From cb4c9b73aecc20ff754341fd2c07f78eb0dce08a Mon Sep 17 00:00:00 2001
From: Joel Therrien <joelt@sfu.ca>
Date: Mon, 22 Jul 2019 11:41:25 -0700
Subject: [PATCH] Improve documentation with more references

---
 R/cr_naiveConcordance.R | 13 +++++++++----
 R/wihs.R                | 14 +++++++++-----
 man/naiveConcordance.Rd |  6 ++++++
 man/wihs.Rd             | 12 ++++++++----
 4 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/R/cr_naiveConcordance.R b/R/cr_naiveConcordance.R
index eb6fc77..bb4046a 100644
--- a/R/cr_naiveConcordance.R
+++ b/R/cr_naiveConcordance.R
@@ -16,19 +16,24 @@
 #'   list should correspond to one of the events in the order of event 1 to J,
 #'   and should be a vector of the same length as responses.
 #' @export
+#' @references Section 3.2 of Wolbers, Marcel, Paul Blanche, Michael T. Koller,
+#'   Jacqueline C M Witteman, and Thomas A Gerds. 2014. “Concordance for
+#'   Prognostic Models with Competing Risks.” Biostatistics 15 (3): 526–39.
+#'   https://doi.org/10.1093/biostatistics/kxt059.
+#'
 #' @examples
 #' data <- data.frame(delta=c(1,1,0,0,2,2), T=1:6, x=1:6)
-#' 
+#'
 #' model <- train(CR_Response(delta, T) ~ x, data, ntree=100, numberOfSplits=0, mtry=1, nodeSize=1)
-#' 
+#'
 #' newData <- data.frame(delta=c(1,0,2,1,0,2), T=1:6, x=1:6)
 #' predictions <- predict(model, newData)
-#' 
+#'
 #' mortalities <- list(
 #'   extractMortalities(predictions, 1, 6),
 #'   extractMortalities(predictions, 2, 6)
 #' )
-#' 
+#'
 #' naiveConcordance(CR_Response(newData$delta, newData$T), mortalities)
 #' 
 naiveConcordance <- function(responses, predictedMortalities){
diff --git a/R/wihs.R b/R/wihs.R
index cd97b32..22aaa48 100644
--- a/R/wihs.R
+++ b/R/wihs.R
@@ -15,9 +15,13 @@
 #' @source The data was obtained from the randomForestSRC R package.
 #'
 #' @references Bacon MC, von Wyl V, Alden C, Sharp G, Robison E, Hessol N, Gange
-#'   S, Barranday Y, Holman S, Weber K, Young MA (2005). “The Women’s
-#'   Interagency HIV Study: an Observational Cohort Brings Clinical Sciences to
-#'   the Bench.” Clinical and Vaccine Immunology, 12(9), 1013–1019.
-#'   doi:10.1128/CDLI.12.9.1013-1019.2005.
-#'   
+#' S, Barranday Y, Holman S, Weber K, Young MA (2005). “The Women’s Interagency
+#' HIV Study: an Observational Cohort Brings Clinical Sciences to the Bench.”
+#' Clinical and Vaccine Immunology, 12(9), 1013–1019.
+#' doi:10.1128/CDLI.12.9.1013-1019.2005.
+#'
+#' Ishwaran, H., and Udaya B. Kogalur. 2018. Random Forests for Survival,
+#' Regression, and Classification (Rf-Src). manual.
+#' https://cran.r-project.org/package=randomForestSRC.
+#' 
 "wihs"
\ No newline at end of file
diff --git a/man/naiveConcordance.Rd b/man/naiveConcordance.Rd
index e289e54..3fde795 100644
--- a/man/naiveConcordance.Rd
+++ b/man/naiveConcordance.Rd
@@ -41,3 +41,9 @@ mortalities <- list(
 naiveConcordance(CR_Response(newData$delta, newData$T), mortalities)
 
 }
+\references{
+Section 3.2 of Wolbers, Marcel, Paul Blanche, Michael T. Koller,
+  Jacqueline C M Witteman, and Thomas A Gerds. 2014. “Concordance for
+  Prognostic Models with Competing Risks.” Biostatistics 15 (3): 526–39.
+  https://doi.org/10.1093/biostatistics/kxt059.
+}
diff --git a/man/wihs.Rd b/man/wihs.Rd
index fad12bc..1891a1a 100644
--- a/man/wihs.Rd
+++ b/man/wihs.Rd
@@ -25,9 +25,13 @@ time may also be censored.
 }
 \references{
 Bacon MC, von Wyl V, Alden C, Sharp G, Robison E, Hessol N, Gange
-  S, Barranday Y, Holman S, Weber K, Young MA (2005). “The Women’s
-  Interagency HIV Study: an Observational Cohort Brings Clinical Sciences to
-  the Bench.” Clinical and Vaccine Immunology, 12(9), 1013–1019.
-  doi:10.1128/CDLI.12.9.1013-1019.2005.
+S, Barranday Y, Holman S, Weber K, Young MA (2005). “The Women’s Interagency
+HIV Study: an Observational Cohort Brings Clinical Sciences to the Bench.”
+Clinical and Vaccine Immunology, 12(9), 1013–1019.
+doi:10.1128/CDLI.12.9.1013-1019.2005.
+
+Ishwaran, H., and Udaya B. Kogalur. 2018. Random Forests for Survival,
+Regression, and Classification (Rf-Src). manual.
+https://cran.r-project.org/package=randomForestSRC.
 }
 \keyword{datasets}