From noreply at r-forge.r-project.org  Fri Mar 11 20:17:00 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 11 Mar 2016 20:17:00 +0100 (CET)
Subject: [Diagnosismed-commits] r21 - in pkg/DiagnosisMed: . R man
Message-ID: <20160311191700.17548188035@r-forge.r-project.org>

Author: tak101
Date: 2016-03-11 20:16:59 +0100 (Fri, 11 Mar 2016)
New Revision: 21

Added:
   pkg/DiagnosisMed/NAMESPACE
Modified:
   pkg/DiagnosisMed/DESCRIPTION
   pkg/DiagnosisMed/R/LRgraph.r
   pkg/DiagnosisMed/R/ROC.r
   pkg/DiagnosisMed/R/TGROC.r
   pkg/DiagnosisMed/R/diagnosis.r
   pkg/DiagnosisMed/R/interact.ROC.r
   pkg/DiagnosisMed/R/plot.ROC.r
   pkg/DiagnosisMed/R/plot.TGROC.r
   pkg/DiagnosisMed/R/plot.diag.r
   pkg/DiagnosisMed/R/print.ROC.r
   pkg/DiagnosisMed/R/print.TGROC.r
   pkg/DiagnosisMed/R/print.diag.r
   pkg/DiagnosisMed/R/summary.diag.R
   pkg/DiagnosisMed/R/zzz.r
   pkg/DiagnosisMed/man/LRgrgaph.Rd
   pkg/DiagnosisMed/man/ROC.Rd
   pkg/DiagnosisMed/man/TGROC.Rd
   pkg/DiagnosisMed/man/diagnosis.Rd
   pkg/DiagnosisMed/man/interact.ROC.Rd
Log:
Revision 21 Version 2.3.4 CRAN ready  Hans Landsheer
NAMESPACE file added
Removed outdated links from Rd files 
Added bare minimum of roxygen comments: #' @export  #' @import
Removed zzz.r Could not get it working and doesn't make much sense
\dontrun{} added to ROC.Rd (Full View not allowed in examples)

Modified: pkg/DiagnosisMed/DESCRIPTION
===================================================================
--- pkg/DiagnosisMed/DESCRIPTION	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/DESCRIPTION	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,10 +1,22 @@
 Package: DiagnosisMed
-Version: 0.2.3
-Date: 2010-03-08
+Version: 0.2.4
+Date: 2016-03-11
 Author: Pedro Brasil <pedro.brasil at ipec.fiocruz.br>
 Maintainer: Pedro Brasil <pedro.brasil at ipec.fiocruz.br>
-Depends: R (>= 2.7.2),epitools, TeachingDemos, tcltk, AMORE,utils,stats
-Title: Diagnostic test accuracy evaluation for medical professionals.
-Description: DiagnosisMed is a package to analyze data from diagnostic test accuracy evaluating health conditions. It is being built to be used by health professionals. This package is able to estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different categorical tests, and estimate reasonble cut-offs of tests and display it in a way commonly used by health professionals. No graphical interface is avalible yet. Partners are most welcome. 
+Depends:
+    R (>= 2.7.2),epitools,
+    TeachingDemos,
+    tcltk,
+    AMORE,utils,stats
+Title: Diagnostic test accuracy evaluation for medical professionals
+Description: DiagnosisMed is a package to analyze data from diagnostic test
+    accuracy evaluating health conditions. It is being built to be used by health
+    professionals. This package is able to estimate sensitivity and specificity
+    from categorical and continuous test results including some evaluations of
+    indeterminate results, or compare different categorical tests, and estimate
+    reasonble cut-offs of tests and display it in a way commonly used by health
+    professionals. No graphical interface is avalible yet. Partners are most
+    welcome.
 License: GPL (>= 2)
-URL: http://r-forge.r-project.org/projects/diagnosismed/
\ No newline at end of file
+URL: http://r-forge.r-project.org/projects/diagnosismed/
+RoxygenNote: 5.0.1

Added: pkg/DiagnosisMed/NAMESPACE
===================================================================
--- pkg/DiagnosisMed/NAMESPACE	                        (rev 0)
+++ pkg/DiagnosisMed/NAMESPACE	2016-03-11 19:16:59 UTC (rev 21)
@@ -0,0 +1,19 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(plot,ROC)
+S3method(plot,TGROC)
+S3method(plot,diag)
+S3method(print,ROC)
+S3method(print,TGROC)
+S3method(print,diag)
+S3method(summary,diag)
+export(LRgraph)
+export(ROC)
+export(TGROC)
+export(diagnosis)
+export(interact.ROC)
+import(AMORE)
+import(TeachingDemos)
+import(epitools)
+import(tcltk)
+import(utils)

Modified: pkg/DiagnosisMed/R/LRgraph.r
===================================================================
--- pkg/DiagnosisMed/R/LRgraph.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/LRgraph.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 LRgraph <- function (tests, lwd = 2, lty = 1, cex = 1, leg.cex = 1.5, pt.cex = 2, ...){
     plot(1 - tests[[6, 1]], tests[[4, 1]], xlim = c(0, 1), ylim = c(0,1), xlab = "False positive rate", ylab = "True positive rate",
         col = 1, cex = cex, lwd = lwd, lty = lty)

Modified: pkg/DiagnosisMed/R/ROC.r
===================================================================
--- pkg/DiagnosisMed/R/ROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/ROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 ROC<-function(gold,
               test,
               CL=0.95,

Modified: pkg/DiagnosisMed/R/TGROC.r
===================================================================
--- pkg/DiagnosisMed/R/TGROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/TGROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,7 @@
+#' @export
+#' @import epitools
+#' @import AMORE
+
 TGROC<-function(gold,
                 test,
                 Cost=1,

Modified: pkg/DiagnosisMed/R/diagnosis.r
===================================================================
--- pkg/DiagnosisMed/R/diagnosis.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/diagnosis.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,5 @@
+#' @export
+#' @import epitools
 diagnosis <- function(a,b=NULL,c=NULL,d=NULL,CL=0.95,print=TRUE,plot=FALSE){
   #require(epitools)
   if(is.numeric(a)){

Modified: pkg/DiagnosisMed/R/interact.ROC.r
===================================================================
--- pkg/DiagnosisMed/R/interact.ROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/interact.ROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,7 @@
+#' @export
+#' @import TeachingDemos 
+#' @import tcltk
+
 interact.ROC<-function(gold,test){
   # require(TeachingDemos)
   # require(tcltk)

Modified: pkg/DiagnosisMed/R/plot.ROC.r
===================================================================
--- pkg/DiagnosisMed/R/plot.ROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/plot.ROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,4 +1,5 @@
-  # the plot commands
+#' @export
+# the plot commands
 plot.ROC<-function(x,Plot.point="Min.ROC.Dist",cex.sub=.85,p.cex=1,...){
 
     if(Plot.point!="None" & Plot.point!="Min.ROC.Dist" & Plot.point!="Max.Accuracy" &

Modified: pkg/DiagnosisMed/R/plot.TGROC.r
===================================================================
--- pkg/DiagnosisMed/R/plot.TGROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/plot.TGROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 plot.TGROC<-function(x,...,
                 Plot="Both",
                 Plot.inc.range=TRUE,

Modified: pkg/DiagnosisMed/R/plot.diag.r
===================================================================
--- pkg/DiagnosisMed/R/plot.diag.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/plot.diag.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 plot.diag<-function(x,print=FALSE,...){
   #to do - include an error rate curve
   #consider ohter graphic parameters

Modified: pkg/DiagnosisMed/R/print.ROC.r
===================================================================
--- pkg/DiagnosisMed/R/print.ROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/print.ROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,4 +1,6 @@
+#' @export
 print.ROC<-function(x,Full=FALSE,...){
+  ## View cannot be used in examples !!!
   if (Full==TRUE){ View(x$test.diag.table[,-c(2:5,24:34)])}
   cat("          Sample size:",x$sample.size,"\n")
   cat("    Sample prevalence:",round(x$sample.prevalence,digits = 4),"\n")

Modified: pkg/DiagnosisMed/R/print.TGROC.r
===================================================================
--- pkg/DiagnosisMed/R/print.TGROC.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/print.TGROC.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 print.TGROC<-function(x,...){
   cat("                Sample size:",x$sample.size,"\n")
   cat("          Sample prevalence:",round(x$sample.prevalence,digits = 4),"\n")

Modified: pkg/DiagnosisMed/R/print.diag.r
===================================================================
--- pkg/DiagnosisMed/R/print.diag.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/print.diag.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 print.diag <- function(x,...){
   cat("Reference standard:",x$reference.name,"\n")
   cat("Index test        :",x$index.name,"\n")  

Modified: pkg/DiagnosisMed/R/summary.diag.R
===================================================================
--- pkg/DiagnosisMed/R/summary.diag.R	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/summary.diag.R	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,3 +1,4 @@
+#' @export
 summary.diag <- function(object,...){
   diag.tab <- matrix(
         c(object$n,NA,paste(formatC(object$p*100,digits=2,format="f")),NA,

Modified: pkg/DiagnosisMed/R/zzz.r
===================================================================
--- pkg/DiagnosisMed/R/zzz.r	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/R/zzz.r	2016-03-11 19:16:59 UTC (rev 21)
@@ -1,13 +1,16 @@
-# first and last
-.First.lib <- function(lib, pkg)
-{
-#require("epitools","TeachingDemos","tcltk",quietly=TRUE,warn.conflicts=FALSE)
-# if (.Platform$OS.type=="windows")
-see <- packageDescription(pkg,fields="Version")
-cat("'DiagnosisMed' library",see," loaded\n",sep=" ")
-}
-
-.Last.lib <- function(libpath)
-{
-# nothing so far
-}
+# #' @import utils
+# 
+# # first and last
+# .onLoad <- function(lib, pkg)
+# {
+# #require("epitools","TeachingDemos","tcltk",quietly=TRUE,warn.conflicts=FALSE)
+# # if (.Platform$OS.type=="windows")
+# see <- utils::packageDescription(pkg,fields="Version") # see=''
+# mess <- .makeMessage("'DiagnosisMed' library ",see," loaded")
+# packageStartupMessage(mess)
+# }
+# 
+# .Last.lib <- function(libpath)
+# {
+# # nothing so far
+# }

Modified: pkg/DiagnosisMed/man/LRgrgaph.Rd
===================================================================
--- pkg/DiagnosisMed/man/LRgrgaph.Rd	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/man/LRgrgaph.Rd	2016-03-11 19:16:59 UTC (rev 21)
@@ -35,11 +35,13 @@
 mytest1<-diagnosis(90,10,10,90,print=FALSE)
 
 # mytest2 has lower sensitivity but higher specificity.
-# mytest2 is better to identify the presence of the target condition compared to mytest5.
+# mytest2 is better to identify the presence of the target condition compared to 
+# mytest5.
 mytest2<-diagnosis(72,28,3,97,print=FALSE)
 
 # mytest3 has higher sensitivity but lower specificity.
-# mytest3 is better to identify the absence of the target condition compared to mytest5.
+# mytest3 is better to identify the absence of the target condition compared to 
+# mytest5.
 mytest3<-diagnosis(92,8,37,63,print=FALSE)
 
 # mytest41 has lower sensitivity and specificity.

Modified: pkg/DiagnosisMed/man/ROC.Rd
===================================================================
--- pkg/DiagnosisMed/man/ROC.Rd	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/man/ROC.Rd	2016-03-11 19:16:59 UTC (rev 21)
@@ -59,10 +59,10 @@
   \item{Print}{If FALSE, no results (detailed below in values section) will be displayed on the output window. Default is TRUE}
   \item{Full}{If TRUE, a table with sensitivity, specificity, predictive values and likelihood ratios (and respective confidence limits) for each decision threshold will be displayed. Default is FALSE.}
   \item{x}{For the \command{plot} and \command{print} functions, x is an object storing \command{ROC} function output.}    
-  \item{...}{Other plot or print parameters form \link[graphics]{plot.default}}  
+  \item{...}{Other plot or print parameters from \link[graphics]{plot.default}}  
 }
 \details{
-   Tests results matching the cut-off values will be considered a positive test. \command{ROC} assumes that subjects with higher values of the test are with the target condition and those with lower values are without the target condition. Tests that behave like glucose (middle values are supposed to be normal and extreme values are supposed to be abnormal) and immunefluorescence (lower values - higher dilutions - are suppose to be abnormal) will not be correctly analyzed. In the latter, multiplying the test results by -1 or other transformation before analysis could make it work. 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 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. If \command{ROC} output is assign to an object (see example), tests results could be easily exported to a spreadsheet and other graphics that might be of interest could be easily done.
+   Tests results matching the cut-off values will be considered a positive test. \command{ROC} assumes that subjects with higher values of the test are with the target condition and those with lower values are without the target condition. Tests that behave like glucose (middle values are supposed to be normal and extreme values are supposed to be abnormal) and immunefluorescence (lower values - higher dilutions - are suppose to be abnormal) will not be correctly analyzed. In the latter, multiplying the test results by -1 or other transformation before analysis could make it work. 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 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 \command{diagnosis} function. If \command{ROC} output is assign to an object (see example), tests results could be easily exported to a spreadsheet and other graphics that might be of interest could be easily done.
    
    Diagnostic odds ratio: \eqn{DOR = (TP*TN)/(FN*FP); the same as: DOR = PLR/NLR}
 
@@ -103,50 +103,70 @@
 \author{Pedro Brasil; Beranrdo Rangel Tura - \email{diagnosismed-list at lists.r-forge.r-project.org}}
 \note{Bug reports, malfunctioning, or suggestions for further improvements or contributions can be sent, preferentially, through the DiagnosisMed email list, or R-Forge website \url{https://r-forge.r-project.org/projects/diagnosismed/}.
 }
-\seealso{\link[epitools]{binom.conf.int},\code{\link{diagnosis}},\code{\link{interact.ROC}},\code{\link{TGROC}},\link[ROCR]{performance},\link[nonbinROC]{contROC}}
+\seealso{\code{epitools::binom.conf.int}, \code{\link{diagnosis}}, \code{\link{interact.ROC}}, \code{\link{TGROC}}, \code{ROCR::performance}, \code{nonbinROC::performance} }
 \examples{
 # loading a dataset
 data(rocdata)
+
 # Attaching the data set.
 attach(rocdata)
+
 # A little description of the data set to check if it is ok!
 str(rocdata)
-# Running ROC analysis with the full table option 
-# and storing ROC objects into 'x' from which there are tables to draw the graphs below.
-x<-DiagnosisMed::ROC(Gold,test2,Full=TRUE) 
-# There is no need to stick the package name before the function if it is loaded as first in search path!
+
+# Running ROC analysis with the full table option and storing ROC objects into 
+# 'x' from which there are tables to draw the graphs below.
+\dontrun{
+x<-DiagnosisMed::ROC(Gold,test2,Full=TRUE) }
+x<-DiagnosisMed::ROC(Gold,test2,Full=FALSE) 
+# There is no need to stick the package name before the function if it is loaded  
+# first in search path!
+
 # Adding a title to the graph.
 title(main="ROC graph")
+
 # Some graphs that may be of interest. Validity measures at each test value. 
 # Setting the plot window to get nine graphs
-# Some graphs showing some validity measures and some indexes variations used to choose good cut-offs
+# Some graphs showing some validity measures and some indexes variations used 
+# to choose good cut-offs
 par(mfrow=c(3,3))
-plot(x$test.diag.table$test.values,x$test.diag.table$DOR,type="l",ylab="DOR",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$DOR,type="l",ylab="DOR",
+      xlab="Test values")
 title(main="Test values x DOR")
-plot(x$test.diag.table$test.values,x$test.diag.table$MCT,type="l",ylab="MCT",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$MCT,type="l",ylab="MCT",
+      xlab="Test values")
 title(main="Test values x MCT")
-plot(x$test.diag.table$test.values,x$test.diag.table$Efficiency,type="l",ylab="Efficiency",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$Efficiency,type="l",
+      ylab="Efficiency",xlab="Test values")
 title(main="Test values x Efficiency")
-plot(x$test.diag.table$test.values,x$test.diag.table$Youden,type="l",ylab="Youden index",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$Youden,type="l",
+      ylab="Youden index",xlab="Test values")
 title(main="Test values x Youden index")
-plot(x$test.diag.table$test.values,x$test.diag.table$PLR,type="l",ylim=c(0,49),ylab="Likelihood ratios",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$PLR,type="l",ylim=c(0,49),
+      ylab="Likelihood ratios",xlab="Test values")
 lines(x$test.diag.table$test.values,x$test.diag.table$NLR,type="l",lty=2)
 legend("right",lty=c(1,2),legend=c("PLR","NLR"),bty = 'n')
 title(main="Test values x Likelihood ratios")
-plot(x$test.diag.table$test.values,x$test.diag.table$PPV,type="l",ylab="Predictive values",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$PPV,type="l",
+      ylab="Predictive values",xlab="Test values")
 lines(x$test.diag.table$test.values,x$test.diag.table$NPV,type="l",lty=2)
 legend("bottomright",lty=c(1,2),legend=c("PPV","NPV"),bty = 'n')
 title(main="Test values x Predictive values")
-plot(x$test.diag.table$test.values,x$test.diag.table$Accuracy.area,type="l",,ylab="Accuracy area",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$Accuracy.area,type="l",
+      ylab="Accuracy area",xlab="Test values")
 title(main="Test values x Accuracy area")
-plot(x$test.diag.table$test.values,x$test.diag.table$MinRocDist,type="l",,ylab="ROC distance",xlab="Test values")
+plot(x$test.diag.table$test.values,x$test.diag.table$MinRocDist,type="l",
+      ylab="ROC distance",xlab="Test values")
 title(main="Test values x ROC distance")
-plot(x$test.diag.table$test.values,x$test.diag.table$Accuracy,type="l",ylab="Error rate & Accuracy",xlab="Test values",ylim=c(0,1))
-lines(x$test.diag.table$test.values,x$test.diag.table$Error.rate,type="l",lty=2)#,xlim=c(0,2.5))
+plot(x$test.diag.table$test.values,x$test.diag.table$Accuracy,type="l",
+      ylab="Error rate & Accuracy",xlab="Test values",ylim=c(0,1))
+lines(x$test.diag.table$test.values,x$test.diag.table$Error.rate,type="l",lty=2)
+#,xlim=c(0,2.5))
 legend("bottomright",lty=c(1,2),legend=c("Accuracy","Error rate"),bty = 'n')
 par(mfrow=c(1,1))
 
-# Also, results from ROC analysis could easily exported to a spreadsheet file or to a odt file by OdfWeave.
+# Also, results from ROC analysis could easily exported to a spreadsheet file 
+# or to a odt file by OdfWeave.
 # Exporting the full table:
 # write.csv(x$test.diag.table[,-c(2:5,24:34)],'MytestFulltable.csv')
 # Exporting AUC summary:
@@ -154,7 +174,7 @@
 # Exporting Test summary:
 # write.csv(x$test.summary,'MytestSummary.csv')
 # Exporting Test best-cut-offs table:
-# write.csv(x$test.best.cutoff,'MytestBestcutof.csv')                                                
+# write.csv(x$test.best.cutoff,'MytestBestcutof.csv')
 rm(rocdata,x)
 }
 \keyword{iplot}

Modified: pkg/DiagnosisMed/man/TGROC.Rd
===================================================================
--- pkg/DiagnosisMed/man/TGROC.Rd	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/man/TGROC.Rd	2016-03-11 19:16:59 UTC (rev 21)
@@ -99,7 +99,7 @@
 \author{Pedro Brasil; - \email{diagnosismed-list at lists.r-forge.r-project.org}}
 \note{Bug reports, malfunctioning, or suggestions for further improvements or contributions can be sent, preferentially, through the DiagnosisMed email list, or R-Forge website \url{https://r-forge.r-project.org/projects/diagnosismed/}.
 }
-\seealso{\code{\link{interact.ROC}},\code{\link{ROC}},\code{\link{diagnosis}},\link[ROCR]{performance},\link[epitools]{binom.conf.int},\link[nonbinROC]{contROC}}
+\seealso{\code{\link{interact.ROC}},\code{\link{ROC}},\code{\link{diagnosis}},\link[ROCR]{performance},\link[epitools]{binom.conf.int},\code{ nonbinROC::performance}}
 \examples{
 # Loading a dataset.
 data(tutorial)

Modified: pkg/DiagnosisMed/man/diagnosis.Rd
===================================================================
--- pkg/DiagnosisMed/man/diagnosis.Rd	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/man/diagnosis.Rd	2016-03-11 19:16:59 UTC (rev 21)
@@ -70,8 +70,8 @@
 \author{Pedro Brasil - \email{diagnosismed-list at lists.r-forge.r-project.org}}
 \note{Bug reports, malfunctioning, or suggestions for further improvements or contributions can be sent, preferentially, through the DiagnosisMed email list, or R-Forge website \url{https://r-forge.r-project.org/projects/diagnosismed/}.
 }
-\seealso{\code{\link{LRgraph}}, \code{\link{ROC}},\code{\link{LRgraph}},\link[epitools]{binom.conf.int},
- \link[epibasix]{sensSpec},\link[epiR]{epi.tests},\link[Design]{nomogram},\link[epiR]{epi.nomogram}}
+\seealso{\code{ LRgraph}, \code{ ROC},\code{ epitools::binom.conf.int},
+ \code{ epibasix::sensSpec},\code{ epiR::epi.tests},\code{ Design::nomogram},\code{ epiR::epi.nomogram}} 
 \examples{
 # Simulating a dataset
 mydata <- as.data.frame(rbind(

Modified: pkg/DiagnosisMed/man/interact.ROC.Rd
===================================================================
--- pkg/DiagnosisMed/man/interact.ROC.Rd	2010-03-09 04:03:04 UTC (rev 20)
+++ pkg/DiagnosisMed/man/interact.ROC.Rd	2016-03-11 19:16:59 UTC (rev 21)
@@ -27,7 +27,7 @@
 \author{Pedro Brasil - \email{diagnosismed-list at lists.r-forge.r-project.org}}
 \note{Bug reports, malfunctioning, or suggestions for further improvements or contributions can be sent, preferentially, through the DiagnosisMed email list, or R-Forge website \url{https://r-forge.r-project.org/projects/diagnosismed/}.
 }
-\seealso{\code{\link{diagnosis}},\code{\link{ROC}},\code{\link{TGROC}},\link[ROCR]{performance},\link[TeachingDemos]{roc.demo},\link[nonbinROC]{contROC}}
+\seealso{\code{diagnosis},\code{ ROC},\code{ TGROC},\code{ ROCR::performance},\code{ TeachingDemos::roc.demo}, \code{ nonbinROC::performance}}
 \examples{
 data(rocdata)
 attach(rocdata)