Archived Analyses

Thome JC, Rebeiro PF, Spieker AJ, Shepherd BE. Understanding difference in differences methods to evaluate policy effects with staggered adoption: an application to Medicaid and HIV. (submitted) did_tutorial_code.R  
Castilho JL, Fonseca FF, Kim A, et al. Prenatal syphilis and adverse pregnancy outcomes in women with HIV receiving ART in Brazil. (submitted)  
Castilho JL, Bian A, Jenkins CA, et al. CD4/CD8 ratio and cancer risk among adults with HIV. Journal of the National Cancer Institute 2022; 114: 854-862. Analysis code  
Castillo-Rozas G, Tu S, Mejias F, et al. Clinical outcomes and risk factors for immune recovery and all-cause mortality in Latin American-Caribbean patients living with HIV on virological success: a retrospective cohort study. (submitted) Analysis code  
Norwood J, Jenkins CA, Bhatta M, Turner M, Bian A, Nelson J, Ransby I, Hughes D, Koethe JR, Sterling TR, Shepherd BE, Castilho J. Hormonal contraception and risk of cardiometabolic disease in women with HIV. (submitted)  
Audet CM, Pettapiece-Phillips M, Tian Y, et al. If it weren't for my traditional healer, I would be dead: engaging people living with HIV in rural Mozambique. PLOS ONE 2022; 17: e0270565 De-identified Data  
Li C, Tian Y, Zeng D, Shepherd BE. Asymptotic properties for cumulative probability models for continuous outcomes. Mathematics 2023; 11: 4896 R-code  
Sneed NM, Heerman WJ, Shaw PA, et al. Associations between gestational weight gain, gestational diabetes, and childhood obesity incidence: a retrospective cohort study. Maternal and Child Health Journal (in press). R-code  
Bhatta M, Bian A, Norwood J, et al. Low rates of contraception use in women with HIV. OFID 2022; 9: ofac113. R-code  
Sack DE, Gange SJ, Althoff KN, et al. Visualizing the geography of HIV observational cohorts with density-adjusted cartograms. JAIDS (in revision) R-code  
Eden SK, Li C, Shepherd BE. Spearman-like correlation measure adjusting for covariates in bivariate survival data. Biometrical Journal 2023; 65: 2200137. CCASAnetData  
Nunez I, Crabtree-Ramirez B, Shepherd BE, et al. Late-onset opportunistic infections while receiving anti-retroviral therapy in Latin America: burden and risk factors. International Journal of Infectious Diseases 2022; 122: 469-475 analysis-code  
Crabtree-Ramirez B, Jenkins CA, Shepherd BE, et al. Tuberculosis Treatment Intermittency in the Continuation Phase and Mortality in HIV-Positive Persons Receiving Antiretroviral Therapy. BMC Infectious Diseases 2022; 22: 341.  
Shepherd BE, Han K, Chen T, et al. Analysis of error-prone electronic health records with multi-wave validation sampling. Biometrics 2023; 79: 2649-2663.  
Pettit AC, Bian A, Schember CO, et al. Development and validation of a multivariable prediction model for missed HIV healthcare provider visits in a large United States clinical cohort. Open Forum Infectious Diseases 2021; 8: ofab130. code  
Wudil UJ, Aliyu MH, Prigmore HL, et al. Apoliproprotein-1 (APOL1) Risk Variants and Associated Kidney Phenotypes in an HIV Cohort in Nigeria. Kidney International 2021; 100: 146-154. code  
Castilho JL, Kim A, Jenkins CA, et al. Antiretroviral therapy and Kaposi's sarcoma trends and outcomes in Latin America. JIAS 2021; 23: e25658.  
Eden SK, Li C, Shepherd BE. Non-parametric estimation of Spearman's rank correlation with bivariate survival data. Biometrics 2022; 78: 421-434.  
Pereira GFM, Kim A, Jalil EM, et al. Dolutegravir and pregnancy outcomes among women on ART in Brazil: a national cohort study. Lancet HIV 2021; 8: e33-e41. R-scripts  
Koenig SP, Kim A, Shepherd BE, et al. Increased mortality after tuberculosis treatment completion in persons with HIV in Latin America. Clinical Infectious Diseases 2020; 71: 215-217. R-scripts  
Tian Y, Hothorn T, Li C, Harrell FE, Shepherd BE. An empirical comparison of two novel transformation models. Statistics in Medicine 2020; 39: 562-576. R-scripts  
Pettit AC, Jenkins CA, Peratikos MB, et al. Directly Observed Therapy and Risk of Unfavorable Tuberculosis Treatment Outcomes Among an International Cohort of People Living with HIV in Medium and Low-Income Countries. Journal of the International AIDS Society 2019; 22: e25423. R-scripts  
Giganti MJ, Shepherd BE, Caro-Vega Y, et al. The impact of data quality and source data verification on epidemiologic inference: a practical application using HIV observational data. BMC Public Health 2019; 19: 1748. R-scripts  
Pettit AC, Giganti MJ, Ingle SM, et al. Increased non-AIDS mortality among persons with AIDS defining events after antiretroviral therapy initiation. Journal of the International AIDS Society 2018; 21: e25031. R-scripts  
Shepherd BE, Liu Q, Wanga V, Li C. Probability-scale residuals in HIV/AIDS research: diagnostics and inference. Quantitative Methods for HIV/AIDS Research, editors Clan C, Hudgens HG, and Chow SC. 2017. Chapman and Hall/CRC. R-scripts  
Caro-Vega Y, Belaunzaran-Zamudio PF, Crabtree-Ramirez B, Shepherd BE, et al. Trends in proportion of older HIV-infected people in care in Latin America and the Caribbean: a growing challenge. Epidemiology and Infection 2018; 146: 1308-1311. R-scripts  
Fink V, Jenkins CA, et al. Survival after cancer diagnosis in a cohort of HIV-infected individuals in Latin America. Infectious Agents and Cancer 2018; 13:16. R-scripts  
Liu Q, Li C, Wanga V, Shepherd BE. Covariate-adjusted Spearman's rank correlation with probability-scale residuals. Biometrics 2018; 74: 595-605. R-scripts  
Carriquiry G, Giganti MJ, Castilho J, Jayathilake K, Cahn P, Grinsztejn B, Cortes C, Pape JW, Padgett D, Madero JS, McGowan CC, Shepherd BE, Gotuzzo E. Virologic Failure and Mortality in Older ART Initiators in a Multisite Latin American and Caribbean Cohort. Journal of the International AIDS Society 2018; 21: e25088. script-files-original, script-files-simulated Over50TablesFigures.pdf
Belaunzaran-Zamudio PF, Caro-Vega YN, Shepherd BE, et al. Impact of late presentation and delayed antiretroviral therapy on mortality in adults receiving HIV care in Latin America. American Journal of Epidemiology 2020; 189: 564-572. script-files  
Liu Q, Shepherd BE, Li C, Harrell FE. Modeling continuous response variables using ordinal regression. Statistics in Medicine 2017; 36: 4316-4335. script-files
De Boni RB, Blevins M, Shepherd BE, et al. Is Substance Use Associated with HIV Cascade Outcomes in Latin America? PLOS ONE 2018; 13: e0194228. script-files  
Giganti MJ, Shaw PA, Chen G, et al. Accounting for dependent errors in predictors and time-to-event outcomes using validation samples and multiple imputation. Annals of Applied Statistics (in press). script-files  
Carlucci JG, Blevins M, et al. Tuberculosis Treatment Outcomes among HIV/TB Co-Infected Children in Resource-Limited Countries. J Acquir Immune Defic Syndr. 2017; 75: 156-163 script-files  
Shepherd BE, Liu Q. Discussion of 'Regularized Regression for Categorical Data.' Statistical Modelling 16: 238-248. R-scripts  
Koethe JR, Jenkins CA, Lau B, Shepherd BE, et al. Higher Time-Updated Body Mass Index: Association With Improved CD4+ Cell Recovery on HIV Treatment. J Acquir Immune Defic Syndr. 2016 Oct 1; 73(2): 197-204. LongTermCD4.Rnw  
De Boni R, et al. Substance use and adherence among people living with HIV/AIDS receiving cART in Latin America. AIDS and Behavior 2016; 20: 2692-2699.  
Shepherd BE, Li C, and Liu Q. Probability-scale residuals for continuous, discrete, and censored data. Canadian Journal of Statistics 2016; 44: 463-479. R code  
Moon TD, Hayes CB, Blevins M, et al. Factors associated with the use of mosquito bed nets: results from a cross-sectional household survey in Zambézia Province, Mozambique. Malaria Journal 2016; 15: 196. script-files  
Crabtree-Ramirez B, Caro-Vega Y, Shepherd BE, et al. Time to HAART initiation after diagnosis and treatment of opportunistic infections in patients with AIDS at the CCASAnet cohort. PLOS ONE 2016; 11: e0153921. R-code, Sweave-file  
Shepherd BE, Rebeiro PF and CCASAnet. Assessing and interpreting the association between continuous covariates and outcomes in observational studies of HIV using splines. Journal of Acquired Immune Deficiency Syndromes 2017; 31: 96-104. R and Sweave Code; Stata Code splines-paper-example.pdf
Luque MT, Jenkins CA, Shepherd BE, et al. Mortality among HIV-infected children after initiation of combination antiretroviral therapy: A six-cohort study in Argentina, Brazil, Haiti, and Honduras. Journal of Pediatrics 2017; 182: 245-252. Main program, Functions  
Blevins M. Randomization documentation for SMS Patient Appointment Reminders to Improve Retention in Zambézia Province, Mozambique (protocol) script-file  
Audet CM, Blevins M, et al. Engagement of men in antenatal care services: HIV testing and treatment uptake in a community participatory action program in Mozambique. AIDS and Behavior 2016; 20: 2090-100 script-files  
Rebeiro PF, Cesar C, Shepherd BE, et al. Assessing the HIV Care Continuum in Latin America: progress in clinical retention, cART use, and viral suppression. Journal of the International AIDS Society 2016; 19: 20636. script-file  
Wolff MJ, Giganti MJ, Cortes CP, Cahn P, Grinsztejn B, et al. A decade of HAART in Latin America: a longitudinal continuum of care among the first wave of HIV patients to receive antiretroviral. PLoS ONE 2017; 12: e0179769.;
Belaunzaran-Zamudio PF, Caro-Vega YN, Shepherd BE, et al. CD4 and HIV viral load monitoring practices and associated costs for HIV-infected patients receiving antiretroviral therapy in Latin America and the Caribbean. Bulletin of the World Health Organization 2015; 93: 529-539. cd4-monitoring.pdf
Cesar C, Jenkins CA, Shepherd BE, et al. Failure of initial cART in the Caribbean, Central, and South America. Lancet HIV 2015; 2: e492-500. first_failure3_for_posting.R  
Luz PM and the CCASAnet writing committee. CD4 response up to 5 years following combination antiretroviral therapy in HIV-infected patients in Latin America and the Caribbean. Open Forum Infectious Diseases 2015; 2:ofv079. script-files  
Carriquiry G, Fink V, Koethe JR, et al. Mortality and loss to follow-up among HIV-infected persons on long-term antiretroviral therapy in Latin America and the Caribbean. Journal of the International AIDS Society 2015; 18: 20016. long-term-mortality.pdf
Kipp AM, Blevins M, Haley CA, et al. Factors associated with declining under-five mortality rates from 2000 to 2011: An ecological analysis of 46 African countries. British Medical Journal Open 2016; 6:e007675. link  
Quinn CE, Sivasubramaniam P, Blevins M, et al. Risk Factors for Neonatal Intensive Care Unit Admission in Amman, Jordan. East Mediterr Health J 2016; 22: 163-174. script-files  
Sivasubramaniam P, Quinn CE, Blevins M, et al. Neonatal Outcomes of Infants Admitted to a Large Government Hospital in Amman, Jordan. 2014. Global Journal of Health Science; Vol. 7, No. 4; 2015 script-files  
Shepherd BE, Liu Q, Mercaldo N, Jenkins CA, Lau B, Cole SR, Saag MS, Sterling TR. Comparing results from two methods for estimating when to start antiretroviral therapy. Statisticis in Medicine 2016; 35: 4335-4351. scripts-MI; scripts-dMSM-data-setup; scripts-dMSM-analysis; Bootstrap Comparison; simulation-code  
da Silva M, Blevins M, et al. (2014) Patient loss to follow-up before antiretroviral therapy initiation in rural Mozambique. AIDS and Behavior, 1-13. script-files  
Koethe JR, Jenkins CA et al. (2015) Body mass index and the risk of incident non-communicable disease after starting antiretroviral therapy. HIV Medicine 16: 67-72. script-files: Sweave and R scripts for analysis  
Silvestri D, Blevins M et al. (2014) Medical and nursing students' intentions to work abroad or in rural areas: a cross-sectional survey in Asia and Africa. Bulletin of the World Health Organization 92 (10), 750-759. link  
Canipe A, Chidumayo T, Blevins M et al. (2014) A 12 week longitudinal study of microbial translocation and systemic inflammation in undernourished HIV-infected Zambians initiating antiretroviral therapy. BMC infectious diseases 14 (1), 521. script-files  
Wolff M, Shepherd BE, Cortes C, et al. Clinical and virology outcomes after changes in first antiretroviral regimen at 7 sites in the Caribbean, Central, and South America Network (CCASAnet). Journal of Acquired Immune Deficiency Syndromes 2016; 71:102-110. script-files  
Cesar C, Shepherd BE, Jenkins CA, Ghidinelli M, Castro JL, Veloso V, Cortes CM, Padgett D, Crabtree-Ramirez B, Gotuzzo E, Fink V, Bacon M, Sued O, McGowan C, Cahm P. (2014) Use of third line antiretroviral therapy in Latin America. PLoS ONE 9: e1086887. script-file  
Crabtree-Ramirez B, Caro Vega YN, Shepherd BE, et al. The changing demographics of HIV infection in the U.S. and the Caribbean and Central and South America. AIDS and Behavior 2015; 19: 1599-1608. VCCC-script-files, CCASAnet-script-files, combined-script-files  
Aliyu MH, Blevins M, et al. (2014) Correlates of suboptimal entry into early infant diagnosis in rural north central Nigeria. Journal of Acquired Immune Deficiency Syndromes 67 (1) e19-26. script-files  
Duda SN, Farr AM, Lindegren ML, Blevins M, et al. (2014) Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration. Journal of the International AIDS Society 17 (1). script-files  
Giganti MJ, Luz PM, Caro-Vega Y, et al. A comparison of seven Cox regression-based models to account for heterogeneity across multiple HIV treatment cohorts in Latin America and the Caribbean. AIDS Research and Human Retroviruses. 2015; 31: 496-503. script-files  
Blevins M, Jose, Bilhete et al. Two-year death and loss to follow-up outcomes by source of referral to HIV care for HIV-infected patients initiating antiretroviral therapy in rural Mozambique. AIDS Research and Human Retroviruses. 2015; 31: 198-207. script-files  
Audet CA, Blevins M, et al. (2014). Symptomatic HIV-positive persons in rural Mozambique who first consult a traditional healer have delays in HIV testing: A cross-sectional study. Journal of Acquired Immune Deficiency Syndromes 66 (4) e80-6. script-files  
Lou J, Blevins M, et al. (2014) Modeling the impact on HIV incidence of combination prevention strategies among men who have set with men in Beijing, China. PloS one, 9(3), e90985. script-files supplement  
Kapambwe S, Sahasrabuddhe VV, Blevins M, et al. Age distribution and determinants of invasive cervical cancer in a 'screen-and-treat' program integrated with HIV/AIDS care in Zambia. Journal of Acquired Immune Deficiency Syndromes 2015; 70: e20-26. script-files  
Cohen JJ, Blevins M, et al. (2013). Overcoming the perceived barriers to health care access among single mothers in coastal Kenya. International Journal of Public Health, 1-8. script-files pdf of analysis  
Castilho JL, Jenkins CA, Shepherd BE, et al. Hormonal Contraception and Risk of Non-communicable Diseases in HIV-infected Women. Journal of Women's Health 2015; 24: 481-488. hc_msm3_forPosting.R  
Mukolo A, Blevins M, et al. (2013) Community stigma endorsement and voluntary counseling and testing behavior and attitudes among female heads of households in Zambézia Province, Mozambique. BMC Public Health, 13(1), 1155. script-files  
Mukolo A, Blevins M, et al. (2013) Correlates of social exclusion and negative labeling and devaluation of people living with HIV/AIDS in rural settings: Evidence from a general household survey in Zambézia Province, Mozambique. PloS one, 8(10), e75744. script-files  
Parrish DD, Blevins M, Megazzini KM, et al. Hemoglobin recovery among HIV-1 infected patients initiated on Zidovudine-based antiretroviral therapy and other regimens in North-central Nigeria. International journal of STD & AIDS 2014; 25: 355-359. script-files pdf of analysis (not yet posted)  
Khuri-Bulos N, Lang RD, Blevins M et al. (2013) Vitamin D deficiency among newborns in Amman, Jordan. Global journal of health science, 6(1). script-files pdf of analysis (not yet posted)  
Koethe, JR, et al. (2010) Regional and total adipose tissue mass is associated with higher circulating proinflammatory cytokines, but lower soluble CD14, in treated HIV infection. JohnRoCytokine.R  
Shepherd BE, Jenkins CA, Parrish DD, et al. (2013) Higher rates of AIDS during the first year of therapy among migrants: the importance of tuberculosis. AIDS 2013; 27: 1321-1329. artcc.nw, modelfun.R and analysis-public2.R  
Aliyu, MH, Blevins M, et al. (2013) Risk Factors for Delayed Initiation of Combination Antiretroviral Therapy in Rural North Central Nigeria. Journal of Acquired Immune deficiency Syndromes, 65(2), e41. script-file pdf of analysis  
Audet C, Sidat M, Blevins M, et al. HIV knowledge and health seeking behavior in Zambézia Province, Mozambique. SAHARA-J 9(1): 41-46. script-file pdf of analysis  
Koethe JR, Blevins M, Bosire C, et al. Self-reported dietary intake and appetite predict early treatment outcome among low body mass index adults initiating HIV treatment in sub-Saharan Africa. Public Health Nutrition 2012; 13:1-10. script-file pdf of analysis  
Wester CW, Eden SK, Shepherd BE, et al. Risk factors for symptomatic hyperlactatemia and lactic acidosis among combination antiretroviral therapy-treated adults in Botswana: results from a clinical trial. AIDS Research and Human Retroviruses 2012; 28:759-65. Lactic Acidosis 2011  
Miller EK, Hernandez JZ, Wimmenauer V, et al. A mechanistic role for type III interferon lambda in asthma exacerbations mediated by human rhinovirus. American Journal of Respiratory and Critical Care Medicine 2012; 185: 508-516. script-file pdf of analysis  
Miller EK, Bugna J, Libster R, et al. Human rhinoviruses in severe respiratory disease in very low birth weight infants. Pediatrics 2012; 129: e60-7. premature.nw  
Moon T, Burlison J, Blevins M, et al. Enrollment and programmatic trends and predictors of ART initiation from PEPFAR-supported public HIV care and treatment sites in rural Mozambique. Int J of STD AIDS 2011; 22(11):621-627. script-file pdf of analysis  
Koethe JR, Jenkins CA, Shepherd BE, et al. An optimal body mass index range associated with improved immune reconstitution among HIV-infected adults initiating antiretroviral therapy. Clinical Infectious Diseases 2011; 53: 952-960. BMI_CD4_for_posting.R  
Pettit AC, Jenkins CA, Stinnette S, et al. Tuberculosis risk before and after highly active antiretroviral therapy initiation: Does HAART increase the short-term TB risk in a low incidence TB setting? Journal of Acquired Immune Deficiency Syndromes 2011; 57: 305-310. TBIncidencePostedCode.R  
Wester CW, Koethe JR, Shepherd BE, et al. Non-AIDS defining events among HIV-1 infected adults receiving combination antiretroviral therapy in urban settings in Sub-Saharan Africa and the United States. AIDS 2011; 25: 1471-1479. Wester et al., 2011, AIDS  

Simulated CCASAnet Data for Quasi-Reproducible Research

The following datasets were simulated from the CCASAnet cohort. These simulated data are made available so that select CCASAnet analyses in the above table are quasi-reproducible. We do not have permission to post the original CCASAnet datasets, so instead we have posted simulated datasets. We also include our simulation code, a second set of simulated datasets that simulates new data from our first simulated datasets so that the simulation procedure itself is quasi-reproducible (labeled "Simulated Dataset2"), and code for this second set of simulations (labeled "Code2"). Multiple datasets are included so that each time we update our simulated data to make them suitable for a new analysis, we do not need to re-run all other previous analyses on this same dataset. Results generated from these simulated datasets may not be generalizeable to the CCASAnet cohort. Additional discussion is in Shepherd BE, Peratikos MB, Rebeiro PF, Duda SN, McGowan CC. A pragmatic approach for reproducible research with sensitive data. American Journal of Epidemiology. 2017; 186: 387-392.

Date Simulated Dataset Code Simulated Dataset2 Code2
21 Dec, 2016 mock-ccasanet-data-2016-12-21 datasim-2016-12-21.R mock-ccasanet-data2-2016-12-21 datasim2-2016-12-21.R
19 Jan, 2017 mock-ccasanet-data-2017-01-19 datasim-2017-01-19.R mock-ccasanet-data2-2017-01-19 datasim2-2017-01-19.R

Topic revision: r175 - 16 Feb 2024, BryanShepherd
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