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This paper describes two analysis approaches under the framework of linear modeling that were used for assessing veterinary medical students’ clinical skills at their 4th year of the curriculum at a large public university in the United States. The study intends to investigate and improve the fairness and validity of a performance based assessment, called Clinical Proficiency Examination, by investigating whether external factors have impacts on estimating students’ clinical ability. Statistical analysis results have shown that the effects of rater, task, and exam time may confound the interpretation of students’ exam scores. Implications to educational practice of the exam and future studies are discussed.