Compbdt: an R program to compare two binary diagnostic tests subject to a paired design.

BACKGROUND: The comparison of the performance of two binary diagnostic tests is an important topic in Clinical Medicine. The most frequent type of sample design to compare two binary diagnostic tests is the paired design. This design consists of applying the two binary diagnostic tests to all of the individuals in a random sample, where the disease status of each individual is known through the application of a gold standard. This article presents an R program to compare parameters of two binary tests subject to a paired design. RESULTS: The "compbdt" program estimates the sensitivity and the specificity, the likelihood ratios and the predictive values of each diagnostic test applying the confidence intervals with the best asymptotic performance. The program compares the sensitivities and specificities of the two diagnostic tests simultaneously, as well as the likelihood ratios and the predictive values, applying the global hypothesis tests with the best performance in terms of type I error and power. When the global hypothesis test is significant, the causes of the significance are investigated solving the individual hypothesis tests and applying the multiple comparison method of Holm. The most optimal confidence intervals are also calculated for the difference or ratio between the respective parameters. Based on the data observed in the sample, the program also estimates the probability of making a type II error if the null hypothesis is not rejected, or estimates the power if the if the alternative hypothesis is accepted. The "compbdt" program provides all the necessary results so that the researcher can easily interpret them. The estimation of the probability of making a type II error allows the researcher to decide about the reliability of the null hypothesis when this hypothesis is not rejected. The "compbdt" program has been applied to a real example on the diagnosis of coronary artery disease. CONCLUSIONS: The "compbdt" program is one which is easy to use and allows the researcher to compare the most important parameters of two binary tests subject to a paired design. The "compbdt" program is available as supplementary material.

Approximate confidence intervals for the likelihood ratios of a binary diagnostic test in the presence of partial disease verification.

The classic parameters used to assess the accuracy of a binary diagnostic test (BDT) are sensitivity and specificity. Other parameters used to describe the performance of a BDT are likelihood ratios (LRs). The LRs depend on the sensitivity and the specificity of the diagnostic test, and they reflect how much greater the probability of a positive or negative diagnostic test result for individuals with the disease than that for the individuals without the disease. In this study, several confidence intervals are studied for the LRs of a BDT in the presence of missing data. Two confidence intervals were studied through the method of maximum likelihood and seven confidence intervals were studied by applying the multiple imputation by chained equations method. A program in R software has been written that allows us to solve the estimation problem posed. The results obtained have been applied to the two real examples.

Combination of the weighted kappa coefficients of two binary diagnostic tests.

The combination of two binary diagnostic tests in order to increase the accuracy of the diagnosis of a disease is a frequent procedure in clinical practice. When considering the losses associated with an erroneous classification with a binary diagnostic test, the parameter that is used to assess the diagnostic test is the weighted kappa coefficient. The weighted kappa coefficient depends on the sensitivity and the specificity of the diagnostic test, on the disease prevalence and on the weighting index. In this article, we study the combination of the weighted kappa coefficients of two binary diagnostic tests, defining the parameters and studying the conditions under which the combination of the two diagnostic tests increases the value of the weighted kappa coefficient of the combination. The Fieller method has been applied to obtain a confidence interval for the ratio between the combined weighted kappa coefficient and the weighted kappa coefficient of each diagnostic test. A program in R has been written to solve the problem studied and it is available as complementary material. The results have been applied to a real example.

Sperm chromatin structure assay and classical semen parameters: systematic review.

The present study is based on a PubMed search and compares the clinical validity of classical semen parameters (CSP) and the sperm chromatin structure assay (SCSA) in different clinical contexts. The PubMed database was searched using keywords on the sperm diagnostic test for pregnancy in three clinical scenarios: (i) couples attempting to conceive; (ii) couples who had been attempting to conceive for 12months without success; and (iii) couples treated with intrauterine insemination (IUI). There was a considerable heterogeneity among the studies included. For couples attempting to conceive following a SCSA that produced an abnormal result, the likelihood of male factor infertility ranged from a pre-test value of 7.5% to a post-test value of 32.1% [95% confidence interval (CI) 15.7-54.5], while after CSP with an abnormal result, the post-test probability was 17.3% (95% CI 11.8-24.5). For a pre-test prevalence of male factor infertility of 50%, the post-test probability of male factor infertility after an abnormal test is very similar for both SCSA and CSP. In couples treated with IUI, the clinical validity of SCSA is higher than that of sperm morphology alone, but not enough to introduce SCSA as a test in male infertility work-up.

El volumen plaquetario en el diagnóstico diferencial de las trombopenias centrales y periféricas / Platelet volume in the differential diagnosis of central and peripheral thrombocytopenia

Objetivos. Analizar la utilidad del volumen plaquetario medio (VPM) en el diagnóstico diferencial de las trombopenias centrales y periféricas. Casuística. Métodos: Se estudiaron 26 trombopenias centrales y 54 trombopenias periféricas, 20 de estas se estudiaron también después de la curación. El recuento de plaquetas y el volumen plaquetario se realizaron en un autoanalizador multicanal acoplado al contador automático de partículas. Se estudiaron 20 controles normales. Resultados: En el grupo control el VPM es significativamente mayor que en las trombopenias centrales. El VPM es significativamente mayor en las trombopenias periféricas que en los controles y que en las trombopenias centrales. Conclusiones. El VPM es una determinación rápida, útil y fácil para el diagnóstico diferencial entre las trombopenias centrales (microtrombocitarias) de las perioféricas (macrotombocitarias)

Objectives: To analyses the usefulness of mean platelet volume (MPV) in the differential diagnosis of central and peripheral thrombocytopenia. Population and methods: Twenty-six patients with central thrombocytopenia, fifty-four patients with peripheral thrombocytopenia and twenty healthy controls were included. Twenty of these patients were studied after the resolution of the process too. Platelet count an MPV were performed in all subjects using a multichannel autoanalyzer connected to an automatic particle counter. Results: MPV was significantly higher in the control group when compared with the central thrombocytopenia group. MPV was significantly higher in the peripheral thrombocytopenia group than in both the control and the central thrombocytopenia groups. Conclusions: MPV is an easy fast and useful determination for the differential diagnosis between central (microthrombocytic) and peripheral (macrothombocytic) thrombocytopenia

Comparing the likelihood ratios of two binary diagnostic tests in the presence of partial verification.

The comparison of the efficiency of two binary diagnostic tests requires one to know the disease status for all patients in the sample, by applying a gold standard. In two-phase studies the gold standard is not applied to all patients in a sample, and the problem of partial verification of the disease arises. At present, one of the approaches most used for comparing two binary diagnostic tests are the likelihood ratios. In this study, the maximum likelihood estimators of likelihood ratios are obtained. The tests of hypothesis to compare the likelihood ratios of two binary diagnostic tests when both are applied to the same random sample in the presence of verification bias are deduced, and simulation experiments are performed in order to investigate the asymptotic behaviour of the tests of hypothesis. The results obtained have been applied to the study of Alzheimer's disease.

Análisis de la estacionalidad de la mortalidad por patología isquémica cerebral / Analysis of the seasonality of mortality due to cerebral ischemic pathology

Objetivos: Estudiar las tasas de moralidad por accidente cerebrovascular isquémico en la Comunidad Autónoma de Andalucía (España) durante el período 1976-1996 en hombres y mujeres con edades iguales o superiores a 55 años. Casuística. Métodos. Se analizaron todas las personas con edades iguales o superiores a 55 años residentes en Andalucía fallecidas por patología isquémica cerebral entre 1976 y 1996. Como referencia temporal se consideraron el mes y el año. Calculándose las tasas específicas mensuales y anuales de mortalidad por sexos, por lo que se obtuvieron 252 observaciones mensuales de mortalidad y 21 anuales tanto para los hombres como para las mujeres. Resultados. El análisis de cada una de las dos series temporales de mortalidad dio como resultado un modelo ARIMA estacional. En ambos sexos, las tasas de mortalidad fueron mayores en los meses de invierno, mientras que las tasas menores se obtuvieron en los meses de verano. Las tasas anuales de mortalidad fueron, en los 21 años estudiados, superiores en las mujeres que en los hombres. Tanto en los hombres como en las mujeres se observa una clara tendencia descendente de la mortalidad durante el periodo analizado. Conclusiones. El análisis de la mortalidad en Andalucía permite confirmar que en el periodo 1976-1996 existen. a) tasas de mortalidad claramente descendientes, b) mayores tasas de mortalidad en las mujeres que en los hombres y c) mayores tasas de mortalidad en invierno que en verano

Objectives. Investigate the mortality rates for ischemic cerebrovascular events in the region of Andalucia (Spain) during the period between 1976-1996 in women and men 55 years old and older. Population and methods. We analysed all the people with ages 55 years resident in Andalucía deceised of ischaemic cerebral pathology between 1976 and 1996. We considered as temporal reference the month and year. We calculated the specific monthly and annual rates for both sexes, obtaining 252 monthly mortality observations and 21 annuals, both for men ad women. Results. The analysis of each of the temporal mortality series resulted in a seasonal ARIMA model. Mortality rates were higher in winter for both sexes with the lowest rates being found in the summer months. Annual morality rates were, for the 21 year studied, higher in women than in men. In both sexes, there is a clear descendant tendency in mortality for the period analysed. Conclusions. The mortality analysis in Andalucía permits to confirm that in the period 1976-1996 there are a) clearly descending mortality rates, b) higher mortality rates in women compared to men and, c) higher mortality rates in winter compared to summer