Dear Colleagues I need someone to kindly help me solving this problem. A sample of 89 patients was tested for 4 tumor types (T1, T2, T3, T4). The results of the operative predicted T stage and those of the pathology tests are tabulated in the following table:
.------------.-----------------------------------------------. . . Operative predicted T stage . . ------------------------------------------------. . Pathology . T1 . T2 . T3 T4 . .------------.----------------------------------------------. . T1 . 1 . 0 . 0 . 0 . .------------.---------------------------------------------. . T2 . 0 . 24 . 2 . 0 . .------------.--------------------------------------------. . T3 . 0 . 1 . 49 3 . .------------.--------------------------------------------. . T4 . 0 . 0 . 0 . 9 . .----------------------------------------------------------- I need to calculate the sensitivity, specificity,accuracy,positive and negative prediction values, p-value and kappa value of these tests. I tried to convert the tabulated results into a two-class (0,1) table and use the function (confusionMatrix) taking the pathology results as the (goldstandard), but unfortunately,I got unreasonable output. Most probably,I used the function wrongly. Thank you and regards Hamed [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.