From 8f768240fa9ddbabf9dd00e05b59be5c86a7d72e Mon Sep 17 00:00:00 2001 From: john Date: Wed, 1 Jan 2025 02:04:10 +0200 Subject: [PATCH] remove unused references --- R/bibentries.R | 380 ++----------------------------------------------- 1 file changed, 10 insertions(+), 370 deletions(-) diff --git a/R/bibentries.R b/R/bibentries.R index f747e6ce..990e7714 100644 --- a/R/bibentries.R +++ b/R/bibentries.R @@ -1,26 +1,4 @@ -bibentries = c( # nolint start - aalen_1978 = bibentry("article", - title = "Nonparametric Inference for a Family of Counting Processes", - author = "Odd Aalen", - year = 1978, - journal = "The Annals of Statistics", - publisher = "Institute of Mathematical Statistics", - volume = 6, - number = 4, - pages = "701--726", - url = "https://www.jstor.org/stable/2958850" - ), - begg_2000 = bibentry("article", - title = "Comparing tumour staging and grading systems: a case study and a review of the issues, using thymoma as a model", - author = "Colin B. Begg and Laura D. Cramer and E. S. Venkatraman and Juan Rosai", - year = 2000, - journal = "Statistics in Medicine", - publisher = "Wiley", - volume = 19, - number = 15, - pages = "1997--2014", - doi = "10.1002/1097-0258(20000815)19:15<1997::aid-sim511>3.0.co;2-c" - ), +bibentries = c( breiman_1984 = bibentry("book", title = "Classification And Regression Trees", author = "Leo Breiman and Jerome H. Friedman and Richard A. Olshen and Charles J. Stone", @@ -28,60 +6,6 @@ bibentries = c( # nolint start publisher = "Routledge", doi = "10.1201/9781315139470" ), - 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", - ), - buehlmann_2003 = bibentry("article", - title = "Boosting With the L2 Loss", - author = "Peter B\u00fchlmann and Bin Yu", - year = 2003, - month = "jun", - journal = "Journal of the American Statistical Association", - publisher = "Informa {UK} Limited", - volume = 98, - number = 462, - pages = "324--339", - doi = "10.1198/016214503000125" - ), - buehlmann_2006 = bibentry("article", - title = "Boosting for High-Dimensional Linear Models", - author = "Peter B\u00fchlmann", - year = 2006, - journal = "The Annals of Statistics", - publisher = "Institute of Mathematical Statistics", - volume = 34, - number = 2, - pages = "559--583", - url = "https://www.jstor.org/stable/25463430" - ), - buehlmann_2007 = bibentry("article", - title = "Boosting Algorithms: Regularization, Prediction and Model Fitting", - author = "Peter B\u00fchlmann and Torsten Hothorn", - year = 2007, - month = "nov", - journal = "Statistical Science", - publisher = "Institute of Mathematical Statistics", - volume = 22, - number = 4, - pages = "477--505", - doi = "10.1214/07-sts242" - ), - burges_2010 = bibentry("techreport", - title = "From RankNet to LambdaRank to LambdaMART: An Overview", - author = "Burges, Chris J.C.", - year = 2010, - month = "jun", - number = "MSR-TR-2010-82", - url = "https://www.microsoft.com/en-us/research/publication/from-ranknet-to-lambdarank-to-lambdamart-an-overview/", - institution = "Microsoft Research" - ), chambless_2006 = bibentry("article", title = "Estimation of time-dependent area under the {ROC} curve for long-term risk prediction", author = "Lloyd E. Chambless and Guoqing Diao", @@ -105,82 +29,6 @@ bibentries = c( # nolint start pages = "187--202", doi = "10.1111/j.2517-6161.1972.tb00899.x" ), - freund_1996 = bibentry("inproceedings", - title = "Experiments with a new boosting algorithm", - author = "Freund, Yoav and Schapire, Robert E and others", - year = 1996, - booktitle = "In: Thirteenth International Conference on ML", - volume = 96, - pages = "148--156", - organization = "Citeseer" - ), - freund_1997 = bibentry("article", - title = "A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting", - author = "Yoav Freund and Robert E Schapire", - year = 1997, - month = "aug", - journal = "Journal of Computer and System Sciences", - publisher = "Elsevier {BV}", - volume = 55, - number = 1, - pages = "119--139", - doi = "10.1006/jcss.1997.1504" - ), - friedman_2000 = bibentry("article", - title = "Additive logistic regression: a statistical view of boosting (With discussion and a rejoinder by the authors)", - author = "Jerome Friedman and Trevor Hastie and Robert Tibshirani", - year = 2000, - month = "apr", - journal = "The Annals of Statistics", - publisher = "Institute of Mathematical Statistics", - volume = 28, - number = 2, - pages = "337--407", - doi = "10.1214/aos/1016218223" - ), - friedman_2001 = bibentry("article", - title = "Greedy Function Approximation: A Gradient Boosting Machine", - author = "Jerome H. Friedman", - year = 2001, - journal = "The Annals of Statistics", - publisher = "Institute of Mathematical Statistics", - volume = 29, - number = 5, - pages = "1189--1232", - url = "https://www.jstor.org/stable/2699986" - ), - friedman_2002 = bibentry("article", - title = "Stochastic gradient boosting", - author = "Jerome H. Friedman", - year = 2002, - month = "feb", - journal = "Computational Statistics & Data Analysis", - publisher = "Elsevier {BV}", - volume = 38, - number = 4, - pages = "367--378", - doi = "10.1016/s0167-9473(01)00065-2" - ), - friedman_2010 = bibentry("article", - title = "Regularization Paths for Generalized Linear Models via Coordinate Descent", - author = "Jerome Friedman and Trevor Hastie and Robert Tibshirani", - year = 2010, - journal = "Journal of Statistical Software", - publisher = "Foundation for Open Access Statistic", - volume = 33, - number = 1, - doi = "10.18637/jss.v033.i01" - ), - goeman_2009 = bibentry("article", - title = "L1Penalized Estimation in the Cox Proportional Hazards Model", - author = "Jelle J. Goeman", - year = 2009, - month = "nov", - journal = "Biometrical Journal", - publisher = "Wiley", - pages = "NA--NA", - doi = "10.1002/bimj.200900028" - ), goenen_2005 = bibentry("article", title = "Concordance probability and discriminatory power in proportional hazards regression", author = "Mithat Goenen and Glenn Heller", @@ -215,40 +63,6 @@ bibentries = c( # nolint start number = 18, pages = "2543--2546" ), - hofner_2012 = bibentry("article", - title = "Model-based boosting in R: a hands-on tutorial using the R package mboost", - author = "Benjamin Hofner and Andreas Mayr and Nikolay Robinzonov and Matthias Schmid", - year = 2012, - month = "dec", - journal = "Computational Statistics", - publisher = "Springer Science and Business Media {LLC}", - volume = 29, - number = "1-2", - pages = "3--35", - doi = "10.1007/s00180-012-0382-5" - ), - hothorn_2006 = bibentry("article", - title = "Unbiased Recursive Partitioning: A Conditional Inference Framework", - author = "Torsten Hothorn and Kurt Hornik and Achim Zeileis", - year = 2006, - month = "sep", - journal = "Journal of Computational and Graphical Statistics", - publisher = "Informa {UK} Limited", - volume = 15, - number = 3, - pages = "651--674", - doi = "10.1198/106186006x133933" - ), - hothorn_2010 = bibentry("article", - title = "Model-based boosting 2.0", - author = "Hothorn, Torsten and B\u00fchlmann, Peter and Kneib, Thomas and Schmid, Matthias and Hofner, Benjamin", - year = 2010, - journal = "Journal of Machine Learning Research", - volume = 11, - number = "Aug", - pages = "2109--2113", - url = "https://www.jmlr.org/papers/v11/hothorn10a.html" - ), hung_2010 = bibentry("article", title = "Estimation methods for time-dependent AUC models with survival data", author = "Hung Hung and Chin-Tsang Chiang", @@ -275,7 +89,7 @@ bibentries = c( # nolint start author = "John D. Kalbfleisch and Ross L. Prentice", year = 2002, month = "aug", - publisher = "John Wiley & Sons, Inc.", + publisher = "John Wiley & Sons, Inc.", doi = "10.1002/9781118032985" ), kaplan_1958 = bibentry("article", @@ -290,25 +104,6 @@ bibentries = c( # nolint start pages = "457--481", doi = "10.1080/01621459.1958.10501452" ), - kneib_2008 = bibentry("article", - title = "Variable Selection and Model Choice in Geoadditive Regression Models", - author = "Thomas Kneib and Torsten Hothorn and Gerhard Tutz", - year = 2008, - month = "aug", - journal = "Biometrics", - publisher = "Wiley", - volume = 65, - number = 2, - pages = "626--634", - doi = "10.1111/j.1541-0420.2008.01112.x" - ), - kriegler_2007 = bibentry("phdthesis", - title = "Cost-Sensitive Stochastic Gradient Boosting Within a Quantitative Regression Framework", - author = "Kriegler, Brian", - year = 2007, - url = "https://dl.acm.org/citation.cfm?id=1354603", - school = "University of California at Los Angeles" - ), nagelkerke_1991 = bibentry("article", title = "A note on a general definition of the coefficient of determination", author = "Nagelkerke, Nico JD and others", @@ -319,30 +114,6 @@ bibentries = c( # nolint start number = 3, pages = "691--692" ), - nelson_1969 = bibentry("article", - title = "Hazard Plotting for Incomplete Failure Data", - author = "Wayne Nelson", - year = 1969, - month = "jan", - journal = "Journal of Quality Technology", - publisher = "Informa {UK} Limited", - volume = 1, - number = 1, - pages = "27--52", - doi = "10.1080/00224065.1969.11980344" - ), - nelson_1972 = bibentry("article", - title = "Theory and Applications of Hazard Plotting for Censored Failure Data", - author = "Wayne Nelson", - year = 1972, - month = "nov", - journal = "Technometrics", - publisher = "Informa {UK} Limited", - volume = 14, - number = 4, - pages = "945--966", - doi = "10.1080/00401706.1972.10488991" - ), oquigley_2005 = bibentry("article", title = "Explained randomness in proportional hazards models", author = "John O'Quigley and Ronghui Xu and Janez Stare", @@ -354,37 +125,6 @@ bibentries = c( # nolint start pages = "479--489", doi = "10.1002/sim.1946" ), - ridgeway_1999 = bibentry("article", - title = "The state of boosting", - author = "Ridgeway, Greg", - year = 1999, - journal = "Computing Science and Statistics", - number = 31, - pages = "172--181" - ), - royston_2002 = bibentry("article", - title = "Flexible parametric proportional-hazards and proportional-odds models for censored survival data, with application to prognostic modelling and estimation of treatment effects", - author = "Patrick Royston and Mahesh K. B. Parmar", - year = 2002, - journal = "Statistics in Medicine", - publisher = "Wiley", - volume = 21, - number = 15, - pages = "2175--2197", - doi = "10.1002/sim.1203" - ), - schmid_2008 = bibentry("article", - title = "Boosting additive models using component-wise P-Splines", - author = "Matthias Schmid and Torsten Hothorn", - year = 2008, - month = "dec", - journal = "Computational Statistics & Data Analysis", - publisher = "Elsevier {BV}", - volume = 53, - number = 2, - pages = "298--311", - doi = "10.1016/j.csda.2008.09.009" - ), song_2008 = bibentry("article", title = "A semiparametric approach for the covariate specific ROC curve with survival outcome", author = "Song, Xiao and Zhou, Xiao-Hua", @@ -416,40 +156,6 @@ bibentries = c( # nolint start pages = "n/a--n/a", doi = "10.1002/sim.4154" ), - vanbelle_2010 = bibentry("article", - title = "Improved performance on high-dimensional survival data by application of Survival-{SVM}", - author = "V. Van Belle and K. Pelckmans and S. Van Huffel and J. A. K. Suykens", - year = 2010, - month = "nov", - journal = "Bioinformatics", - publisher = "Oxford University Press ({OUP})", - volume = 27, - number = 1, - pages = "87--94", - doi = "10.1093/bioinformatics/btq617" - ), - vanbelle_2011 = bibentry("article", - title = "Support vector methods for survival analysis: a comparison between ranking and regression approaches", - author = "Vanya Van Belle and Kristiaan Pelckmans and Sabine Van Huffel and Johan A.K. Suykens", - year = 2011, - month = "oct", - journal = "Artificial Intelligence in Medicine", - publisher = "Elsevier {BV}", - volume = 53, - number = 2, - pages = "107--118", - doi = "10.1016/j.artmed.2011.06.006" - ), - wright_2017 = bibentry("article", - title = "ranger: A Fast Implementation of Random Forests for High Dimensional Data in {C++} and {R}", - author = "Wright, Marvin N. and Ziegler, Andreas", - year = 2017, - journal = "Journal of Statistical Software", - volume = 77, - number = 1, - pages = "1--17", - doi = "10.18637/jss.v077.i01" - ), xu_1999 = bibentry("article", title = "A R2 type measure of dependence for proportional hazards models", author = "Ronghui Xu and John O'Quigley", @@ -462,47 +168,16 @@ bibentries = c( # nolint start pages = "83--107", doi = "10.1080/10485259908832799" ), - jaeger_2019 = bibentry("article", - title = "Oblique random survival forests", - volume = "13", - url = "https://projecteuclid.org/euclid.aoas/1571277776", - doi = "10.1214/19-AOAS1261", - language = "EN", - number = "3", - urldate = "2019-10-19", - journal = "The Annals of Applied Statistics", - author = "Jaeger, Byron C. and Long, D. Leann and Long, Dustin M. and Sims, Mario and Szychowski, Jeff M. and Min, Yuan-I. and Mcclure, Leslie A. and Howard, George and Simon, Noah", - month = "sep", - year = "2019", - pages = "1847--1883" - ), silverman_1986 = bibentry("book", address = "London", author = "Silverman, B. W.", biburl = "https://www.bibsonomy.org/bibtex/25c3b630fb0a76da55942a77551fde8a2/pierpaolo.pk81", - description = "WSD", + description = "WSD", publisher = "Chapman & Hall", timestamp = "2007-02-27T16:22:14.000+0100", title = "Density Estimation for Statistics and Data Analysis", year = 1986 ), - chen_2016 = bibentry("article", - title = "{XGBoost}: {A} {Scalable} {Tree} {Boosting} {System}", - url = "https://arxiv.org/abs/1603.02754", - journal = "Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '16", - author = "Chen, Tianqi and Guestrin, Carlos", - year = "2016", - note = "arXiv: 1603.02754", - pages = "785--794" - ), - binder_2009 = bibentry("article", - author = "Binder, H. and Allignol, A. and Schumacher, M. and Beyersmann, J.", - year = "2009", - title = "Boosting for high-dimensional time-to-event data with competing risks", - journal = "Bioinformatics", - pages = "890--896", - volume = "25" - ), schemper_2000 = bibentry("article", author = "Schemper, Michael and Henderson, Robin", doi = "10.1002/sim.1486", @@ -567,18 +242,6 @@ bibentries = c( # nolint start volume = "61", year = "2016" ), - jackson_2014 = bibentry("article", - author = "Jackson, Dan and White, Ian R. and Seaman, Shaun and Evans, Hannah and Baisley, Kathy and Carpenter, James", - doi = "10.1002/sim.6274", - journal = "Statistics in Medicine", - month = "nov", - number = "27", - pages = "4681--4694", - publisher = "John Wiley and Sons Ltd", - title = "Relaxing the independent censoring assumption in the Cox proportional hazards model using multiple imputation", - volume = "33", - year = "2014" - ), klein_2003 = bibentry("book", author = "Klein, John P and Moeschberger, Melvin L", edition = "2", @@ -587,19 +250,6 @@ bibentries = c( # nolint start title = "Survival analysis: techniques for censored and truncated data", year = "2003" ), - buckley_1979 = bibentry("article", - author = "Buckley, Jonathan and James, Ian", - doi = "10.2307/2335161", - journal = "Biometrika", - month = "apr", - number = "3", - pages = "429--436", - publisher = "Oxford University Press, Biometrika Trust", - title = "Linear Regression with Censored Data", - url = "https://www.jstor.org/stable/2335161", - volume = "66", - year = "1979" - ), haider_2020 = bibentry("article", author = "Haider, Humza and Hoehn, Bret and Davis, Sarah and Greiner, Russell", journal = "Journal of Machine Learning Research", @@ -610,16 +260,6 @@ bibentries = c( # nolint start url = "https://jmlr.org/papers/v21/18-772.html", year = "2020" ), - dcalib = bibentry("article", - author = "Humza Haider and Bret Hoehn and Sarah Davis and Russell Greiner", - title = "Effective Ways to Build and Evaluate Individual Survival Distributions", - journal = "Journal of Machine Learning Research", - year = "2020", - volume = "21", - number = "85", - pages = "1-63", - url = "https://jmlr.org/papers/v21/18-772.html" - ), breslow_1972 = bibentry("article", author = "Norman Breslow", title = "Discussion of 'Regression Models and Life-Tables' by D.R. Cox", @@ -676,13 +316,13 @@ bibentries = c( # nolint start url = "https://doi.org/10.1093/biomet/81.3.515" ), tutz_2016 = bibentry("book", - author = "Tutz, Gerhard and Schmid, Matthias", - title = "Modeling Discrete Time-to-Event Data", - year = "2016", - publisher = "Springer International Publishing", - series = "Springer Series in Statistics", - isbn = "978-3-319-28156-8 978-3-319-28158-2", - url = "http://link.springer.com/10.1007/978-3-319-28158-2" + author = "Tutz, Gerhard and Schmid, Matthias", + title = "Modeling Discrete Time-to-Event Data", + year = "2016", + publisher = "Springer International Publishing", + series = "Springer Series in Statistics", + isbn = "978-3-319-28156-8 978-3-319-28158-2", + url = "http://link.springer.com/10.1007/978-3-319-28158-2" ), sonabend_2022 = bibentry("article", author = "Sonabend, Raphael and Bender, Andreas and Vollmer, Sebastian",