Bayesian Statistics

adaptBayes

  • This package contains R functions implementing the adaptive priors described in Boonstra and Barbaro (2018).
  • Language(s): R
  • Faculty: Philip S. Boonstra. Download: Github.
  • Reference: Boonstra, Philip S. and Barbaro, Ryan P., "Incorporating Historical Models with Adaptive Bayesian Updates" (2018) Biostatistics https://doi.org/10.1093/biostatistics/kxy053

baker

  • Bayesian Analytic Kit for Etiology Research.
  • Faculty: Zhenke Wu. Download: Github, Website.
  • Reference: Wu, Z., Deloria-Knoll, M. and Zeger, S.L., 2016. Nested partially latent class models for dependent binary data; estimating disease etiology. Biostatistics, 18(2), pp.200-213. <doi:10.1093/biostatistics/kxw037>.

Bama

  • Mediation analysis in the presence of high-dimensional mediators based on the potential outcome framework. Bayesian Mediation Analysis (BAMA), developed by Song et al (2018) <doi:10.1101/467399>.
  • Faculty: Bhramar Mukherjee, Min Zhang, Xiang Zhou. Download: CRAN.
  • Song, Y., Zhou, X., Zhang, M., Zhao, W., Liu, Y., Kardia, S., Roux, A.D., Needham, B., Smith, J.A. and Mukherjee, B., 2018. Bayesian Shrinkage Estimation of High Dimensional Causal Mediation Effects in Omics Studies. bioRxiv, p.467399.

BEHAVIOUR

CoxClusterProcess

  • Bayesian meta-analysis of functional neuroimaging data.
  • Faculty: Jian Kang. Download: Website.

eSIR

  • Extended state-space SIR epidemiological models.
  • Language(s): R
  • Faculty: Peter X.K. Song. Author: Lili Wang.
  • Download: Github.

GeneNetwork

  • Gene sub-network analysis via Bayesian nonparametric methods.
  • Faculty: Jian Kang. Download: Website.

iBAG

lcra

  • A user-friendly interface for doing joint Bayesian latent class and regression analysis with binary and continuous outcomes.
  • Language(s): R
  • Faculty: Michael Elliott. Download: Github.
  • Reference: “Methods to account for uncertainty in latent class assignments when using latent classes as predictors in regression models, with application to acculturation strategy measures” (2020) In press at Epidemiology. doi:10.1097/EDE.0000000000001139

MMCR

mpcr

  • Package for estimating treatment effects in matched-pair cluster randomized trials (MPCR) using covariate calibration.
  • Faculty: Zhenke Wu. Download: Github, Website.
  • Reference: Wu, Z., Frangakis, C.E., Louis, T.A. and Scharfstein, D.O., 2014. Estimation of treatment effects in matched‐pair cluster randomized trials by calibrating covariate imbalance between clusters. Biometrics, 70(4), pp.1014-1022. <doi:10.1111/biom.12214>.

PRECISE

  • Proteomic based integrated subject-specific networks in cancer.
  • Faculty: Veera Baladandayuthapani. Download: Github, Website.
  • Reference: Ha, M.J., Banerjee, S., Akbani, R., Liang, H., Mills, G.B., Do, K.A. and Baladandayuthapani, V., 2018. Personalized Integrated Network Modeling of the Cancer Proteome Atlas. Scientific Reports, 8(1), p.14924. <doi:10.1038/s41598-018-32682-x>.

ReverseInference

  • A Bayesian spatial point pattern classifier.
  • Faculty: Jian Kang. Download: Website.

rewind

  • Package for fitting Bayesian restricted latent class models.
  • Faculty: Zhenke Wu. Download: Github.
  • Reference: Wu, Z., Casciola-Rosen, L., Rosen, A. and Zeger, S.L., 2018. A Bayesian approach to restricted latent class models for scientifically-structured clustering of multivariate binary outcomes. arXiv preprint arXiv:1808.08326. <doi:10.1101/400192>.

rstap

  • Spatial Temporal Aggregated Predictor Models via STAN.
  • Faculty: Brisa Sanchez. Download: Website, Github.
  • Reference: Peterson, Adam, and Brisa Sanchez. "rstap: An R Package for Spatial Temporal Aggregated Predictor Models." arXiv preprint arXiv:1812.10208 (2018).

sbams

  • Bayesian model selection in complex linear systems.
  • Faculty: Xiaoquan William Wen. Download: Github.
  • Reference: Wen, X. "Bayesian Model Selection in Complex Linear Systems, as Illustrated in Genetic Association Studies", submit to Biometrics.

snSMART 

  • Small n Sequential, Multiple Assignment, Randomized Trial (snSMART) calculation applet.
  • Faculty: Kelley Kidwell. Download: Website.
  • Reference: Wei, B., Braun, T.M., Tamura, R.N. and Kidwell, K.M., 2018. A Bayesian analysis of small n sequential multiple assignment randomized trials (snSMARTs). Statistics in Medicine, 37(26), pp.3723-3732.

spotgear

  • Package for fitting Bayesian two-dimensional image dewarping models and estimating disease subsets and signatures.
  • Faculty: Zhenke Wu. Download: Github, Website.
  • Reference: Wu, Z., Casciola-Rosen, L., Shah, A.A., Rosen, A. and Zeger, S.L., 2017. Estimating autoantibody signatures to detect autoimmune disease patient subsets. Biostatistics, 20(1), pp.30-47. <doi:10.1093/biostatistics/kxx061>.

STGP

  • This package focus on spatial variable selection for scalar-on-image regression. It uses a new class of Bayesian nonparametric models, soft-thresholded Gaussian processes and the developed efficient posterior computation algorithms.
  • Faculty: Jian Kang. Download: Website.
  • References: Kang, J., Reich, B.J. and Staicu, A.M., 2018. Scalar-on-image regression via the soft-thresholded Gaussian process. Biometrika, 105(1), pp.165-184.

TGLG

  • This package implements a novel prior model for Bayesian network marker selection in the generalized linear model (GLM) framework.
  • Faculty: Jian Kang. Download: Website.
  • References: Cai, Q., Kang, J. and Yu, T., 2018. Bayesian network marker selection via the thresholded graph Laplacian Gaussian prior. Bayesian Analysis.