Archived Analyses

Manuscript Code Report with Simulated Data
Shepherd BE, Liu Q, Wanga V, Li C. Probability-scale residuals in HIV/AIDS research: diagnostics and inference. Quantitative Methods for HIV/AIDS Research (in press) R-scripts  
Fink V, Jenkins CA, et al. Survival after cancer diagnosis in a cohort of HIV-infected individuals in Latin America. (submitted) R-scripts  
Liu Q, Li C, Wanga V, Shepherd BE. Covariate-adjusted Spearman's rank correlation with probability-scale residuals. (submitted) 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 suppression and mortality in older ART initiators in a multisite Latin American and Caribbean cohort. (submitted) script-files Over50TablesFigures.pdf
Belaunzaran-Zamudio PF, Shepherd BE, Caro-Vega YN, et al. High mortality attributable to late presentation and delayed antiretroviral therapy initiation in HIV-infected adults receiving care in Latin America: a CCASAnet observational cohort study. (submitted) script-files  
Liu Q, Shepherd BE, Li C, Harrell FE. Modeling continuous response variables using ordinal regression. Statistics in Medicine. (in press) script-files  
De Boni RB, Blevins M, Shepherd BE, et al. Is Substance Use Associated with HIV Cascade Outcomes in Latin America? (submitted) 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. (submitted) script-files  
Carlucci JG, Blevins M, et al. Tuberculosis Treatment Outcomes among HIV/TB Co-Infected Children in Resource-Limited Countries. (submitted) script-files  
Shepherd BE, Liu Q. Discussion of 'Regularized Regression for Categorical Data.' Statistical Modelling 16: 238-248. R-scripts  
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 (in press) 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 (in press) 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. The first ten years of highly active antiretroviral therapy in a multiregional Latin American cohort. (submitted);
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. (submitted). 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. (in press)

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: r117 - 14 Jul 2017, BryanShepherd

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