Methodology Papers

Jones G, Johnson WO, Vink WD, French N. A framework for the joint modeling of longitudinal diagnostic outcome data and latent infection status: application to investigating the temporal relationship between infection and disease. Biometrics 2012; 68(2):371-379. DOI: 10.1111/j.1541-0420.2011.01687.x.

Cheng D, Branscum AJ, Johnson WO. Sample size calculations for ROC studies: parametric robustness and Bayesian nonparametrics. Statistics in Medicine 2012; 31(2):131–142. DOI: 10.1002/sim.4396.

Gastwirth JL, Johnson WO, Hikawa H. Estimating the fraction of ‘non-genuine’ artwork by Henry Moore for sale on eBay: application of latent class screening test methodology. Journal of the Royal Statistical Society: Series A (Statistics in Society) 2011; 174(3):805–822. DOI: 10.1111/j.1467-985X.2011.00682.x.

Dhand N, Johnson WO, Torribo JA. A Bayesian approach to estimate OJD prevalence from pooled faecal samples of variable pool size. Journal of Agricultural, Biological, and Environmental Statistics 2010; 15(4):452-473. DOI: 10.1007/s13253-010-0032-8.

Related link: WinBUGS file: OJDPrev wo data.odc 

Jones G, Johnson WO, Hanson TE, Christensen R. Identifiability of models for multiple diagnostic testing in the absence of a gold standard. Biometrics 2010; 66(3):855-863. DOI: 10.1111/j.1541-0420.2009.01330.x.

Jafarzadeh SR, Johnson WO, Utts JM, Gardner IA. Bayesian estimation of the receiver operating characteristic curve for a diagnostic test with a limit of detection in the absence of a gold standard. Statistics in Medicine 2010; 29(20):2090-2106. DOI: 10.1002/sim.3975.

Related link: ROC curve estimation for qPCR assay in the absence of a gold standard using a mixture model with point mass and truncation

Johnson WO, Gardner IA, Metoyer CN, Branscum AJ. On the interpretation of test sensitivity in the two-test two-population problem: Assumptions matter. Preventive Veterinary Medicine 2009; 91(2-4):116-121. DOI: 10.1016/j.prevetmed.2009.06.006.

Jones G, Johnson WO, Vink WD. Evaluating a continuous biomarker for infection by using observed disease status with covariate effects on disease. Journal of the Royal Statistical Society: Series C (Applied Statistics) 2009; 58(5):705-717. DOI: 10.1111/j.1467-9876.2009.00681.x.

Kostoulas P, Leontides L, Browne WJ, Gardner IA. Bayesian estimation of variance partition coefficients adjusted for imperfect test sensitivity and specificity. Preventive Veterinary Medicine 2009; 89(3-4):155-162. DOI: 10.1016/j.prevetmed.2009.02.008.

Norris M, Johnson WO, Gardner IA. Modeling bivariate longitudinal diagnostic outcome data in the absence of a gold standard. Statistics and Its Interface 2009; 2:171-185.

Branscum AJ, Johnson WO, Hanson TE, Gardner IA. Bayesian semiparametric ROC curve estimation and disease diagnosis. Statistics in Medicine 2008; 27(13):2474-2496. DOI: 10.1002/sim.3250.

Hanson TE, Kottas A, Branscum AJ. Modelling stochastic order in the analysis of receiver operating characteristic data: Bayesian non-parametric approaches. Journal of the Royal Statistical Society: Series C (Applied Statistics) 2008; 57(2):207-225. DOI: 10.1111/j.1467-9876.2007.00609.x.

Hanson TE, Branscum AJ, Gardner IA. Multivariate mixtures of Polya trees for modeling ROC data. Statistical Modelling 2008; 8(1):81-96. DOI: 10.1177/1471082X0700800106.

Su CL, Gardner IA, Johnson WO. Bayesian estimation of aggregate test accuracy based on different sampling schemes. Journal of Agricultural, Biological, and Environmental Statistics 2007; 12(2):250-271. DOI: 10.1198/108571107X198895.

Branscum AJ, Johnson WO, Gardner IA. Sample size calculations for studies designed to estimate diagnostic test accuracy. Journal of Agricultural, Biological, and Environmental Statistics 2007; 12(1):112-127. DOI: 10.1198/108571107X177519.

Related link: S-PLUS and WinBUGS codes file: SampleSizeCode_ScreeningTestEvaluation.txt

Branscum AJ, Johnson WO, Gardner IA. Sample size calculations for disease freedom and prevalence estimation surveys. Statistics in Medicine 2006; 25(15):2658-2674. DOI: 10.1002/sim.2449.

Muñoz-Zanzi CA, Thurmond MC, Heitala S, Johnson WO. Factors affecting sensitivity and specificity of pooled-sample testing for diagnosis of low prevalence infections. Preventive Veterinary Medicine 2006; 74(4):309-322. DOI: 10.1016/j.prevetmed.2005.12.006.

Choi YK, Johnson WO, Collins MT, Gardner IA. Bayesian estimation of ROC curves in the absence of a gold standard. Journal of Agricultural, Biological, and Environmental Statistics 2006; 11(2):210-229. DOI: 10.1198/108571106X110883.

Related links:

Estimating ROC curves and corresponding AUC’s based on a gold standard

Estimating ROC curves and corresponding AUC’s in the absence of a gold standard

Choi YK, Johnson WO, Thurmond MC. Diagnosis using predictive probabilities without cut-offs. Statistics in Medicine 2006; 25(4):699-717. DOI: 10.1002/sim.2365.

Hanson TE, Johnson WO, Gastwirth JL. Bayesian inference for prevalence and diagnostic test accuracy based on dual-pooled screening. Biostatistics 2006; 7(1):41-57. DOI: 10.1093/biostatistics/kxi039.

Georgiadis MP, Johnson WO, Gardner IA. Sample size determination for estimation of the accuracy of two conditionally independent tests in the absence of a gold standard. Preventive Veterinary Medicine 2005; 71(1-2):1-10. DOI: 10.1016/j.prevetmed.2005.04.004.

Related link:

2 independent tests, 2 populations, no gold standard - spreadsheet workbook to estimate Se and Sp, and for frequentist sample size calculations [Microsoft Excel file: HWsamplesize.xls ]

Branscum AJ, Gardner IA, Wagner BA, McInturff PS, Salman MD. Effect of diagnostic testing error on intracluster correlation coefficient estimation. Preventive Veterinary Medicine 2005; 69(1-2):63-75. DOI: 10.1016/j.prevetmed.2005.01.015.

Branscum AJ, Gardner IA, Johnson WO. Estimation of diagnostic-test sensitivity and specificity through Bayesian modeling. Preventive Veterinary Medicine 2005; 68(2-4):145-163. DOI: 10.1016/j.prevetmed.2004.12.005.

Related links:

2 independent tests, 2 populations, no gold standard

2 dependent tests, 1 population, no gold standard

2 dependent tests, 2 populations, no gold standard

3 tests (2 dependent and 1 independent), 1 population, no gold standard

Johnson WO, Hanson TE. Comment on "On model expansion, model contraction, identifiability and prior information: Two illustrative scenarios involving mismeasured variables". Statistical Science 2005; 20(2):131-134. DOI: 10.1214/088342305000000098.

Branscum AJ, Gardner IA, Johnson WO. Bayesian modeling of animal- and herd-level prevalences. Preventive Veterinary Medicine 2004; 66(1-4):101-112. DOI: 10.1016/j.prevetmed.2004.09.009.

Related links:

1 test, 1 population - binomial sampling

1 test, multiple populations - estimation of herd-level prevalence

2 tests, multiple populations - estimation of prevalence distribution

Su CL, Gardner IA, Johnson WO. Diagnostic test accuracy and prevalence inferences based on joint and sequential testing with finite population sampling. Statistics in Medicine 2004; 23(14):2237-2255. DOI: 10.1002/sim.1809.

Thurmond MC, Johnson WO. Effect of multiple sampling on diagnostic sensitivity. Journal of Veterinary Diagnostic Investigation 2004; 16(3):233-236. DOI: 10.1177/104063870401600311.

McInturff P, Johnson WO, Cowling D, Gardner IA. Modelling risk when binary outcomes are subject to error. Statistics in Medicine 2004; 23(7):1095-1109. DOI: 10.1002/sim.1656.

Related links:

Logistic Regression, outcome measured perfectly - ordinary logistic model

Logistic Regression, outcome based on imperfect test results, and measured imperfectly or with “error”

Johnson WO, Su CL, Gardner IA, Christensen R. Sample size calculations for surveys to substantiate freedom of populations from infectious agents. Biometrics. 2004; 60(1):165-171. DOI: 10.1111/j.0006-341X.2004.00143.x.

Related link:

Bayesfreecalc: Posterior probability of herd freedom from disease and sample size calculation

Hanson TE, Johnson WO, Gardner IA, Georgiadis MP. Determining the infection status of a herd. Journal of Agricultural, Biological, and Environmental Statistics 2003; 8(4):469-485. DOI: 10.1198/1085711032561.


Hanson TE, Johnson WO, Gardner IA. Hierarchical models for estimating herd prevalence and test accuracy in the absence of a gold standard. Journal of Agricultural, Biological, and Environmental Statistics 2003; 8(2):223-239. DOI: 10.1198/1085711031526.

Georgiadis MP, Johnson WO, Gardner IA, Singh R. Correlation-adjusted estimation of sensitivity and specificity of two diagnostic tests. Journal of the Royal Statistical Society: Series C (Applied Statistics) 2003; 52(1):63-76. DOI: 10.1111/1467-9876.00389.

Suess EA, Gardner IA, Johnson WO. Hierarchical Bayesian model for prevalence inferences and determination of a country's status for an animal pathogen. Preventive Veterinary Medicine 2002; 55(3):155-171. DOI: 10.1016/S0167-5877(02)00092-2.

Thurmond MC, Johnson WO, Muñoz-Zanzi CA, Su CL, Hietala SK. A method of probability diagnostic assignment that applies bayes theorem for use in serologic diagnostics, using an example of Neospora caninum infection in cattle. American Journal of Veterinary Research 2002; 63(3):318-325. DOI: 10.2460/ajvr.2002.63.318.

Pouillot R, Gerbier G, Gardner IA. "TAGS", a program for the evaluation of test accuracy in the absence of a gold standard. Preventive Veterinary Medicine 2002; 53(1-2):67-81. DOI: 10.1016/S0167-5877(01)00272-0.

Related link:

2 independent tests, 2 populations, no gold standard (TAGS) - frequentist approach

Johnson WO, Gastwirth JL, Pearson LM. Screening without a "gold standard": The Hui-Walter paradigm revisited. American Journal of Epidemiology 2001; 153(9):921-924. DOI: 10.1093/aje/153.9.921.

Hanson TE, Gardner IA, Johnson WO. Log-linear and logistic modeling of dependence among diagnostic tests. Preventive Veterinary Medicine 2000; 45(1-2):123-137. DOI: 10.1016/S0167-5877(00)00120-3.

Gardner IA, Stryhn H, Lind P, Collins MT. Conditional dependence between tests affects the diagnosis and surveillance of animal diseases. Preventive Veterinary Medicine 2000; 45(1-2):107-122. DOI: 10.1016/S0167-5877(00)00119-7.

Christensen J, Gardner IA. Herd-level interpretation of test results for epidemiologic studies of animal diseases. Preventive Veterinary Medicine 2000; 45(1-2):83-106. DOI: 10.1016/S0167-5877(00)00118-5.

Enøe C, Georgiadis MP, Johnson WO. Estimation of sensitivity and specificity of diagnostic tests and disease prevalence when the true disease state is unknown. Preventive Veterinary Medicine 2000; 45(1-2):61-81. DOI: 10.1016/S0167-5877(00)00117-3.

Greiner M, Gardner IA. Application of diagnostic tests in veterinary epidemiologic studies. Preventive Veterinary Medicine 2000; 45(1-2):43-59. DOI: 10.1016/S0167-5877(00)00116-1.

Greiner M, Pfeiffer D, Smith RD. Principles and practical application of the receiver-operating characteristic analysis for diagnostic tests. Preventive Veterinary Medicine 2000; 45(1-2):23-41. DOI: 10.1016/S0167-5877(00)00115-X.

Greiner M, Gardner IA. Epidemiologic issues in the validation of veterinary diagnostic tests. Preventive Veterinary Medicine 2000; 45(1-2):3-22. DOI: 10.1016/S0167-5877(00)00114-8.

Muñoz-Zanzi CA, Johnson WO, Thurmond MC, Hietala SK. Pooled-sample testing as a herd-screening tool for detection of bovine viral diarrhea virus persistently infected cattle. Journal of Veterinary Diagnostic Investigation 2000; 12(3):195-203. DOI: 10.1177/104063870001200301.

Johnson WO, Gastwirth JL. Dual group screening. Journal of Statistical Planning and Inference 2000; 83(2):449-473. DOI: 10.1016/S0378-3758(99)00100-7. 

Cowling DW, Gardner IA, Johnson WO. Comparison of methods for estimation of individual-level prevalence based on pooled samples. Preventive Veterinary Medicine 1999; 39(3):211-225. DOI: 10.1016/S0167-5877(98)00131-7.

Johnson WO, Pearson LM. Dual screening. Biometrics 1999; 55(3):867-873. DOI: 10.1111/j.0006-341X.1999.00867.x.

Bedrick EJ, Christensen R, Johnson WO. A new perspective on priors for generalized linear models. Journal of the American Statistical Association 1996; 91(436):1450-1460. DOI: 10.1080/01621459.1996.10476713.

Related link: Logistic Regression, outcome based on imperfect test results, and measured imperfectly or with “error”

Gastwirth JL, Johnson WO. Screening with cost-effective quality control: Potential applications to HIV and drug testing. Journal of the American Statistical Association 1994; 89(427):972-981. DOI: 10.1080/01621459.1994.10476831.

Geisser S, Johnson WO. Optimal administration of dual screening tests for detecting a characteristic with special reference to low prevalence diseases. Biometrics 1992; 48(3):839-852. DOI: 10.2307/2532349.

Gastwirth JL, Johnson WO, Reneau DM. Bayesian analysis of screening data: Application to AIDS in blood donors. Canadian Journal of Statistics 1991; 19(2):135-150. DOI: 10.2307/3315793.

Johnson WO, Gastwirth JL. Bayesian inference for medical screening tests: Approximations useful for the analysis of acquired immune deficiency syndrome. Journal of the Royal Statistical Society. Series B (Methodological) 1991; 53(2):427-439.


Lombard JE, Gardner IA, Jafarzadeh SR, Fossler CP, Harris B, Capsel RT, Wagner BA, Johnson WO. Herd-level prevalence of Mycobacterium avium subsp. paratuberculosis infection in United States dairy herds in 2007. Preventive Veterinary Medicine 2012; In Press. DOI: 10.1016/j.prevetmed.2012.08.006.

Aly SS, Anderson RJ, Whitlock RH, Fyock TL, McAdams SC, Byrem TM, Jiang J, Adaska JM, Gardner IA. Cost-effectiveness of diagnostic strategies to identify Mycobacterium avium subspecies paratuberculosis super-shedder cows in a large dairy herd using antibody enzyme-linked immunosorbent assays, quantitative real-time polymerase chain reaction, and bacterial culture. Journal of Veterinary Diagnostic Investigation 2012; 24(5):821-832. DOI: 10.1177/1040638712452107.

Morton JM, McCoy RJ, Kann RK, Gardner IA, Meers J. Validation of real-time polymerase chain reaction tests for diagnosing feline immunodeficiency virus infection in domestic cats using Bayesian latent class models. Preventive Veterinary Medicine 2012; 104(1-2):136-148. DOI: 10.1016/j.prevetmed.2011.10.009.

Tavornpanich S, Wells SJ, Fossler CP, Roussel AJ, Gardner IA. Evaluation of an alternative method of herd classification for infection with paratuberculosis in cattle herds in the United States. American Journal of Veterinary Research 2012; 73(2):248-256. DOI: 10.2460/ajvr.73.2.248.

Buijze GA, Mallee WH, Beeres FJ, Hanson TE, Johnson WO, Ring D. Diagnostic performance tests for suspected scaphoid fractures differ with conventional and latent class analysis. Clinical Orthopaedics and Related Research 2011; 469(12):3400-3407. DOI: 10.1007/s11999-011-2074-9.

Gardner IA, Nielsen SS, Whittington RJ, Collins MT, Bakker D, Harris B, Sreevatsan S, Lombard JE, Sweeney R, Smith DR, Gavalchin J, Eda S. Consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis in ruminants. Preventive Veterinary Medicine 2011; 101(1-2):18-34. DOI: 10.1016/j.prevetmed.2011.04.002.


Nielsen SS, Toft N, Gardner IA. Structured approach to design of diagnostic test evaluation studies for chronic progressive infections in animals. Veterinary Microbiology 2011; 150(1-2):115-125. DOI: 10.1016/j.vetmic.2011.01.019.

Houe H, Gardner IA, Nielsen LR. Use of information on disease diagnoses from databases for animal health economic, welfare and food safety purposes: strengths and limitations of recordings. Acta Veterinaria Scandinavica 2011; 53 Suppl 1:S7. DOI: 10.1186/1751-0147-53-S1-S7.

Gastwirth JL, Johnson WO. Dare you buy a Henry Moore on eBay? Significance 2011; 8(1):10–14. DOI: 10.1111/j.1740-9713.2011.00470.x.

Schumaker BA, Corso BA, Rhyan JC, Philo LM, Salman MD, Gardner IA. Evaluation of the fluorescence polarization assay for the detection of Brucella abortus antibodies in bison in a natural setting. Comparative Immunology, Microbiology and Infectious Diseases 2010; 33(6): 119-125. DOI: 10.1016/j.cimid.2010.07.001.

Gardner IA. Quality standards are needed for reporting of test accuracy studies for animal diseases. Preventive Veterinary Medicine 2010; 97(3-4):136-143. DOI: 10.1016/j.prevetmed.2010.09.009.

Messam LL, O'Brien JM, Hietala SK, Gardner IA. Effect of changes in testing parameters on the cost-effectiveness of two pooled test methods to classify infection status of animals in a herd. Preventive Veterinary Medicine 2010; 94(3-4):202-212. DOI: 10.1016/j.prevetmed.2010.01.005.

Norton S, Johnson WO, Jones G, Heuer C. Evaluation of diagnostic tests for Johne's disease (Mycobacterium avium subspecies paratuberculosis) in New Zealand dairy cows. Journal of Veterinary Diagnostic Investigation 2010; 22(3):341-351. DOI: 10.1177/104063871002200301.

Gardner IA, Greiner M, Dubey JP. Statistical evaluation of test accuracy studies for Toxoplasma gondii in food animal intermediate hosts. Zoonoses and Public Health 2010; 57(1):82-94. DOI: 10.1111/j.1863-2378.2009.01281.x.

Buijze GA, Hanson TE, Johnson WO, Ring D. Latent class analysis to determine the accuracy of diagnostic tests in orthopaedics. Orthopaedic Journal at Harvard Medical School 2010; 12:106-108.

Vink WD, Jones G, Johnson WO, Brown J, Demirkan I, Carter SD, French NP. Diagnostic assessment without cut-offs: application of serology for the modelling of bovine digital dermatitis infection. Preventive Veterinary Medicine 2009; 92(3):235-248. DOI: 10.1016/j.prevetmed.2009.08.018.

Tavornpanich S, Johnson WO, Anderson RJ, Gardner IA. Herd characteristics and management practices associated with seroprevalence of Mycobacterium avium subsp paratuberculosis infection in dairy herds. American Journal of Veterinary Research 2008; 69(7):904-911. DOI: 10.2460/ajvr.69.7.904.

Messam LL, Branscum AJ, Collins MT, Gardner IA. Frequentist and Bayesian approaches to prevalence estimation using examples from Johne's disease. Animal Health Research Reviews 2008; 9(1):1-23. DOI: 10.1017/S1466252307001314.

Tavornpanich S, Muñoz-Zanzi CA, Wells SJ, Raizman EA, Carpenter TE, Johnson WO, Gardner IA. Simulation model for evaluation of testing strategies for detection of paratuberculosis in midwestern US dairy herds. Preventive Veterinary Medicine 2008; 83(1):65-82. DOI: 10.1016/j.prevetmed.2007.06.010.

Gardner IA, Greiner M. Receiver-operating characteristic curves and likelihood ratios: improvements over traditional methods for the evaluation and application of veterinary clinical pathology tests. Veterinary Clinical Pathology 2006; 35(1):8-17. DOI: 10.1111/j.1939-165X.2006.tb00082.x.

Tavornpanich S, Gardner IA, Carpenter TE, Johnson WO, Anderson RJ. Evaluation of cost-effectiveness of targeted sampling methods for detection of Mycobacterium avium subsp paratuberculosis infection in dairy herds. American Journal of Veterinary Research 2006; 67(5):821-828. DOI: 10.2460/ajvr.67.5.821.

Robbe-Austerman S, Gardner IA, Thomsen BV, Morrical DG, Martin BM, Palmer MV, Thoen CO, Ewing C. Sensitivity and specificity of the agar-gel-immunodiffusion test, ELISA and the skin test for detection of paratuberculosis in United States Midwest sheep populations. Veterinary Research 2006; 37(4):553-364. DOI: 10.1051/vetres:2006018.

Miller WA, Gardner IA, Atwill ER, Leutenegger CM, Miller MA, Hedrick RP, Melli AC, Barnes NM, Conrad PA. Evaluation of methods for improved detection of Cryptosporidium spp. in mussels (Mytilus californianus). Journal of Microbiological Methods 2006; 65(3):367-379. DOI: 10.1016/j.mimet.2005.08.011.

Payne MA, Wetzlich SE, Robb EJ, Brown SA, Gardner IA, Cullor JS, Craigmill AL. Comparison of the use of regulatory assays and high-performance liquid chromatography for detection of residues of ceftiofur sodium metabolites in tissue specimens of culled dairy cattle. American Journal of Veterinary Research 2004; 65(12):1730-1733.  DOI: 10.2460/ajvr.2004.65.1730.

Gross DK, Stover SM, Hill AE, Gardner IA. Observer variation in visual assessment of forelimb horseshoe characteristics on Thoroughbred racehorses. American Journal of Veterinary Research 2004; 65(12):1674-1679.  DOI: 10.2460/ajvr.2004.65.1674.

Hoar BR, Carpenter TE, Singer RS, Gardner IA. Probability of introduction of exotic strains of bluetongue virus into the US and into California through importation of infected cattle. Preventive Veterinary Medicine 2004; 66(1-4):79-91. DOI: 10.1016/j.prevetmed.2004.08.006.

Gardner IA. An epidemiologic critique of current microbial risk assessment practices: the importance of prevalence and test accuracy data. Journal of Food Protection 2004; 67(9):2000-2007.

Tavornpanich S, Gardner IA, Anderson RJ, Shin S, Whitlock RH, Fyock T, Adaska JM, Walker RL, Hietala SK. Evaluation of microbial culture of pooled fecal samples for detection of Mycobacterium avium subsp paratuberculosis in large dairy herds. American Journal of Veterinary Research 2004; 65(8):1061-1070. DOI: 10.2460/ajvr.2004.65.1061.

Liu Y, Johnson WO, Gold EB, Lasley BL. Bayesian analysis of risk factors for anovulation. Statistics in Medicine 2004; 23(12):1901-1919. DOI: 10.1002/sim.1773.

Fosgate GT, Adesiyun AA, Hird DW, Johnson WO, Hietala SK, Schurig GG, Ryan J. Estimation of receiver-operating characteristic curves to determine accuracy of a competitive enzyme-linked immunosorbent assay for the serodiagnosis of Brucella infection in domestic water buffalo (Bubalus bubalis) and cattle. American Journal of Veterinary Research 2003; 64(1):57-64. DOI: 10.2460/ajvr.2003.64.57.

Gardner IA. The utility of Bayes' theorem and Bayesian inference in veterinary clinical practice and research. Australian Veterinary Journal 2002; 80(12):758-761. DOI: 10.1111/j.1751-0813.2002.tb11347.x.

Fosgate GT, Adesiyun AA, Hird DW, Johnson WO, Hietala SK, Schurig GG, Ryan J. Comparison of serologic tests for detection of Brucella infections in cattle and water buffalo (Bubalus bubalis). American Journal of Veterinary Research 2002; 63(11):1598-1605. DOI: 10.2460/ajvr.2002.63.1598.

Singer RS, Boyce WM, Gardner IA, Johnson WO, Fisher AS. Evaluation of bluetongue virus diagnostic tests in free-ranging bighorn sheep. Preventive Veterinary Medicine 1998; 35(4):265-282. DOI: 10.1016/S0167-5877(98)00067-1.