From 379882237f19c2c1fc39d749435921c932360a37 Mon Sep 17 00:00:00 2001 From: john Date: Tue, 22 Oct 2024 12:20:57 +0200 Subject: [PATCH] add more references --- R/PipeOpBreslow.R | 2 ++ R/TaskGeneratorCoxed.R | 2 ++ R/TaskGeneratorSimsurv.R | 2 ++ R/pipelines.R | 5 +++++ man/mlr_graphs_survtoclassif_IPCW.Rd | 6 ++++++ man/mlr_graphs_survtoclassif_disctime.Rd | 6 ++++++ man/mlr_pipeops_compose_breslow_distr.Rd | 11 +++++++++++ man/mlr_task_generators_coxed.Rd | 6 ++++++ man/mlr_task_generators_simsurv.Rd | 6 ++++++ 9 files changed, 46 insertions(+) diff --git a/R/PipeOpBreslow.R b/R/PipeOpBreslow.R index 7a0ae6455..4fc3d2daf 100644 --- a/R/PipeOpBreslow.R +++ b/R/PipeOpBreslow.R @@ -39,6 +39,8 @@ #' This is useful for changing the prediction `distr` from one model form to #' another. #' @seealso [pipeline_distrcompositor] +#' @references +#' `r format_bib("cox_1972", "lin_2007")` #' @export #' @family survival compositors #' @examplesIf mlr3misc::require_namespaces(c("mlr3pipelines"), quietly = TRUE) diff --git a/R/TaskGeneratorCoxed.R b/R/TaskGeneratorCoxed.R index f4e5e32b5..7ae38f02b 100644 --- a/R/TaskGeneratorCoxed.R +++ b/R/TaskGeneratorCoxed.R @@ -16,6 +16,8 @@ #' @template task_generator #' #' @template seealso_task_generator +#' @references +#' `r format_bib("harden_2019")` #' @examplesIf mlr3misc::require_namespaces(c("coxed"), quietly = TRUE) #' library(mlr3) #' diff --git a/R/TaskGeneratorSimsurv.R b/R/TaskGeneratorSimsurv.R index 0396b4a59..2765102f8 100644 --- a/R/TaskGeneratorSimsurv.R +++ b/R/TaskGeneratorSimsurv.R @@ -20,6 +20,8 @@ #' @template task_generator #' #' @template seealso_task_generator +#' @references +#' `r format_bib("brilleman_2021")` #' @examplesIf mlr3misc::require_namespaces(c("simsurv"), quietly = TRUE) #' # generate 20 samples with Weibull survival distribution #' gen = tgen("simsurv") diff --git a/R/pipelines.R b/R/pipelines.R index ba916da1e..ffff3b68e 100644 --- a/R/pipelines.R +++ b/R/pipelines.R @@ -562,6 +562,8 @@ pipeline_survtoregr = function(method = 1, regr_learner = lrn("regr.featureless" #' 4. Optionally: [PipeOpModelMatrix][mlr3pipelines::PipeOpModelMatrix] is used to transform the formula of the task #' before fitting the learner. #' +#' @references +#' `r format_bib("tutz_2016")` #' @examplesIf mlr3misc::require_namespaces(c("mlr3pipelines", "mlr3learners"), quietly = TRUE) #' \dontrun{ #' library(mlr3) @@ -636,6 +638,9 @@ pipeline_survtoclassif_disctime = function(learner, cut = NULL, max_time = NULL, #' 3. [PipeOpPredClassifSurvIPCW] transforms the resulting [PredictionClassif][mlr3::PredictionClassif] #' to [PredictionSurv]. #' +#' @references +#' `r format_bib("vock_2016")` +#' #' @examplesIf mlr3misc::require_namespaces(c("mlr3pipelines", "mlr3learners"), quietly = TRUE) #' \dontrun{ #' library(mlr3) diff --git a/man/mlr_graphs_survtoclassif_IPCW.Rd b/man/mlr_graphs_survtoclassif_IPCW.Rd index 0fe388f31..da86e587e 100644 --- a/man/mlr_graphs_survtoclassif_IPCW.Rd +++ b/man/mlr_graphs_survtoclassif_IPCW.Rd @@ -85,6 +85,12 @@ Additional alias id for pipeline construction: } \dontshow{\}) # examplesIf} } +\references{ +Vock, M D, Wolfson, Julian, Bandyopadhyay, Sunayan, Adomavicius, Gediminas, Johnson, E P, Vazquez-Benitez, Gabriela, O'Connor, J P (2016). +\dQuote{Adapting machine learning techniques to censored time-to-event health record data: A general-purpose approach using inverse probability of censoring weighting.} +\emph{Journal of Biomedical Informatics}, \bold{61}, 119--131. +\doi{https://doi.org/10.1016/j.jbi.2016.03.009}, \url{https://www.sciencedirect.com/science/article/pii/S1532046416000496}. +} \seealso{ Other pipelines: \code{\link{mlr_graphs_crankcompositor}}, diff --git a/man/mlr_graphs_survtoclassif_disctime.Rd b/man/mlr_graphs_survtoclassif_disctime.Rd index aee1e38df..577589cbe 100644 --- a/man/mlr_graphs_survtoclassif_disctime.Rd +++ b/man/mlr_graphs_survtoclassif_disctime.Rd @@ -85,6 +85,12 @@ ppl("survtoclassif_disctime") } \dontshow{\}) # examplesIf} } +\references{ +Tutz, Gerhard, Schmid, Matthias (2016). +\emph{Modeling Discrete Time-to-Event Data}, series Springer Series in Statistics. +Springer International Publishing. +ISBN 978-3-319-28156-8 978-3-319-28158-2, \url{http://link.springer.com/10.1007/978-3-319-28158-2}. +} \seealso{ Other pipelines: \code{\link{mlr_graphs_crankcompositor}}, diff --git a/man/mlr_pipeops_compose_breslow_distr.Rd b/man/mlr_pipeops_compose_breslow_distr.Rd index 95e016ca5..ad6652726 100644 --- a/man/mlr_pipeops_compose_breslow_distr.Rd +++ b/man/mlr_pipeops_compose_breslow_distr.Rd @@ -70,6 +70,17 @@ another. } \dontshow{\}) # examplesIf} } +\references{ +Cox DR (1972). +\dQuote{Regression Models and Life-Tables.} +\emph{Journal of the Royal Statistical Society: Series B (Methodological)}, \bold{34}(2), 187--202. +\doi{10.1111/j.2517-6161.1972.tb00899.x}. + +Lin, Y. D (2007). +\dQuote{On the Breslow estimator.} +\emph{Lifetime Data Analysis}, \bold{13}(4), 471-480. +\doi{10.1007/s10985-007-9048-y}. +} \seealso{ \link{pipeline_distrcompositor} diff --git a/man/mlr_task_generators_coxed.Rd b/man/mlr_task_generators_coxed.Rd index e22a25017..a6feb7574 100644 --- a/man/mlr_task_generators_coxed.Rd +++ b/man/mlr_task_generators_coxed.Rd @@ -54,6 +54,12 @@ tgen("coxed") gen$generate(50) \dontshow{\}) # examplesIf} } +\references{ +Harden, J. J, Kropko, Jonathan (2019). +\dQuote{Simulating Duration Data for the Cox Model.} +\emph{Political Science Research and Methods}, \bold{7}(4), 921--928. +\doi{10.1017/PSRM.2018.19}. +} \seealso{ \itemize{ \item \link[mlr3misc:Dictionary]{Dictionary} of \link[mlr3:TaskGenerator]{TaskGenerators}: \link[mlr3:mlr_task_generators]{mlr3::mlr_task_generators} diff --git a/man/mlr_task_generators_simsurv.Rd b/man/mlr_task_generators_simsurv.Rd index 81ccac464..7f9379eab 100644 --- a/man/mlr_task_generators_simsurv.Rd +++ b/man/mlr_task_generators_simsurv.Rd @@ -51,6 +51,12 @@ tgen("simsurv") head(task) \dontshow{\}) # examplesIf} } +\references{ +Brilleman, L. S, Wolfe, Rory, Moreno-Betancur, Margarita, Crowther, J. M (2021). +\dQuote{Simulating Survival Data Using the simsurv R Package.} +\emph{Journal of Statistical Software}, \bold{97}(3), 1--27. +\doi{10.18637/JSS.V097.I03}. +} \seealso{ \itemize{ \item \link[mlr3misc:Dictionary]{Dictionary} of \link[mlr3:TaskGenerator]{TaskGenerators}: \link[mlr3:mlr_task_generators]{mlr3::mlr_task_generators}