rework refs

ropensci · Jan 10, 2024 · 9d2d565 · 9d2d565
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diff --git a/R/bibentries.R b/R/bibentries.R
@@ -0,0 +1,127 @@
+# nocov start
+
+cite = function(entry){
+
+ out <- switch(
+  entry,
+  breiman_2001 = bibentry(
+   "article",
+   title       = "Random Forests",
+   author      = "Breiman, Leo",
+   year        = "2001",
+   journal     = "Machine Learning",
+   volume      = "45",
+   number      = "1",
+   pages       = "5--32",
+   doi         = "10.1023/A:1010933404324",
+   issn        = "1573-0565"
+  ),
+  ishwaran_2008 = bibentry(
+   "article",
+   doi         = "10.1214/08-aoas169",
+   url         = "https://doi.org/10.1214/08-aoas169",
+   year        = "2008",
+   month       = "9",
+   publisher   = "Institute of Mathematical Statistics",
+   volume      = "2",
+   number      = "3",
+   author      = "Hemant Ishwaran and Udaya B. Kogalur and Eugene H. Blackstone and Michael S. Lauer",
+   title       = "Random survival forests",
+   journal     = "The Annals of Applied Statistics"
+  ),
+  jaeger_2019 = bibentry(
+   "article",
+   doi           = "10.1214/19-aoas1261",
+   year          = "2019",
+   month         = "9",
+   publisher     = "Institute of Mathematical Statistics",
+   volume        = "13",
+   number        = "3",
+   author        = "Byron C. Jaeger and D. Leann Long and Dustin M. Long and Mario Sims and Jeff M. Szychowski and Yuan-I Min and Leslie A. Mcclure and George Howard and Noah Simon",
+   title         = "Oblique random survival forests",
+   journal       = "The Annals of Applied Statistics"
+  ),
+  jaeger_2022 = bibentry(
+   "article",
+   title         = "Accelerated and interpretable oblique random survival forests",
+   author        = "Byron C. Jaeger and Sawyer Welden and Kristin Lenoir and Jaime L. Speiser and Matthew W. Segar and Ambarish Pandey and Nicholas M. Pajewski",
+   journal       = "Journal of Computational and Graphical Statistics",
+   doi           = "10.1080/10618600.2023.2231048",
+   year          = "2023",
+   month         = "8",
+   publisher     = "Taylor & Francis",
+   pages         = "1--16"
+  ),
+  hooker_2021 = bibentry(
+   "article",
+   title     = "Unrestricted permutation forces extrapolation: variable importance requires at least one more model, or there is no free variable importance",
+   author    = "Hooker, Giles and Mentch, Lucas and Zhou, Siyu",
+   journal   = "Statistics and Computing",
+   volume    = "31",
+   pages     = "1--16",
+   year      = "2021",
+   publisher = "Springer"
+  ),
+  harrell_1982 = bibentry(
+   "article",
+   title     = "Evaluating the yield of medical tests",
+   author    = "Harrell, Frank E and Califf, Robert M and Pryor, David B and Lee, Kerry L and Rosati, Robert A",
+   journal   = "Jama",
+   volume    = "247",
+   number    = "18",
+   pages     = "2543--2546",
+   year      = "1982",
+   publisher ="American Medical Association"
+  ),
+  menze_2011 = bibentry(
+   "inproceedings",
+   title        = "On oblique random forests",
+   author       = "Menze, Bjoern H and Kelm, B Michael and Splitthoff, Daniel N and Koethe, Ullrich and Hamprecht, Fred A",
+   booktitle    = "Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD 2011, Athens, Greece, September 5-9, 2011, Proceedings, Part II 22",
+   pages        = "453--469",
+   year         = "2011",
+   organization = "Springer"
+  ),
+  simon_2011 = bibentry(
+   "article",
+   title     = "Regularization paths for Cox’s proportional hazards model via coordinate descent",
+   author    = "Simon, Noah and Friedman, Jerome and Hastie, Trevor and Tibshirani, Rob",
+   journal   = "Journal of statistical software",
+   volume    = "39",
+   number    = "5",
+   pages     = "1",
+   year      = "2011",
+   publisher = "NIH Public Access"
+  ),
+  horst_2022 = bibentry(
+   "article",
+   title   = "Palmer Archipelago Penguins Data in the palmerpenguins R Package-An Alternative to Anderson's Irises",
+   author  = "Horst, Allison M and Hill, Alison Presmanes and Gorman, Kristen B",
+   journal = "R Journal",
+   volume  = "14",
+   number  = "1",
+   year    = "2022"
+  ),
+  penguins_2020 = bibentry(
+   "manual",
+   title  = "palmerpenguins: Palmer Archipelago (Antarctica) penguin data",
+   author = "Allison Marie Horst and Alison Presmanes Hill and Kristen B Gorman",
+   year   = "2020",
+   note   = "R package version 0.1.0",
+   url    = "https://allisonhorst.github.io/palmerpenguins/"
+  ),
+  greenwell_2018 = bibentry(
+   "article",
+   title   = "A simple and effective model-based variable importance measure",
+   author  = "Greenwell, Brandon M and Boehmke, Bradley C and McCarthy, Andrew J",
+   journal = "arXiv preprint arXiv:1805.04755",
+   year    = "2018"
+  ),
+  stop("unrecognized entry")
+ )
+
+ format(out)
+
+}
+
+# nocov end
diff --git a/R/orsf.R b/R/orsf.R
@@ -301,23 +301,20 @@
 #'
 #' @references
 #'
-#' `r roxy_cite_harrell_1982()`
-#'
-#' `r roxy_cite_breiman_2001()`
-#'
-#' `r roxy_cite_ishwaran_2008()`
-#'
-#' `r roxy_cite_menze_2011()`
-#'
-#' `r roxy_cite_jaeger_2019()`
-#'
-#' `r roxy_cite_jaeger_2023()`
+#' 1. `r cite("harrell_1982")`
+#' 1. `r cite("breiman_2001")`
+#' 1. `r cite("ishwaran_2008")`
+#' 1. `r cite("menze_2011")`
+#' 1. `r cite("jaeger_2019")`
+#' 1. `r cite("jaeger_2022")`
 #'
 #' @includeRmd Rmd/orsf_examples.Rmd
 #'
 #' @export
 #'
 
+
+
 orsf <- function(data,
                  formula,
                  control = NULL,

diff --git a/R/orsf_control.R b/R/orsf_control.R
@@ -174,7 +174,7 @@ orsf_control_cph <- function(method = 'efron',
 #'
 #' @references
 #'
-#' `r roxy_cite_simon_2011()`
+#' 1. `r cite("simon_2011")`
 #'
 
 orsf_control_net <- function(alpha = 1/2,

diff --git a/R/orsf_pd.R b/R/orsf_pd.R
@@ -121,7 +121,7 @@ pred_spec_auto <- function(...){
 #'
 #' @references
 #'
-#' `r roxy_cite_hooker_2021()`
+#' 1. `r cite("hooker_2021")`
 #'
 #' @includeRmd Rmd/orsf_pd_examples.Rmd
 #'

diff --git a/R/orsf_vi.R b/R/orsf_vi.R
@@ -69,14 +69,10 @@
 #'
 #' @references
 #'
-#'
-#' `r roxy_cite_harrell_1982()`
-#'
-#' `r roxy_cite_breiman_2001()`
-#'
-#' `r roxy_cite_menze_2011()`
-#'
-#' `r roxy_cite_jaeger_2023()`
+#' 1. `r cite("harrell_1982")`
+#' 1. `r cite("breiman_2001")`
+#' 1. `r cite("menze_2011")`
+#' 1. `r cite("jaeger_2022")`
 #'
 #'
 orsf_vi <- function(object,

diff --git a/R/orsf_vint.R b/R/orsf_vint.R
@@ -34,7 +34,7 @@
 #'
 #' @references
 #'
-#' `r roxy_cite_greenwell_2018()`
+#' 1. `r cite("greenwell_2018")`
 #'
 #' @examples
 #'

diff --git a/R/roxy.R b/R/roxy.R
@@ -138,166 +138,6 @@ roxy_na_action_impute_meanmode <- function(data_label){
 }
 
 
-# citations ---------------------------------------------------------------
-
-
-
-roxy_cite <- function(authors,
-                      title,
-                      journal = NULL,
-                      date,
-                      number=NULL,
-                      doi=NULL,
-                      url=NULL){
-
- if(!is.null(number)) number <- paste0('; ', number)
- if(!is.null(doi)) doi <- paste(" DOI:", doi)
- if(!is.null(url)) url <- paste(" URL:", url)
- if(!is.null(journal)) journal <- paste0('*', journal, '*. ')
-
- ending <- paste(c(doi, url), collapse = '.')
-
- paste0(
-  authors, '. ',
-  title, '. ',
-  journal,
-  date,
-  number, '.',
-  ending
- )
-}
-
-roxy_cite_breiman_2001 <- function(){
-
- roxy_cite(
-  authors = "Breiman L",
-  title = "Random forests",
-  journal = "Machine learning",
-  date = "2001 Oct",
-  number = "45(1):5-32",
-  doi = "10.1023/A:1010933404324"
- )
-
-}
-
-roxy_cite_ishwaran_2008 <- function(){
-
- roxy_cite(
-  authors = "Ishwaran H, Kogalur UB, Blackstone EH, Lauer MS",
-  title = "Random survival forests",
-  journal = "Annals of applied statistics",
-  date = "2008 Sep",
-  number = "2(3):841-60",
-  doi = "10.1214/08-AOAS169"
- )
-
-}
-
-roxy_cite_jaeger_2019 <- function(){
-
- roxy_cite(
-  authors = "Jaeger BC, Long DL, Long DM, Sims M, Szychowski JM, Min YI, Mcclure LA, Howard G, Simon N",
-  title = "Oblique random survival forests",
-  journal = "Annals of applied statistics",
-  date = "2019 Sep",
-  number = "13(3):1847-83",
-  doi = "10.1214/19-AOAS1261"
- )
-
-}
-
-roxy_cite_jaeger_2023 <- function(){
-
- roxy_cite(
-  authors = "Jaeger BC, Welden S, Lenoir K, Speiser JL, Segar MW, Pandey A, Pajewski NM",
-  title = "Accelerated and interpretable oblique random survival forests",
-  journal = "Journal of Computational and Graphical Statistics",
-  date = "Published online 08 Aug 2023",
-  number = NULL,
-  doi = "10.1080/10618600"
- )
-
-}
-
-roxy_cite_hooker_2021 <- function(){
-
- roxy_cite(
-  authors = "Giles Hooker, Lucas Mentch, Siyu Zhou",
-  title = "Unrestricted Permutation forces Extrapolation: Variable Importance Requires at least One More Model, or There Is No Free Variable Importance",
-  journal = "arXiv e-prints",
-  date = "2021 Oct",
-  number = 'arXiv-1905',
-  url = "https://doi.org/10.48550/arXiv.1905.03151"
- )
-
-}
-
-roxy_cite_harrell_1982 <- function(){
-
- roxy_cite(
-  authors = "Harrell FE, Califf RM, Pryor DB, Lee KL, Rosati RA",
-  title = "Evaluating the Yield of Medical Tests",
-  journal = "JAMA",
-  date = "1982",
-  number = '247(18):2543-2546',
-  doi = "10.1001/jama.1982.03320430047030"
- )
-
-}
-
-roxy_cite_menze_2011 <- function(){
-
- roxy_cite(
-  authors = "Menze BH, Kelm BM, Splitthoff DN, Koethe U, Hamprecht FA",
-  title = "On oblique random forests",
-  journal = "Joint European Conference on Machine Learning and Knowledge Discovery in Databases",
-  date = "2011 Sep 4",
-  number = 'pp. 453-469',
-  doi = "10.1007/978-3-642-23783-6_29"
- )
-
-}
-
-roxy_cite_simon_2011 <- function(){
-
- roxy_cite(
-  authors = "Simon N, Friedman J, Hastie T, Tibshirani R",
-  title = "Regularization paths for Cox's proportional hazards model via coordinate descent",
-  journal = "Journal of statistical software",
-  date = "2011 Mar",
-  number = '39(5):1',
-  doi = "10.18637/jss.v039.i05"
- )
-
-}
-
-roxy_cite_penguins <- function(){
-
- roxy_cite(
-  authors = "Horst AM, Hill AP, Gorman KB",
-  title = "palmerpenguins: Palmer Archipelago (Antarctica) penguin data. R package version 0.1.0",
-  date = "2020",
-  doi = "10.5281/zenodo.3960218"
- )
-
-}
-
-roxy_cite_greenwell_2018 <- function(){
-
- roxy_cite(
-  authors = "Greenwell BM, Boehmke BC, McCarthy AJ",
-  title = "A simple and effective model-based variable importance measure",
-  journal = "arXiv e-prints",
-  date = "2018 May 12",
-  number = 'arXiv:1805.04755',
-  url = "https://doi.org/10.48550/arXiv.1805.04755"
-
- )
-
-}
-
-
-
 # ... ---------------------------------------------------------------------
 
 roxy_dots <- function(){

diff --git a/README.Rmd b/README.Rmd
@@ -294,19 +294,12 @@ For survival analysis, comparisons between `aorsf` and existing software are pre
 
 ## References
 
-```{r results='asis', echo=FALSE}
+1. `r aorsf:::cite("jaeger_2019")`
+1. `r aorsf:::cite("jaeger_2022")`
+1. `r aorsf:::cite("penguins_2020")`
+1. `r aorsf:::cite("menze_2011")`
+1. `r aorsf:::cite("greenwell_2018")`
 
-cat("1. ", aorsf:::roxy_cite_jaeger_2019(), '\n\n')
-
-cat("2. ", aorsf:::roxy_cite_jaeger_2023(), '\n\n')
-
-cat("3. ", aorsf:::roxy_cite_penguins(),  '\n\n')
-
-cat("4. ", aorsf:::roxy_cite_menze_2011(), '\n\n')
-
-cat("5. ", aorsf:::roxy_cite_greenwell_2018())
-
-```
 
 
 ## Funding