diff --git a/README.Rmd b/README.Rmd index c043206d..8c3f4f29 100644 --- a/README.Rmd +++ b/README.Rmd @@ -28,7 +28,7 @@ knitr::opts_chunk$set( [![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/532_status.svg)](https://github.com/ropensci/software-review/issues/532/) [![CRAN status](https://www.r-pkg.org/badges/version/aorsf)](https://CRAN.R-project.org/package=aorsf) -[![DOI](https://zenodo.org/badge/394311897.svg)](https://zenodo.org/badge/latestdoi/394311897) +[![DOI](https://zenodo.org/badge/394311897.svg)](https://zenodo.org/doi/10.5281/zenodo.7116854) Fit, interpret, and make predictions with oblique random survival forests (ORSFs). diff --git a/README.md b/README.md index 56d46957..79e8b3e6 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ Review](https://badges.ropensci.org/532_status.svg)](https://github.com/ropensci [![CRAN status](https://www.r-pkg.org/badges/version/aorsf)](https://CRAN.R-project.org/package=aorsf) -[![DOI](https://zenodo.org/badge/394311897.svg)](https://zenodo.org/badge/latestdoi/394311897) +[![DOI](https://zenodo.org/badge/394311897.svg)](https://zenodo.org/doi/10.5281/zenodo.7116854) Fit, interpret, and make predictions with oblique random survival @@ -113,7 +113,7 @@ fit #> N trees: 500 #> N predictors total: 17 #> N predictors per node: 5 -#> Average leaves per tree: 12 +#> Average leaves per tree: 10 #> Min observations in leaf: 5 #> Min events in leaf: 1 #> OOB stat value: 0.83 @@ -144,21 +144,20 @@ using `aorsf`: important the variable. This technique is promising b/c it does not require permutation and it emphasizes variables with larger coefficients in linear combinations, but it is also relatively new and - hasn’t been studied as much as permutation importance. See [Jaeger, - 2023](https://doi.org/10.1080/10618600.2023.2231048) for more details - on this technique. + hasn’t been studied as much as permutation importance. See + Jaeger, (2023) for more details on this technique. ``` r orsf_vi_negate(fit) - #> bili sex copper ast age - #> 0.1190290560 0.0619448918 0.0290622719 0.0260108174 0.0251263919 - #> stage protime edema ascites hepato - #> 0.0237725455 0.0158527871 0.0117258458 0.0105685230 0.0092045115 - #> albumin chol trt alk.phos spiders - #> 0.0082732463 0.0041510636 0.0036632967 0.0010256161 -0.0003298163 - #> trig platelet - #> -0.0011060747 -0.0045517701 + #> bili sex copper stage age + #> 0.1162463868 0.0517905362 0.0375565841 0.0240450064 0.0239056901 + #> ast protime hepato edema ascites + #> 0.0191083400 0.0158014897 0.0139536512 0.0119264604 0.0100865906 + #> albumin chol spiders trt trig + #> 0.0085394443 0.0037903802 0.0030727468 0.0020617896 0.0018361632 + #> alk.phos platelet + #> 0.0006586211 -0.0044967624 ``` - **permutation**: Each variable is assessed separately by randomly @@ -172,14 +171,14 @@ using `aorsf`: ``` r orsf_vi_permute(fit) - #> bili copper ast age sex - #> 0.0514033622 0.0170611427 0.0142515581 0.0140224052 0.0131459748 - #> stage protime ascites edema albumin - #> 0.0119768965 0.0102950158 0.0098067817 0.0081730899 0.0080652857 - #> hepato chol alk.phos trig spiders - #> 0.0069734562 0.0032811220 0.0015862128 0.0014943484 0.0007825752 + #> bili copper age stage sex + #> 0.0523994364 0.0187964038 0.0152246586 0.0115192591 0.0110127557 + #> ast hepato edema ascites albumin + #> 0.0100104477 0.0082889176 0.0079183046 0.0077834483 0.0070642325 + #> protime trig chol spiders alk.phos + #> 0.0066513097 0.0015656325 0.0014474560 0.0006015308 0.0001369292 #> trt platelet - #> -0.0007067631 -0.0022338286 + #> -0.0013984860 -0.0022427356 ``` - **analysis of variance (ANOVA)**3: A p-value is computed @@ -195,12 +194,12 @@ using `aorsf`: ``` r orsf_vi_anova(fit) - #> ascites bili edema sex copper age ast - #> 0.39107612 0.36316990 0.36316238 0.24720893 0.20547180 0.19213732 0.19029233 - #> albumin stage hepato trig chol protime alk.phos - #> 0.17219680 0.17068758 0.16126761 0.13379872 0.12964021 0.12659698 0.12352611 - #> spiders platelet trt - #> 0.11728395 0.08997135 0.07305095 + #> bili ascites edema copper stage sex age + #> 0.48778004 0.44943820 0.41677872 0.31865585 0.26675095 0.26458616 0.25448430 + #> ast hepato albumin chol protime trig spiders + #> 0.21743929 0.19945726 0.18191604 0.15240328 0.15076561 0.13709677 0.11833550 + #> alk.phos platelet trt + #> 0.10113636 0.06302021 0.05019305 ``` You can supply your own R function to estimate out-of-bag error when @@ -222,20 +221,20 @@ variables as you ask it to, using sensible values. orsf_summarize_uni(fit, n_variables = 2) #> -#> -- bili (VI Rank: 1) ---------------------------- +#> -- bili (VI Rank: 1) --------------------------- #> -#> |----------------- Risk -----------------| -#> Value Mean Median 25th % 75th % -#> 0.70 0.2094827 0.09046313 0.03827429 0.3184979 -#> 1.3 0.2283358 0.11078307 0.05347112 0.3492104 -#> 3.2 0.3090977 0.21368937 0.11889617 0.4412656 +#> |---------------- Risk ----------------| +#> Value Mean Median 25th % 75th % +#> 0.70 0.1986719 0.1044026 0.04354701 0.2968290 +#> 1.3 0.2132847 0.1210276 0.05245387 0.3208855 +#> 3.2 0.2883814 0.1917119 0.11951296 0.4147258 #> -#> -- sex (VI Rank: 2) ----------------------------- +#> -- sex (VI Rank: 2) ---------------------------- #> -#> |----------------- Risk -----------------| +#> |---------------- Risk ----------------| #> Value Mean Median 25th % 75th % -#> m 0.3667488 0.2614335 0.15611841 0.5836574 -#> f 0.2507675 0.1051310 0.04355687 0.3596206 +#> m 0.3394141 0.2313787 0.13762339 0.5311308 +#> f 0.2390067 0.1112093 0.04782891 0.3773551 #> #> Predicted risk at time t = 1826.25 for top 2 predictors ``` @@ -288,8 +287,7 @@ examples](https://docs.ropensci.org/aorsf/reference/orsf.html#tidymodels) 2. Jaeger BC, Welden S, Lenoir K, Speiser JL, Segar MW, Pandey A, Pajewski NM. Accelerated and interpretable oblique random survival forests. *Journal of Computational and Graphical Statistics* - Published online 08 Aug 2023. URL: - + Published online 08 Aug 2023. DOI: 10.1080/10618600.2023.2231048 3. Menze BH, Kelm BM, Splitthoff DN, Koethe U, Hamprecht FA. On oblique random forests. *Joint European Conference on Machine Learning and diff --git a/cran-comments.md b/cran-comments.md index 7ae11bdd..56b56f58 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,7 @@ ## Version 0.1.1 +This version is being submitted to CRAN early due to a memory error that was identified in version 1.0.0. I apologize for the oversight. As `aorsf` would be removed from CRAN if the issue is not fixed before October 28, I would like to request an expedited submission. I have run the current submission's tests and examples with valgrind to ensure the memory error has been fixed. + ## R CMD check results Duration: 4m 8.3s