diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 7fc135d0..24126b3c 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 0.0.1 -Date: 2022-08-22 18:00:32 UTC -SHA: ebf0254a9ce00f29f47458d176b0d7cc5bc9a1d6 +Date: 2022-08-23 12:19:47 UTC +SHA: 35dd46f06b82ff711b23781dc7374723737096df diff --git a/DESCRIPTION b/DESCRIPTION index 9781b2aa..49c405df 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,12 +19,7 @@ Authors@R: c( email = "chris.jackson@mrc-bsu.cam.ac.uk", role = "rev") ) -Description: Fit, interpret, and make predictions with oblique random - survival forests. Oblique decision trees are notoriously slow compared - to their axis based counterparts, but 'aorsf' runs as fast or faster than - axis-based decision tree algorithms for right-censored time-to-event - outcomes. Methods to accelerate and interpret the oblique random survival - forest are described in Jaeger et al., (2022) . +Description: Fit, interpret, and make predictions with oblique random survival forests. Oblique decision trees are notoriously slow compared to their axis based counterparts, but 'aorsf' runs as fast or faster than axis-based decision tree algorithms for right-censored time-to-event outcomes. Methods to accelerate and interpret the oblique random survival forest are described in Jaeger et al., (2022) . License: MIT + file LICENSE Encoding: UTF-8 LazyData: true diff --git a/LICENSE b/LICENSE index 2796da36..fdffc5b5 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2021 -COPYRIGHT HOLDER: orsf2 authors +YEAR: 2022 +COPYRIGHT HOLDER: aorsf authors (Byron C. Jaeger, Sawyer Welden, and Nicholas M. Pajewski) diff --git a/LICENSE.md b/LICENSE.md index bf0b0566..7b8e7f04 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ # MIT License -Copyright (c) 2021 aorsf authors +Copyright (c) 2022 aorsf authors (Byron C. Jaeger, Sawyer Welden, and Nicholas M. Pajewski) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/cran-comments.md b/cran-comments.md index 3e24eec1..eb97d310 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -29,4 +29,16 @@ Updates: Updates: -- the trailing slash on URL's to the arXiv paper was removed. +- the trailing slash on URL's to the arXiv paper was removed in the readme. + +## Revision 3, 2022-08-22 + +Updates: + +- the trailing slash on URL's to the arXiv paper was removed in the aorsf vignette. + +## Revision 4, 2022-08-23 + +- Extra spaces in `DESCRIPTION` removed. + +- `LICENSE` file fixed and names of authors added. diff --git a/man/orsf.Rd b/man/orsf.Rd index 2e5b5b94..089abb09 100644 --- a/man/orsf.Rd +++ b/man/orsf.Rd @@ -291,9 +291,11 @@ library(tidymodels) ## x purrr::discard() masks scales::discard() ## x dplyr::filter() masks stats::filter() ## x dplyr::first() masks aorsf::first() +## x purrr::is_null() masks testthat::is_null() ## x recipes::is_trained() masks aorsf::is_trained() ## x dplyr::lag() masks stats::lag() ## x dplyr::last() masks aorsf::last() +## x tidyr::matches() masks rsample::matches(), dplyr::matches(), testthat::matches() ## x recipes::step() masks stats::step() ## x purrr::transpose() masks aorsf::transpose() ## * Dig deeper into tidy modeling with R at https://www.tmwr.org @@ -308,16 +310,20 @@ library(tidymodels) ## v stringr 1.4.0 ## -- Conflicts ------------------------------------- tidyverse_conflicts() -- -## x dplyr::between() masks aorsf::between() -## x readr::col_factor() masks scales::col_factor() -## x purrr::discard() masks scales::discard() -## x dplyr::filter() masks stats::filter() -## x dplyr::first() masks aorsf::first() -## x stringr::fixed() masks recipes::fixed() -## x dplyr::lag() masks stats::lag() -## x dplyr::last() masks aorsf::last() -## x readr::spec() masks yardstick::spec() -## x purrr::transpose() masks aorsf::transpose() +## x dplyr::between() masks aorsf::between() +## x readr::col_factor() masks scales::col_factor() +## x purrr::discard() masks scales::discard() +## x readr::edition_get() masks testthat::edition_get() +## x dplyr::filter() masks stats::filter() +## x dplyr::first() masks aorsf::first() +## x stringr::fixed() masks recipes::fixed() +## x purrr::is_null() masks testthat::is_null() +## x dplyr::lag() masks stats::lag() +## x dplyr::last() masks aorsf::last() +## x readr::local_edition() masks testthat::local_edition() +## x tidyr::matches() masks rsample::matches(), dplyr::matches(), testthat::matches() +## x readr::spec() masks yardstick::spec() +## x purrr::transpose() masks aorsf::transpose() }\if{html}{\out{}} \if{html}{\out{
}}\preformatted{library(randomForestSRC) @@ -623,29 +629,29 @@ glimpse(results) \if{html}{\out{
}}\preformatted{## Rows: 276 ## Columns: 23 -## $ id 7, 36, 52, 65, 67, 72, 79, 88, 89, 100, 127, 154, 161, 167~ -## $ trt placebo, placebo, d_penicill_main, d_penicill_main, placeb~ -## $ age 55.53457, 56.41068, 50.54073, 40.20260, 51.28816, 32.49281~ -## $ sex f, f, m, f, f, f, f, f, f, m, f, m, f, m, f, f, f, f, f, f~ -## $ ascites 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0~ -## $ hepato 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1~ -## $ spiders 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0~ -## $ edema 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,~ -## $ bili 1.0, 0.3, 6.0, 1.2, 1.1, 0.5, 0.8, 0.6, 2.0, 2.3, 0.5, 2.4~ -## $ chol 322, 172, 614, 256, 466, 320, 315, 296, 408, 178, 268, 168~ -## $ albumin 4.09, 3.39, 3.70, 3.60, 3.91, 3.54, 4.24, 4.06, 3.65, 3.00~ -## $ copper 52, 18, 158, 74, 84, 51, 13, 37, 50, 145, 9, 225, 4, 200, ~ -## $ alk.phos 824.0, 558.0, 5084.4, 724.0, 1787.0, 1243.0, 1637.0, 1032.~ -## $ ast 60.45, 71.30, 206.40, 141.05, 328.60, 122.45, 170.50, 80.6~ -## $ trig 213, 96, 93, 108, 185, 80, 70, 83, 98, 122, 95, 75, 180, 1~ -## $ platelet 204, 311, 362, 430, 261, 225, 426, 442, 200, 119, 453, 108~ -## $ protime 9.7, 10.6, 10.6, 10.0, 10.0, 10.0, 10.9, 12.0, 11.4, 12.0,~ -## $ stage 3, 2, 1, 1, 3, 3, 3, 3, 2, 4, 2, 3, 2, 4, 4, 3, 3, 3, 4, 3~ -## $ time 1832, 3611, 2386, 3992, 2769, 4184, 3707, 2452, 1741, 552,~ -## $ status 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0~ -## $ pred_aorsf 0.14427839, 0.01870334, 0.51377784, 0.04334777, 0.21914657~ -## $ pred_rfsrc 0.14732022, 0.03156261, 0.55773866, 0.06502143, 0.16192547~ -## $ pred_ranger 0.14870388, 0.01662689, 0.57519043, 0.05876898, 0.14884980~ +## $ id 7, 36, 52, 65, 67, 72, 79, 88, 89, 100, 127, 154, 161~ +## $ trt placebo, placebo, d_penicill_main, d_penicill_main, p~ +## $ age 55.53457, 56.41068, 50.54073, 40.20260, 51.28816, 32.~ +## $ sex f, f, m, f, f, f, f, f, f, m, f, m, f, m, f, f, f, f,~ +## $ ascites 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,~ +## $ hepato 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1,~ +## $ spiders 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1,~ +## $ edema 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 1, 0, 0, 0, 0, 0, ~ +## $ bili 1.0, 0.3, 6.0, 1.2, 1.1, 0.5, 0.8, 0.6, 2.0, 2.3, 0.5~ +## $ chol 322, 172, 614, 256, 466, 320, 315, 296, 408, 178, 268~ +## $ albumin 4.09, 3.39, 3.70, 3.60, 3.91, 3.54, 4.24, 4.06, 3.65,~ +## $ copper 52, 18, 158, 74, 84, 51, 13, 37, 50, 145, 9, 225, 4, ~ +## $ alk.phos 824.0, 558.0, 5084.4, 724.0, 1787.0, 1243.0, 1637.0, ~ +## $ ast 60.45, 71.30, 206.40, 141.05, 328.60, 122.45, 170.50,~ +## $ trig 213, 96, 93, 108, 185, 80, 70, 83, 98, 122, 95, 75, 1~ +## $ platelet 204, 311, 362, 430, 261, 225, 426, 442, 200, 119, 453~ +## $ protime 9.7, 10.6, 10.6, 10.0, 10.0, 10.0, 10.9, 12.0, 11.4, ~ +## $ stage 3, 2, 1, 1, 3, 3, 3, 3, 2, 4, 2, 3, 2, 4, 4, 3, 3, 3,~ +## $ time 1832, 3611, 2386, 3992, 2769, 4184, 3707, 2452, 1741,~ +## $ status 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0,~ +## $ pred_aorsf 0.14427839, 0.01870334, 0.51377784, 0.04334777, 0.219~ +## $ pred_rfsrc 0.14732022, 0.03156261, 0.55773866, 0.06502143, 0.161~ +## $ pred_ranger 0.14870388, 0.01662689, 0.57519043, 0.05876898, 0.148~ }\if{html}{\out{
}} And finish by aggregating the predictions and computing performance in @@ -743,5 +749,5 @@ Ishwaran H, Kogalur UB, Blackstone EH, Lauer MS. Random survival forests. \emph{ Jaeger BC, Long DL, Long DM, Sims M, Szychowski JM, Min YI, Mcclure LA, Howard G, Simon N. Oblique random survival forests. \emph{Annals of applied statistics} 2019 Sep; 13(3):1847-83. DOI: 10.1214/19-AOAS1261 -Jaeger BC, Welden S, Lenoir K, Speiser JL, Segar MW, Pandey A, Pajewski NM. Accelerated and interpretable oblique random survival forests. \emph{arXiv e-prints} 2022 Aug; arXiv-2208. URL: https://arxiv.org/abs/2208.01129/ +Jaeger BC, Welden S, Lenoir K, Speiser JL, Segar MW, Pandey A, Pajewski NM. Accelerated and interpretable oblique random survival forests. \emph{arXiv e-prints} 2022 Aug; arXiv-2208. URL: https://arxiv.org/abs/2208.01129 } diff --git a/man/orsf_vi.Rd b/man/orsf_vi.Rd index 48b5d45a..66888204 100644 --- a/man/orsf_vi.Rd +++ b/man/orsf_vi.Rd @@ -156,12 +156,12 @@ To get aggregated values across all levels of each factor, use \if{html}{\out{
}}\preformatted{orsf_vi(fit) }\if{html}{\out{
}} -\if{html}{\out{
}}\preformatted{## ascites bili edema copper age albumin protime -## 0.35528942 0.27837977 0.24719876 0.19605331 0.18822292 0.17033964 0.15320911 -## chol stage spiders ast hepato sex trig -## 0.14883599 0.13627743 0.13495783 0.12754159 0.12057626 0.10669014 0.09723320 -## alk.phos platelet trt -## 0.09183673 0.07599581 0.06846999 +\if{html}{\out{
}}\preformatted{## ascites bili edema copper age albumin +## 0.35528942 0.27837977 0.24719876 0.19605331 0.18822292 0.17033964 +## protime chol stage spiders ast hepato +## 0.15320911 0.14883599 0.13627743 0.13495783 0.12754159 0.12057626 +## sex trig alk.phos platelet trt +## 0.10669014 0.09723320 0.09183673 0.07599581 0.06846999 }\if{html}{\out{
}} } @@ -249,5 +249,5 @@ Breiman L. Random forests. \emph{Machine learning} 2001 Oct; 45(1):5-32. DOI: 10 Menze BH, Kelm BM, Splitthoff DN, Koethe U, Hamprecht FA. On oblique random forests. \emph{Joint European Conference on Machine Learning and Knowledge Discovery in Databases} 2011 Sep 4; pp. 453-469. DOI: 10.1007/978-3-642-23783-6_29 -Jaeger BC, Welden S, Lenoir K, Speiser JL, Segar MW, Pandey A, Pajewski NM. Accelerated and interpretable oblique random survival forests. \emph{arXiv e-prints} 2022 Aug; arXiv-2208. URL: https://arxiv.org/abs/2208.01129/ +Jaeger BC, Welden S, Lenoir K, Speiser JL, Segar MW, Pandey A, Pajewski NM. Accelerated and interpretable oblique random survival forests. \emph{arXiv e-prints} 2022 Aug; arXiv-2208. URL: https://arxiv.org/abs/2208.01129 }