase signal and to identify likely causal variants. Performs structure-guided collapsing, which leads to local tests that borrow information from neighboring variants on a protein and that provide association information on a variant-specific level. For details of the implemented method see West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S-M., Wagner M. J., Buse, J. B., Motsinger-Reif, A., Fourches, D., and Tzeng, J-Y. (2019) <doi:10.1371/journal.pcbi.1006722>.

Last updated 1 years ago

1.00 score 3 scripts 189 downloads

tLagInterim - Interim Monitoring of Clinical Trials with Time-Lagged Outcome

Implements inverse and augmented inverse probability weighted estimators for common treatment effect parameters at an interim analysis with time-lagged outcome that may not be available for all enrolled subjects. Produces estimators, standard errors, and information that can be used to compute stopping boundaries using software that assumes that the estimators/test statistics have independent increments. Tsiatis, A. A. and Davidian, M., (2022) <arXiv:2204.10739> .

Last updated 2 years ago

1.00 score 1 stars 143 downloads

CONCUR - Copy Number Profile Curve-Based Association Test

Implements a kernel-based association test for copy number variation (CNV) aggregate analysis in a certain genomic region (e.g., gene set, chromosome, or genome) that is robust to the within-locus and across-locus etiological heterogeneity, and bypass the need to define a "locus" unit for CNVs. Brucker, A., et al. (2020) <doi:10.1101/666875>.

Last updated 2 years ago

1.00 score 208 downloads

FastKM - A Fast Multiple-Kernel Method Based on a Low-Rank Approximation

A computationally efficient and statistically rigorous fast Kernel Machine method for multi-kernel analysis. The approach is based on a low-rank approximation to the nuisance effect kernel matrices. The algorithm is applicable to continuous, binary, and survival traits and is implemented using the existing single-kernel analysis software 'SKAT' and 'coxKM'. 'coxKM' can be obtained from <https://github.com/lin-lab/coxKM>.

Last updated 2 years ago

1.00 score 6 scripts 162 downloads

dtrSurv - Dynamic Treatment Regimes for Survival Analysis

Provides methods for estimating multi-stage optimal dynamic treatment regimes for survival outcomes with dependent censoring. Cho, H., Holloway, S. T., and Kosorok, M. R. (2020) <arXiv:2012.03294>.

Last updated 2 years ago

1.00 score 1 scripts 226 downloads

ChangepointTesting - Change Point Estimation for Clustered Signals

A multiple testing procedure for clustered alternative hypotheses. It is assumed that the p-values under the null hypotheses follow U(0,1) and that the distributions of p-values from the alternative hypotheses are stochastically smaller than U(0,1). By aggregating information, this method is more sensitive to detecting signals of low magnitude than standard methods. Additionally, sporadic small p-values appearing within a null hypotheses sequence are avoided by averaging on the neighboring p-values.

Last updated 2 years ago

1.00 score 2 scripts 234 downloads

ICODS - Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring

Sieve semiparametric likelihood methods for analyzing interval-censored failure time data from an outcome-dependent sampling (ODS) design and from a case-cohort design. Zhou, Q., Cai, J., and Zhou, H. (2018) <doi:10.1111/biom.12744>; Zhou, Q., Zhou, H., and Cai, J. (2017) <doi:10.1093/biomet/asw067>.

Last updated 2 years ago

1.00 score 175 downloads

highTtest - Simultaneous Critical Values for t-Tests in Very High Dimensions

Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion.

Last updated 2 years ago

1.00 score 1 stars 2 scripts 231 downloads

ramsvm - Reinforced Angle-Based Multicategory Support Vector Machines

Provides a solution path for Reinforced Angle-based Multicategory Support Vector Machines, with linear learning, polynomial learning, and Gaussian kernel learning. C. Zhang, Y. Liu, J. Wang and H. Zhu. (2016) <doi:10.1080/10618600.2015.1043010>.

Last updated 2 years ago

1.00 score 2 scripts 166 downloads

subdetect - Detect Subgroup with an Enhanced Treatment Effect

A test for the existence of a subgroup with enhanced treatment effect. And, a sample size calculation procedure for the subgroup detection test.

Last updated 2 years ago

1.00 score 2 scripts 214 downloads