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Improve documentation with more references

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Joel Therrien 2019-07-22 11:41:25 -07:00
parent c36a3d8d37
commit cb4c9b73ae
4 changed files with 32 additions and 13 deletions
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13
R/cr_naiveConcordance.R
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@ -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){

14
R/wihs.R
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@ -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"

6
man/naiveConcordance.Rd
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@ -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.
}

12
man/wihs.Rd
View file

@ -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}