| sensSpec {epibasix} | R Documentation |
Sensitivity and Specificity Analysis of a 2x2 Matrix
Description
This function provides detailed information regarding the comparison of two competing methods, for example self-report and gold-standard treatment through a sensitivity/specificity analysis.
Usage
sensSpec(X, alpha=0.05, CL=TRUE, digits=3)Arguments
X |
A 2x2 matrix, with Gold Standard Class A and B in the columns and Comparison Method A and B in the rows. |
CL |
Logical: If TRUE, Confidence Intervals are calculated and displayed in summary method. |
alpha |
The desired Type I Error Rate for Hypothesis Tests and Confidence Intervals |
digits |
Number of Digits to round calculations |
Details
This function is designed to calculate Sensitivity, Specificity, Youden's J and Percent Agreement. These tools are used to assess the validity of a new instrument or self-report against the current gold standard. In general, self-report is less expensive, but may be subject to information bias. Computational formulae can be found in the reference.
Value
X |
The original input matrix. |
sens |
The point estimate of sensitivity |
spec |
The point estimate of specificity |
PA |
The point estimate of Percent Agreement |
YoudenJ |
The point estimate of Youden's J |
sens.s |
The standard deviation of sensitivity |
spec.s |
The standard deviation of specificity |
PA.s |
The standard deviation of Percent Agreement |
YoudenJ.s |
The standard deviation of Youden's J |
sens.CIL |
The lower bound of the constructed confidence interval for true sensitivity. |
sens.CIU |
The upper bound of the constructed confidence interval for true sensitivity |
spec.CIL |
The lower bound of the constructed confidence interval for true specificity. |
spec.CIU |
The upper bound of the constructed confidence interval for true specificity. |
PA.CIL |
The lower bound of the constructed confidence interval for Percent Agreement. |
PA.CIU |
The upper bound of the constructed confidence interval for Percent Agreement. |
YoudenJ.CIL |
The lower bound of the constructed confidence interval for Youden's J. |
YoudenJ.CIU |
The upper bound of the constructed confidence interval for Youden's J. |
alpha |
The desired Type I Error Rate for Hypothesis Tests and Confidence Intervals |
digits |
Number of Digits to round calculations |
Note
All confidence limits rely on simple asymptotic theory, as such, confidence limits may lie outside of [0,1]. A more accurate method is available in the twoby2 function of the Epi package, which employs a logit transformation.
Author(s)
Michael Rotondi, mrotondi@yorku.ca
References
Szklo M and Nieto FJ. Epidemiology: Beyond the Basics, Jones and Bartlett: Boston, 2007.
See Also
Examples
## Not run: From Szklo and Nieto, p. 315
dat <- cbind(c(18,1), c(19,11));
summary(sensSpec(dat));