Hughes Publications

James Hughes, Ph.D.

Hughes JP, Lettenmaier DP, Guttorp P: A stochastic approach for assessing the effect of changes in regional circulation patterns on local precipitation. Water Resour Res 29:3303-3315, 1993.
Hughes JP, Guttorp P: A class of stochastic models for relating synoptic atmospheric patterns to local hydrologic phenomenon. Water Resour Res 30:1535-1546, 1994.
Hughes JP: Computing the observed information in the hidden Markov model using the EM algorithm. Statistics and Probability Letters 32:107-114, 1997.
Hughes JP, Guttorp P, Charles SP: A nonhomogeneous hidden Markov model for precipitation. Applied Statistics 48: 15-30, 1999.
download software (tarfile) (revised 4/13/99)
Bellone E, Hughes JP, Guttorp P: A hidden Markov model for downscaling synoptic patterns to precipitation amounts. Climate Research 15:1-12, 2000.
Lystig TC, Hughes JP: Exact Computation of the Observed Information Matrix for Hidden Markov Models. JCGS 11:678 - 689, 2002.

Magder LS, Hughes JP: Logistic regression when the outcome is measured with uncertainty. American Journal of Epidemiology 146:195-203, 1997.
download software (S-plus function) (modified 3/18/03)
Richardson BA and Hughes JP: Product limit estimation for infectious disease data when the diagnostic test for the outcome is measured with uncertainty. Biostatistics 1:341-354, 2000.
Bureau A, Shiboski S, Hughes JP: Applications of continuous time hidden Markov models to the study of misclassified disease outcomes. Statistics in Medicine 22:441-462, 2003.
Meier A, Richardson BA, Hughes JP. Discrete Proportional Hazards models for Mismeasured outcomes. Biometrics, 59:947-954, 2003.
Hughes JP, Totten PA. Estimating the accuracy of polymerase chain reaction-based tests using end-point dilution. Biometrics, 59:505-511, 2003.
Ou SS, Hughes JP, Richardson BA. Methods for Assessing the Accuracy of PCR-Based Tests: Comparisons and Extensions. Statistics in Medicine 24:1755-1764, 2005.
Richardson BA, Hughes JP. Statistical methods for determining the accuracy of quantitative polymerase chain reaction-based tests. Statistics in Medicine, 26, 895-902, 2007.

Hughes JP. Using Baseline Data to Design a Group Randomized Trial. Statistics in Medicine 24:1983-1994, 2005.
Hughes JP, Kulich M. Cluster randomized trials for HIV prevention. Current Opinions in HIV and AIDS 1:471-475, 2006.
Hussey MA, Hughes JP. Design and Analysis of Stepped Wedge Cluster Randomized Trials. Contemporary Clinical Trials, 28:182-191, 2007.
excel spreadsheet for SW power calculations (proportions)

excel spreadsheet for SW power calculations (means)
Hughes JP, Granston TS, Heagerty PJ. Current Issues in the Design and Analysis of Stepped Wedge Trials. Contemporary Clinical Trials, 45:55 - 60, 2015.
Hughes JP, Heagerty PJ, Xia F, Ren Y. Robust Inference for the Stepped Wedge Design. Biometrics, in press, 2019.
R package (swCRTdesign.tar.gz) for SW trials

Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, Raugi DN, Sorensen S, Stoddard JN, Zhao H, Deng W, Kahle E, Panteleeff D, Baeten JM, McCutchan FE, Albert J, Leitner T, Wald A, Corey L, Lingappa JR for the Partners in Prevention HSV/HIV Transmission Study Team. Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PloS One 6(3):e16986, 2011.
Eshleman S, Hudelson S, Redd A,Wang L, Debes R, Chen Y,Martens C, Ricklefs S, Selig E,Porcella S, Piwowar-Manning E, McCauleyM, Hosseinipour M, Kumwenda J, Hakim J, Chariyalertsak S, de Bruyn G, Grinsztejn B, Kumarasamy N, Makhema J, Mayer K, Pilotto J, Santos B, Quinn T, Cohen MS, Hughes JP. Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. Journal of Infectious Diseases, 204:1918-1926, 2011.
R code for sequence linkage analysis

Hughes JP: Mixed effects models with censored data with application to HIV RNA levels. Biometrics 55:625-629, 1999.
download software for Splus (tarfile) (revised 2/7/07)

download software for R/Windows (ZIP file) (revised 2/7/07)
Hughes JP and Richardson R: Analysis of a Randomized Trial to Prevent Vertical Transmission of HIV-1. J of Amer. Statist. Assoc. 95:1032-1043.
download software (tarfile) (revised 6/6/00)

download data (tarfile) (revised 6/6/00)
Hughes JP, Baeten JM, Lingappa JR, Magaret AS, Wald A, de Bruyn G, Kiarie J, Inambao M, Kilembe W, Farquhar C, Celum C. Determinants of per coital act HIV-1 infectivity among HIV-1 serodiscordant couples. Journal of Infectious Diseases, 205:358-365, 2012.