Added RdPack to manage references (#271)

DESCRIPTION

@@ -30,6 +30,7 @@ Depends:
     R (>= 4.1.0)
 Imports:
     assertthat,
+    Rdpack,
     checkmate,
     dplyr,
     stringr,
@@ -96,3 +97,4 @@ Collate:
     'simulations_sf.R'
     'zzz.R'
 VignetteBuilder: knitr
+RdMacros: Rdpack

NAMESPACE

@@ -184,6 +184,7 @@ import(checkmate)
 import(ggplot2)
 import(methods)
 import(stringr)
+importFrom(Rdpack,reprompt)
 importFrom(ggplot2,autoplot)
 importFrom(ggplot2.utils,geom_km)
 importFrom(glue,as_glue)

R/SurvivalQuantities.R

@@ -363,13 +363,15 @@ setMethod(
 #'
 #' @description
 #' Derives the Brier Scores (using Inverse Probability of Censoring Weighting)
-#' for the Survival estimates as detailed in Blanche et. al. (2015).
+#' for the Survival estimates as detailed in \insertCite{blanche2015}{jmpost}.
 #'
 #' @inheritParams SurvivalQuantities-Shared
 #' @inheritParams Brier-Score-Shared
 #'
 #' @family brierScore
 #' @family SurvivalQuantities
+#' @references
+#' \insertAllCited{}
 #' @export
 brierScore.SurvivalQuantities <- function(
     object,

R/brier_score.R

@@ -123,13 +123,16 @@ reverse_km_cen_first <- function(t, times, events) {
 #' @inheritParams Brier-Score-Shared
 #'
 #' @description
-#' Implements the Brier Score as detailed in Blanche et. al. (2015)
+#' Implements the Brier Score as detailed in \insertCite{blanche2015}{jmpost}
 #'
 #' @details
 #' - `bs_get_squared_dist()` - implements the squared distance part
 #' of the formula.
 #' - `bs_get_weights()` - implements the IPCW weighting
 #'
+#' @references
+#' \insertAllCited{}
+#'
 #' @keywords internal
 brier_score <- function(
     t,

R/jmpost-package.R

@@ -10,4 +10,5 @@
 #' @importFrom glue as_glue
 #' @importFrom tibble add_case
 #' @importFrom stats acf
+#' @importFrom Rdpack reprompt
 NULL

design/Intro_to_jmpost.Rmd

@@ -15,7 +15,7 @@ header-includes:
   - \usetikzlibrary{shapes.geometric, arrows}   
 output:
   pdf_document: default
-bibliography: bibliography.bib
+bibliography: '`r system.file("REFERENCES.bib", package = "jmpost")`'
 vignette: |
   %\VignetteIndexEntry{Introduction to `jmpost`}
   %\VignetteEncoding{UTF-8}

design/bibliography.bib → inst/REFERENCES.bib

@@ -1,3 +1,21 @@
+
+
+
+@article{blanche2015,
+author = {Blanche, Paul and Proust-Lima, Cécile and Loubère, Lucie and Berr, Claudine and Dartigues, Jean-François and Jacqmin-Gadda, Hélène},
+title = {Quantifying and comparing dynamic predictive accuracy of joint models for longitudinal marker and time-to-event in presence of censoring and competing risks},
+journal = {Biometrics},
+volume = {71},
+number = {1},
+pages = {102-113},
+keywords = {Competing risks, Dynamic prediction, Joint model, Longitudinal data, Prediction accuracy},
+doi = {https://doi.org/10.1111/biom.12232},
+url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/biom.12232},
+eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/biom.12232},
+year = {2015}
+}
+
+
 @article{kerioui2020bayesian,
   title={Bayesian inference using Hamiltonian Monte-Carlo algorithm for nonlinear joint modelling in the context of cancer immunotherapy},
   author={Kerioui, Marion and Mercier, Francois and Bertrand, Julie and Tardivon, Coralie and Bruno, Ren{\'e} and Guedj, J{\'e}r{\'e}mie and Desm{\'e}e, Sol{\`e}ne},

vignettes/statistical-specification.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "Statistical Specifications"
 package: jmpost
-bibliography: '`r system.file("references.bib", package = "jmpost")`'
+bibliography: '`r system.file("REFERENCES.bib", package = "jmpost")`'
 csl: '`r system.file("jss.csl", package = "jmpost")`'
 output:
   rmarkdown::html_vignette: