[Diagnosismed-commits] r9 - in pkg/DiagnosisMed: . R man

[noreply at r-forge.r-project.org]

Author: pedrobrasil
Date: 2009-03-15 04:02:55 +0100 (Sun, 15 Mar 2009)
New Revision: 9

Modified:
   pkg/DiagnosisMed/DESCRIPTION
   pkg/DiagnosisMed/R/ROC.r
   pkg/DiagnosisMed/man/ROC.Rd
Log:


Modified: pkg/DiagnosisMed/DESCRIPTION
===================================================================
--- pkg/DiagnosisMed/DESCRIPTION	2009-03-04 12:27:23 UTC (rev 8)
+++ pkg/DiagnosisMed/DESCRIPTION	2009-03-15 03:02:55 UTC (rev 9)
@@ -1,6 +1,6 @@
 Package: DiagnosisMed
-Version: 0.1.2.1
-Date: 2009-03-03
+Version: 0.1.2.3
+Date: 2009-03-13
 Author: Pedro Brasil <pedro.brasil at ipec.fiocruz.br>
 Maintainer: Pedro Brasil <pedro.brasil at ipec.fiocruz.br>
 Depends: R (>= 2.7.2),epitools,epicalc, TeachingDemos, tcltk

Modified: pkg/DiagnosisMed/R/ROC.r
===================================================================
--- pkg/DiagnosisMed/R/ROC.r	2009-03-04 12:27:23 UTC (rev 8)
+++ pkg/DiagnosisMed/R/ROC.r	2009-03-15 03:02:55 UTC (rev 9)
@@ -50,17 +50,16 @@
   X<-test[gold=="negative"] # pag 209
   Y<-test[gold=="positive"] # pag 209
   }
-  m<-length(X) # pag 209
-  n<-length(Y) # pag 209
+  m<-length(X) # pag 209  
+  n<-length(Y) # pag 209  
   D10X<-function(Xi){(1/n)*sum(Y>=Xi)} # pag 211
   D01Y<-function(Yi){(1/m)*sum(Yi>=X)} # pag 211
-  VAR.AUC<-sum((tapply(X,X,"D10X")-AUC)^2)/(m*(m-1))+sum((tapply(Y,Y,"D01Y")-AUC)^2)/(m*(m-1))
-  VAR.AUC<-(1/(m*(m-1)))*(sum((tapply(X,X,"D10X")-AUC)^2)+(1/(n*(n-1)))*sum((tapply(Y,Y,"D01Y")-AUC)^2)) # pag 211
+  VAR.AUC<-sum((tapply(X,X,"D10X")-AUC)^2)/(m*(m-1))+sum((tapply(Y,Y,"D01Y")-AUC)^2)/(n*(n-1)) # pag 211
   SD.AUC<-sqrt(VAR.AUC)
   alpha<-1-CL
   AUC.summary<-c(AUC- qnorm(1-alpha/2)*SD.AUC,AUC,AUC+ qnorm(1-alpha/2)*SD.AUC)
   names(AUC.summary)<-c("AUC inf conf limit", "AUC","AUC sup conf limit")
-
+  
   #TP sum(test.table[i:nrow(test.table),2])
   #FP sum(test.table[i:nrow(test.table),1])
   #TN sum(test.table[1:i-1,1])

Modified: pkg/DiagnosisMed/man/ROC.Rd
===================================================================
--- pkg/DiagnosisMed/man/ROC.Rd	2009-03-04 12:27:23 UTC (rev 8)
+++ pkg/DiagnosisMed/man/ROC.Rd	2009-03-15 03:02:55 UTC (rev 9)
@@ -88,8 +88,10 @@
    automatically  shows these columns below, therefore one has to be careful when
    relating the corresponding lines. The AUC (area under the ROC curve) is estimated 
    by the trapezoidal method (also known as Mann-Whitney statistic), its confidence
-   interval is estimated by DeLong method. The validity measures such as 
-   Sensitivity, Specificity and Likelihood ratios are estimated as 
+   interval is estimated by DeLong method. The AUC confidence limits should be used only
+   to compare the AUC with the null value for AUC which is 0.5 and not to compare 
+   the AUC from different tests. The validity measures such as Sensitivity, 
+   Specificity and Likelihood ratios and its confidence limits are estimated as 
    in \code{\link{diagnosis}} function.
    
    Diagnostic odds ratio: \eqn{DOR = (TP*TN)/(FN*FP); the same as: DOR = PLR/NLR}