From 8be45013f181c707365496b992dc706b5571f42a Mon Sep 17 00:00:00 2001
From: agdamsbo <agdamsbo@protonmail.com>
Date: Thu, 4 Oct 2018 16:52:09 +0200
Subject: [PATCH] new function

---
 DESCRIPTION          |  4 +++-
 NAMESPACE            |  1 +
 R/rep_epi_tests.R    | 24 ++++++++++++++++++++++++
 man/rep_epi_tests.Rd | 26 ++++++++++++++++++++++++++
 4 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 R/rep_epi_tests.R
 create mode 100644 man/rep_epi_tests.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 226096a..b534adf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,7 +7,9 @@ Description: Tools for Danish health research. A collection of
     functions to ease my work. I'll try to keep it updated for 
     others to use as well.
 Depends: R (>= 3.4.4)
-Imports: broom
+Imports: broom,
+  dplyr,
+  epiR
 License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index 7385056..4b21f71 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,5 +12,6 @@ export(hwe_allele)
 export(hwe_geno)
 export(hwe_sum)
 export(rep_biv)
+export(rep_epi_tests)
 export(rep_glm)
 export(rep_lm)
diff --git a/R/rep_epi_tests.R b/R/rep_epi_tests.R
new file mode 100644
index 0000000..c3a0e19
--- /dev/null
+++ b/R/rep_epi_tests.R
@@ -0,0 +1,24 @@
+#' A repeated epi.tests function
+#'
+#' Repeats the epi.tests from the epiR package.
+#' @description For bivariate analyses. The confint() function is rather slow, causing the whole function to hang when including many predictors and calculating the ORs with CI.
+#' @param gs the test or meassure used as "golden standard". Format as dichotomised factor.
+#' @param test possible predictive tests to evaluate. Format as dichotomised factor.
+#' @keywords ppv npv sensitivity specificity
+#' @export
+#' @examples
+#' rep_epi_tests()
+
+
+rep_epi_tests<-function(gs,test){
+  require(epiR)
+
+  ls<-list()
+  for (i in 1:ncol(test)){
+    t<-table(test[,i],gs)
+    rval <- epi.tests(t, conf.level = 0.95)
+    n<-names(test)[i]
+    ls[[i]]<-list(n,rval)
+  }
+  return(ls)
+}
diff --git a/man/rep_epi_tests.Rd b/man/rep_epi_tests.Rd
new file mode 100644
index 0000000..3eb4d2a
--- /dev/null
+++ b/man/rep_epi_tests.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rep_epi_tests.R
+\name{rep_epi_tests}
+\alias{rep_epi_tests}
+\title{A repeated epi.tests function}
+\usage{
+rep_epi_tests(gs, test)
+}
+\arguments{
+\item{gs}{the test or meassure used as "golden standard". Format as dichotomised factor.}
+
+\item{test}{possible predictive tests to evaluate. Format as dichotomised factor.}
+}
+\description{
+For bivariate analyses. The confint() function is rather slow, causing the whole function to hang when including many predictors and calculating the ORs with CI.
+}
+\details{
+Repeats the epi.tests from the epiR package.
+}
+\examples{
+rep_epi_tests()
+}
+\keyword{npv}
+\keyword{ppv}
+\keyword{sensitivity}
+\keyword{specificity}