software.html

Software:
[Updated: 03/31/2023; * = a student author during the time the work was conducted]

WinBUGS code from Bandyopadhyay D, Reich BJ and Slate E. (2009). Bayesian modeling of multivariate spatial binary data with applications to dental caries, Statistics in Medicine 28, 3492-3508
SAS macro from *Lin L, Bandyopadhyay D, Lipsitz S and Sinha D (2010). Association models for clustered data with binary and continuous responses, Biometrics, 66(1), 287-293
R code from Reich BJ, Bandyopadhyay D. (2010). A latent factor model for spatial data with informative missingness, The Annals of Applied Statistics, 4(1), 439-459
WinBUGS code from Bandyopadhyay D, Sinha D, Lipsitz S, Letourneau E. (2010). Changing approaches of prosecutors towards juvenile repeated sex-offenders: a Bayesian evaluation, The Annals of Applied Statistics, 4(2), 805-829
SAS macro from *Li X, Bandyopadhyay D, Lipsitz S and Sinha D. (2011). Likelihood methods for binary responses of present components in a cluster, Biometrics, 67(2), 629-635
R package 'ordcrm' from
(i) *VanMeter EM, Garett-Mayer E and Bandyopadhyay D. (2011). Proportional odds model for dose finding clinical trial designs with ordinal toxicity grading, Statistics in Medicine 30(17), 2070-2080; &
(ii) *VanMeter EM, Garett-Mayer E and Bandyopadhyay D. (2012). Dose finding clinical trial design for ordinal toxicity grades using the continuation ratio model: an extension of the continual reassessment method, Clinical Trials, 9(3), 303-313
R package 'nlsmsn' from Lachos VH, Bandyopadhyay D and *Garay AM. (2011). Heteroscedastic non-linear regression models based on scale mixtures of skew-normal distributions, Statistics and Probability Letters, 81(8), 1208-1217
R and WinBUGS codes from Lachos VH, Bandyopadhyay D and Dey DK. (2011). Linear and non-linear mixed-effect models for censored HIV viral loads using normal/independent distributions, Biometrics, 67(4), 1594-1604
WinBUGS code from Bandyopadhyay D, Reich BJ and Slate E. (2011). A spatial Beta-Binomial model for clustered count data on dental caries, Statistical Methods in Medical Research, 20, 85-102.
R and WinBUGS codes from Bandyopadhyay D, Lachos VH, Castro LM and Dey DK. (2012). Skew-normal/independent linear mixed models for censored responses with applications to HIV viral loads, Biometrical Journal, 54(3), 405-425
WinBUGS code from *Boehm L, Reich BJ and Bandyopadhyay D. (2013). Bridging conditional and marginal shapes for spatially-referenced binary data, Biometrics, 69(2), 545-554
R code from *Mustvari T, Bandyopadhyay D, Lesaffre E and Declerck D. (2013). A multilevel model for spatially correlated binary data in the presence of misclassification: An application in oral health research, Statistics in Medicine, 32(30), 5241-5259
R code (using MPI) from Reich BJ, Bandyopadhyay D and Bondell H. (2013). A nonparametric spatial model for periodontal data with non-random missingness, Journal of the American Statistical Association, 108, 820-831
WinBUGS code for the full model from *Galvis DM, Bandyopadhyay D and Lachos VH. (2014). Augmented mixed beta regression models for periodontal proportion data, Statistics in Medicine, 33(21), 3759-3771
R code from *Schnell P, Bandyopadhyay D, Reich BJ and Nunn M. (2015). A marginal cure-rate proportional hazards model for spatial survival data, Journal of the Royal Statistical Society - Series C, 64(4), 673-691
R code from *Matos LM, Bandyopadhyay D, Castro LM and Lachos VH. (2015). Influence assessment in censored mixed-effects models using the multivariate Student's-t distribution,Journal of Multivariate Analysis, 141, 104-117
R code for MCMC implementation from Bandyopadhyay D and Canale A. (2016). Nonparametric spatial models for clustered ordered periodontal data, Journal of the Royal Statistical Society - Series C, 65(4), 619-640
R code to implement the fractional-risk-set based (i) weighted log-rank test, and (ii) weighted Kaplan-Meier tests, proposed in:
(i) Bandyopadhyay D and Datta S (2008). Testing equality of survival distributions when the population marks are missing, Journal of Statistical Planning and Inference, 138, 1722-1732 &
(ii) Bandyopadhyay D, Jacome-Pumar A. (2016). Comparing conditional survival functions with missing population marks in a competing risk model, Computational Statistics and Data Analysis, 95, 150-160
C code to implement the Potts model in Jin I-H, Yuan Y and Bandyopadhyay D. (2016). A Bayesian hierarchical spatial model for dental caries assessment using non-Gaussian Markov random fields, The Annals of Applied Statistics, 10(2), 884-905
WinBUGS code from Bandyopadhyay D, *Galvis DM and Lachos VH (2017). Augmented mixed models for clustered proportion data, Statistical Methods in Medical Research, 26(2), 880-897
SAS macro from *Lewis B, Bandyopadhyay D, DeSantis SM and John MT. (2017). Augmented beta regression for periodontal proportion data via the SAS NLMIXED procedure,Journal of Applied Probability and Statistics, 12(1), 49-66
R package 'qrLMM' from *Galarza CE, Lachos VH and Bandyopadhyay D. (2017). Quantile regression for linear mixed models: A stochastic approximation EM approach, Statistics and Its Interface, 10(3), 471-482
R code to generate p-values from the L1-distance tests (see Table 3) for assessing effects of the covariate BMI from Lan L, Bandyopadhyay D and Datta S. (2017). Nonparametric regression in clustered multistate current status data with informative cluster size, Statistica Neerlandica, 71(1), 31-57
R code available in GitHub from *Chernokhouva A, Hussein A, Nkurunziza S and Bandyopadhyay D (2018). Bayesian inference in time-varying additive hazards model with applications to disease mapping, Environmetrics, 29(5-6), e2478 [Special Issue celebrating TIES 25th Anniversary]
R code [with data] from Zhao W, Lian H and Bandyopadhyay D. (2018). A partially linear additive model for clustered proportion data, Statistics in Medicine, 37(6), 1009-1030
R code from Wu X, Guan T, Liu DJ, Leon-Novelo LG and Bandyopadhyay D. (2018). Adaptive-weight burden test for associations between quantitative traits and genotype data with complex correlations, The Annals of Applied Statistics,12(3), 1558-1582
R package 'CensSpatial' from *Ordonez JA, Bandyopadhyay D, Lachos VH and Cabral CR. (2018). Geostatistical estimation and prediction for censored responses, Spatial Statistics, 23, 109-123
R/JAGS codes available in GitHub from *Bhingare A, Sinha D, Pati D, Bandyopadhyay D and Lipsitz SR. (2019). Semiparametric Bayesian latent variable regression for skewed multivariate data, Biometrics, 75(2), 528-538
R code available in GitHub from Zhang L and Bandyopadhyay D. (2020). A graphical model for skewed matrix-variate non-randomly missing data, Biostatistics, 21(2), e80-e97

R code available in GitHub from *Guan Q, Reich BJ, Laber E and Bandyopadhyay D. (2020). Bayesian nonparametric policy search with applications to periodontal recall intervals, Journal of the American Statistical Association - Applications & Case Studies, 105(531), 1066-1078

R code available in GitHub from # Xu J, Bandyopadhyay D, Chakraborty B, Mirzaei S and Michalowicz B. (2020). SMARTp: A SMART design for non-surgical treatment of chronic periodontitis with spatially-referenced and non-randomly missing skewed outcomes, Biometrical Journal, 62(2), 282-310; RShiny link here; R package SMARTp here

Simulation demo (R code zipped) from *Jhuang A-T, Fuentes M, Bandyopadhyay D and Reich BJ. (2020). Spatiotemporal signal detection using continuous shrinkage priors, Statistics in Medicine, 39(13), 1817-1832

R package clordr from *Wang P, Ma TF, Bandyopadhyay D, Tang Y and Zhu J. (2021). Composite likelihood inference for ordinal periodontal data with replicated spatial patterns, Statistics in Medicine, 40(26), 5871-5893

R code available in GitHub from Lock E, Bandyopadhyay D. (2021). Bayesian nonparametric multiway regression for clustered binomial data, Stat, 10(1), e378; Figure

R package BAREB from *Li Y, Bandyopadhyay D, Xie F, Xu Y (2020). BAREB: A Bayesian repulsive biclustering model for periodontal data, Statistics in Medicine, 39(16), 2139-2151

R/C++ code available in GitHub from *Lan Z, Reich BJ and Bandyopadhyay D. (2021). A Bayesian semiparametric mixture modeling of spatially-dependent positive-definite matrices, with applications to diffusion tensor imaging, Canadian Journal of Statistics, 49(1), 129-149

R package RASCO (available from GitHub) to alleviate spatial confounding in disease mapping (GLMMs) & survival analysis; led by PhD co-advisee Douglas Mesquita:
(i) Azevedo DRM, Bandyopadhyay D, Prates MO, Abdel-Salam A-SG and Garcia D. (2020). Assessing spatial confounding in cancer disease mapping using R, Cancer Reports, 3(4), e1263
(ii) Azevedo DRM, Prates MO and Bandyopadhyay D. (2021). MSPOCK: Alleviating spatial confounding in multivariate disease mapping models, Journal of Agricultural, Biological & Environmental Statistics, 26, 464-491

(iii) Azevedo DRM, Prates MO and Bandyopadhyay D. (2022+). Alleviating spatial confounding in frailty models, (Tentatively accepted), Biostatistics

R/C code from Shin Y, Sun S and Bandyopadhyay D. (2020). Impact of adoloscent obesity on middle-age health of women given data MAR, Biometrical Journal, 62(7), 1702-1716

R package ICScure from Lam KF, *Lee CY, Wong KY and Bandyopadhyay D. (2021). Marginal analysis of current status data with informative cluster size using a class of semiparametric transformation cure models, Statistics in Medicine, 40(10), 2400-2412

GitHub implementation for Swihart BJ and Bandyopadhyay D. (2021). Bridged parametric survival models: General paradigm and speed improvements, Computer Methods and Programs in Biomedicine, 206, 106115

GitHub implementation for *Lan Z, Reich BJ and Bandyopadhyay D. (2021). Probabilistic diffusion MRI fiber-tracking using a directed acyclic graph auto-regressive model of positive definite matrices, Journal of Statistical Research, 55(1), 147-158

GitHub implementation for Choi S, *Choi T, Cho H and Bandyopadhyay D. (2022). Weighted least-squares regression with competing risks data, Statistics in Medicine, 41(2), 227-241

R implementation for Ke C, Bandyopadhyay D, Acunzo M and Winn R. (2022). Gene-screening in ultra-high dimensional right-censored lung cancer data, Onco, 2(4), 305-318

R packages skewBART and MultiskewBART available in GitHub from *Um S, Linero AR, Sinha D and Bandyopadhyay D. (2023). Bayesian Additive Regression Trees for Multivariate Skewed Responses, Statistics in Medicine, 42(3), 246-263

R/C++ codes available in GitHub from *Lan Z, Reich BJ, Guiness J, Bandyopadhyay D, Ma L and Moeller G. (2023+). Geostatistical modeling of positive definite matrices: An application to diffusion tensor imaging, (Accepted), Biometrics

GitHub (RStan) implementation from *Acharya S, Pati D, Bandyopadhyay D and Sun S. (2023+). A monotone single-index model for missing-at-random longitudinal proportion data, (Accepted), Journal of Applied Statistics

R package drRML available in GitHub from Choi S, *Choi T, Lee H-Y, *Han SW and Bandyopadhyay D. (2022). Doubly-robust inference for differences in restricted mean lifetimes using pseudo-observations, Pharmaceutical Statistics, 21(6), 1185-1198

R package MMGOR from *Wang T, He K, Ma W, Bandyopadhyay D and Sinha S. (2023+). Minorize-Maximize algorithm for the generalized odds rate model for clustered current status data, (Accepted), Canadian Journal of Statistics

R code for running simulation design from *Zhang CE, Al-Mosawi RR, Bandyopadhyay D, Huang H and Lu X (2023+). Sieve estimation of the additive hazards model for bivariate current status data, (Under Review), Statistics in Biosciences

R package MMIntAdd available in GitHub from Wang T, Bandyopadhyay D and Sinha S. (2023+). Efficient estimation of the additive hazards model for interval-censored data, (Accepted), Book Chapter, Springer Issue on Emerging Topics in Modeling Interval-Censored Data, edited by (Tony) Sun and (Din) Ding-Geng Chen

R package BSTN available in GitHub from *Lee I, Sinha D, Mai Q, Zhang X and Bandyopadhyay D. (2023+). Bayesian regression analysis of skewed tensor responses, (Accepted), Biometrics

R implementation JointCSsurv available in GitHub from *Lee CY, Wong KY, Lam KF and Bandyopadhyay D. (2023+). A semiparametric joint model for cluster size and subunit-specific interval-censored outcomes, (Accepted), Biometrics

R package BSTT available in GitHub from *Lee I, Sinha D, Mai Q and Bandyopadhyay D. (2023+). A new class of skewed tensor distributions, (Under Revision), Bayesian Analysis

R/JAGS implementation in GitHub from Tong X, *Kim S, Bandyopadhyay D and Sun S. (2023+). Association between body fat and body mass index from incomplete longitudinal proportion data: Findings from the Fels study, (Under Review), Journal of Data Science

R package mspack2 available in GitHub from *Anyaso-Samuel S, Bandyopadhyay D and Datta S. (2023+). Pseudo-value regression of clustered current status data with informative cluster size, (Under Review), Statistical Methods in Medical Research

R package rankIC available in GitHub from *Choi T, Choi S and Bandyopadhyay D. (2023+). Rank estimation for the accelerated failure time model with partially interval-censored data, (Under Review), Biometrics

R package ipcwQRPIC available in GitHub from *Kim Y, Choi S, Park S, *Choi S and Bandyopadhyay D. (2023+). Inverse weighted quantile regression with partially interval-censored data, (Under Review), Statistical Methods in Medical Research

GitHub implementation for Lu X, *Wang Y, Bandyopadhyay D and Bakoyannis G. (2023+). Sieve estimation of a class of partially linear transformation models with interval-censored competing risks data, (Accepted), Statistica Sinica

R markdown demo for Ke C, Bandyopadhyay D and Sarkar D (2023). Gene screening for prognosis of non-muscle-invasive bladder carcinoma under competing risks endpoints, Cancers,15(2), 379