From 11ed7a659e445566d6a45a16ec4cec85674369b8 Mon Sep 17 00:00:00 2001 From: byron jaeger Date: Sat, 25 Nov 2023 13:46:01 -0500 Subject: [PATCH] fix yaml, edit for brevity --- README.Rmd | 4 +-- README.md | 84 ++++++++++++++++++++++++---------------------------- _pkgdown.yml | 1 + 3 files changed, 41 insertions(+), 48 deletions(-) diff --git a/README.Rmd b/README.Rmd index ae8e4479..fc14eb86 100644 --- a/README.Rmd +++ b/README.Rmd @@ -62,9 +62,7 @@ remotes::install_github("ropensci/aorsf") ## What is an oblique decision tree? -Decision trees are developed by splitting a set of training data into two new subsets, with the goal of having more similarity within the new subsets than between them. The splitting process is repeated on resulting subsets of data until a stopping criterion is met. - -When the new subsets of data are formed based on a single predictor, the decision tree is said to be *axis-based* because the splits of the data appear perpendicular to the axis of the predictor. When linear combinations of variables are used instead of a single variable, the tree is *oblique* because the splits of the data are neither parallel nor at a right angle to the axis. +Decision trees are grown by splitting a set of training data into non-overlapping subsets, with the goal of having more similarity within the new subsets than between them. When subsets are created with a single predictor, the decision tree is *axis-based* because the subset boundaries are perpendicular to the axis of the predictor. When linear combinations (i.e., a weighted sum) of variables are used instead of a single variable, the tree is *oblique* because the boundaries are neither parallel nor perpendicular to the axis. **Figure**: Decision trees for classification with axis-based splitting (left) and oblique splitting (right). Cases are orange squares; controls are purple circles. Both trees partition the predictor space defined by variables X1 and X2, but the oblique splits do a better job of separating the two classes. diff --git a/README.md b/README.md index 4b0e3e62..174753f7 100644 --- a/README.md +++ b/README.md @@ -52,17 +52,14 @@ remotes::install_github("ropensci/aorsf") ## What is an oblique decision tree? -Decision trees are developed by splitting a set of training data into -two new subsets, with the goal of having more similarity within the new -subsets than between them. The splitting process is repeated on -resulting subsets of data until a stopping criterion is met. - -When the new subsets of data are formed based on a single predictor, the -decision tree is said to be *axis-based* because the splits of the data -appear perpendicular to the axis of the predictor. When linear -combinations of variables are used instead of a single variable, the -tree is *oblique* because the splits of the data are neither parallel -nor at a right angle to the axis. +Decision trees are grown by splitting a set of training data into +non-overlapping subsets, with the goal of having more similarity within +the new subsets than between them. When subsets are created with a +single predictor, the decision tree is *axis-based* because the subset +boundaries are perpendicular to the axis of the predictor. When linear +combinations (i.e., a weighted sum) of variables are used instead of a +single variable, the tree is *oblique* because the boundaries are +neither parallel nor perpendicular to the axis. **Figure**: Decision trees for classification with axis-based splitting (left) and oblique splitting (right). Cases are orange squares; controls @@ -112,10 +109,10 @@ fit #> N trees: 500 #> N predictors total: 17 #> N predictors per node: 5 -#> Average leaves per tree: 10.198 +#> Average leaves per tree: 10.238 #> Min observations in leaf: 5 #> Min events in leaf: 1 -#> OOB stat value: 0.84 +#> OOB stat value: 0.83 #> OOB stat type: Harrell's C-index #> Variable importance: anova #> @@ -149,14 +146,12 @@ using `aorsf`: ``` r orsf_vi_negate(fit) - #> bili sex copper stage age - #> 0.1152040355 0.0550384871 0.0346540451 0.0342394602 0.0212811906 - #> ast protime hepato chol albumin - #> 0.0189147173 0.0179113542 0.0151705980 0.0111316204 0.0107352274 - #> edema ascites spiders trig alk.phos - #> 0.0101276579 0.0097629480 0.0043991365 0.0031611867 0.0030722039 - #> trt platelet - #> 0.0024625381 -0.0005569787 + #> bili sex copper stage age ast + #> 0.117180683 0.058528338 0.033761789 0.026655509 0.022144911 0.019139095 + #> protime hepato edema ascites albumin chol + #> 0.016879701 0.011605852 0.010634489 0.009580159 0.008336260 0.007633992 + #> trt spiders alk.phos trig platelet + #> 0.002705027 0.002662017 0.002413369 0.001197399 -0.003386483 ``` - **permutation**: Each variable is assessed separately by randomly @@ -170,14 +165,12 @@ using `aorsf`: ``` r orsf_vi_permute(fit) - #> bili stage copper age sex - #> 0.0487808290 0.0180334035 0.0178325263 0.0124277288 0.0111897854 - #> ast hepato edema protime ascites - #> 0.0111084077 0.0095618267 0.0082559886 0.0082473977 0.0078725536 - #> albumin chol spiders alk.phos trig - #> 0.0073437819 0.0057881417 0.0033941136 0.0028194077 0.0019933887 - #> platelet trt - #> -0.0002101522 -0.0016860907 + #> bili copper age stage sex ast + #> 0.050536719 0.016394807 0.013793348 0.013204760 0.010261860 0.010101841 + #> edema ascites protime albumin hepato chol + #> 0.008298456 0.008148291 0.007630773 0.006667768 0.006141770 0.002881687 + #> spiders trig alk.phos platelet trt + #> 0.001669604 0.001047642 -0.000301684 -0.001417230 -0.001665785 ``` - **analysis of variance (ANOVA)**3: A p-value is computed @@ -193,12 +186,12 @@ using `aorsf`: ``` r orsf_vi_anova(fit) - #> bili ascites edema sex copper stage age - #> 0.48004315 0.43536122 0.38654727 0.31024531 0.29493088 0.27168950 0.26673985 - #> hepato ast albumin protime chol spiders trig - #> 0.21492921 0.20151679 0.18771331 0.18352060 0.14617169 0.13932292 0.13620489 - #> alk.phos platelet trt - #> 0.09051254 0.07011494 0.06179067 + #> bili copper age stage sex ast + #> 0.050536719 0.016394807 0.013793348 0.013204760 0.010261860 0.010101841 + #> edema ascites protime albumin hepato chol + #> 0.008298456 0.008148291 0.007630773 0.006667768 0.006141770 0.002881687 + #> spiders trig alk.phos platelet trt + #> 0.001669604 0.001047642 -0.000301684 -0.001417230 -0.001665785 ``` You can supply your own R function to estimate out-of-bag error when @@ -224,16 +217,17 @@ orsf_summarize_uni(fit, n_variables = 2) #> #> |---------------- Risk ----------------| #> Value Mean Median 25th % 75th % -#> 0.70 0.2099215 0.1262483 0.05057666 0.3160044 -#> 1.30 0.2244830 0.1472311 0.06196578 0.3369922 -#> 3.18 0.2932736 0.2263620 0.11896921 0.4424589 +#> 0.70 0.2043124 0.1288782 0.05502854 0.3130744 +#> 1.30 0.2193531 0.1430383 0.06680735 0.3352729 +#> 3.18 0.2835984 0.2210419 0.12363028 0.4313679 #> -#> -- ascites (VI Rank: 2) ------------------------ +#> -- copper (VI Rank: 2) ------------------------- #> #> |---------------- Risk ----------------| -#> Value Mean Median 25th % 75th % -#> 0 0.2630294 0.1490837 0.0613327 0.4186542 -#> 1 0.3924844 0.3053928 0.2222267 0.5253717 +#> Value Mean Median 25th % 75th % +#> 39.0 0.2308500 0.1358346 0.05536305 0.3575617 +#> 68.0 0.2415171 0.1482876 0.06189812 0.3682164 +#> 111 0.2725110 0.1846062 0.08723814 0.4047750 #> #> Predicted risk at time t = 1826.25 for top 2 predictors ``` @@ -266,7 +260,7 @@ Comparisons between `aorsf` and existing software are presented in our learners. - runs a simulation study comparing variable importance techniques with - ORSFs, axis based RSFs, and boosted trees. + oblique survival RFs, axis based survival RFs, and boosted trees. - reports the probability that each variable importance technique will rank a relevant variable with higher importance than an irrelevant @@ -295,9 +289,9 @@ examples](https://docs.ropensci.org/aorsf/reference/orsf.html#tidymodels) ## Funding -The developers of `aorsf` receive financial support from the Center for +The developers of `aorsf` received financial support from the Center for Biomedical Informatics, Wake Forest University School of Medicine. We -also receive support from the National Center for Advancing +also received support from the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1TR001420. diff --git a/_pkgdown.yml b/_pkgdown.yml index 7cdc31bf..463524df 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -42,6 +42,7 @@ reference: - contents: - matches("^orsf_ice") - matches("^orsf_pd") + - matches("^pred_spec") - title: Example survival data desc: Datasets used in examples and vignettes. - contents: