joel/largeRCRF
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

Improve documentation with more references

Browse source
This commit is contained in:
Joel Therrien 2019-07-22 11:41:25 -07:00
parent c36a3d8d37
commit cb4c9b73ae
4 changed files with 32 additions and 13 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

13
R/cr_naiveConcordance.R
View file

@ -16,19 +16,24 @@
#' list should correspond to one of the events in the order of event 1 to J, #' 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. #' and should be a vector of the same length as responses.
#' @export #' @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 #' @examples
#' data <- data.frame(delta=c(1,1,0,0,2,2), T=1:6, x=1:6) #' 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) #' 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) #' newData <- data.frame(delta=c(1,0,2,1,0,2), T=1:6, x=1:6)
#' predictions <- predict(model, newData) #' predictions <- predict(model, newData)
#' #'
#' mortalities <- list( #' mortalities <- list(
#' extractMortalities(predictions, 1, 6), #' extractMortalities(predictions, 1, 6),
#' extractMortalities(predictions, 2, 6) #' extractMortalities(predictions, 2, 6)
#' ) #' )
#' #'
#' naiveConcordance(CR_Response(newData$delta, newData$T), mortalities) #' naiveConcordance(CR_Response(newData$delta, newData$T), mortalities)
#' #'
naiveConcordance <- function(responses, predictedMortalities){ naiveConcordance <- function(responses, predictedMortalities){

14
R/wihs.R
View file

@ -15,9 +15,13 @@
#' @source The data was obtained from the randomForestSRC R package. #' @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 #' @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 #' S, Barranday Y, Holman S, Weber K, Young MA (2005). “The Women’s Interagency
#' Interagency HIV Study: an Observational Cohort Brings Clinical Sciences to #' HIV Study: an Observational Cohort Brings Clinical Sciences to the Bench.”
#' the Bench.” Clinical and Vaccine Immunology, 12(9), 1013–1019. #' Clinical and Vaccine Immunology, 12(9), 1013–1019.
#' doi:10.1128/CDLI.12.9.1013-1019.2005. #' 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" "wihs"

6
man/naiveConcordance.Rd
View file

@ -41,3 +41,9 @@ mortalities <- list(
naiveConcordance(CR_Response(newData$delta, newData$T), mortalities) 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{ \references{
Bacon MC, von Wyl V, Alden C, Sharp G, Robison E, Hessol N, Gange 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 S, Barranday Y, Holman S, Weber K, Young MA (2005). “The Women’s Interagency
Interagency HIV Study: an Observational Cohort Brings Clinical Sciences to HIV Study: an Observational Cohort Brings Clinical Sciences to the Bench.”
the Bench.” Clinical and Vaccine Immunology, 12(9), 1013–1019. Clinical and Vaccine Immunology, 12(9), 1013–1019.
doi:10.1128/CDLI.12.9.1013-1019.2005. 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} \keyword{datasets}