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mlr-org / mlr3extralearners

Extra learners for use in mlr3.
https://mlr3extralearners.mlr-org.com/
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Error: Element with key 'surv.bart' not found in DictionaryLearner! Did you mean 'surv.parametric' / 'surv.rpart'? #346

Closed Kuroshiwo closed 6 months ago

Kuroshiwo commented 6 months ago

Description

I wanted to train a BART model but it is not in the DictionaryLearner.

lrn()

with 103 stored values Keys: classif.abess, classif.AdaBoostM1, classif.bart, classif.C50, classif.cforest, classif.ctree, classif.debug, classif.earth, classif.featureless, classif.fnn, classif.gam, classif.gamboost, classif.gausspr, classif.gbm, classif.glmboost, classif.glmer, classif.IBk, classif.imbalanced_rfsrc, classif.J48, classif.JRip, classif.ksvm, classif.liblinear, classif.lightgbm, classif.LMT, classif.lssvm, classif.mob, classif.OneR, classif.PART, classif.priority_lasso, classif.randomForest, classif.rfsrc, classif.rpart, dens.hist, dens.kde, dens.kde_ks, dens.locfit, dens.logspline, dens.mixed, dens.nonpar, dens.pen, dens.plug, dens.spline, regr.abess, regr.bart, regr.cforest, regr.ctree, regr.cubist, regr.debug, regr.earth, regr.featureless, regr.fnn, regr.gam, regr.gamboost, regr.gausspr, regr.gbm, regr.glm, regr.glmboost, regr.IBk, regr.ksvm, regr.liblinear, regr.lightgbm, regr.lmer, regr.M5Rules, regr.mars, regr.mob, regr.priority_lasso, regr.randomForest, regr.rfsrc, regr.rpart, regr.rsm, regr.rvm, surv.akritas, surv.aorsf, surv.blackboost, surv.cforest, surv.coxboost, surv.coxph, surv.coxtime, surv.ctree, surv.cv_coxboost, surv.cv_glmnet, surv.deephit, surv.deepsurv, surv.dnnsurv, surv.flexible, surv.gamboost, surv.gbm, surv.glmboost, surv.glmnet, surv.kaplan, surv.loghaz, surv.mboost, surv.nelson, surv.obliqueRSF, surv.parametric, surv.pchazard, surv.penalized, surv.priority_lasso, surv.ranger, surv.rfsrc, surv.rpart, surv.svm, surv.xgboost

According to this link: https://mlr-org.com/learners.html It is supposed to be available.

So, how do I train the BART model?

I tried this to install BART model install_learners("surv.bart")

But got an error: Error: Element with key 'surv.bart' not found in DictionaryLearner! Did you mean 'surv.parametric' / 'surv.rpart'?

I tried this code chunk but no success

library(mlr3) library(mlr3proba) library(distr6)

Attaching package: ‘distr6’

The following object is masked from ‘package:stats’:

qqplot

The following object is masked from ‘package:base’:

truncate

library(BART) Loading required package: nlme Loading required package: nnet Loading required package: survival learner = mlr3::lrn("surv.bart") Error: Element with key 'surv.bart' not found in DictionaryLearner! Did you mean 'surv.rpart'?

Reproducible example

library(mlr3extralearners) library(mlr3pipelines) library(mlr3proba) library(distr6) library(BART)

lrn()

with 103 stored values Keys: classif.abess, classif.AdaBoostM1, classif.bart, classif.C50, classif.cforest, classif.ctree, classif.debug, classif.earth, classif.featureless, classif.fnn, classif.gam, classif.gamboost, classif.gausspr, classif.gbm, classif.glmboost, classif.glmer, classif.IBk, classif.imbalanced_rfsrc, classif.J48, classif.JRip, classif.ksvm, classif.liblinear, classif.lightgbm, classif.LMT, classif.lssvm, classif.mob, classif.OneR, classif.PART, classif.priority_lasso, classif.randomForest, classif.rfsrc, classif.rpart, dens.hist, dens.kde, dens.kde_ks, dens.locfit, dens.logspline, dens.mixed, dens.nonpar, dens.pen, dens.plug, dens.spline, regr.abess, regr.bart, regr.cforest, regr.ctree, regr.cubist, regr.debug, regr.earth, regr.featureless, regr.fnn, regr.gam, regr.gamboost, regr.gausspr, regr.gbm, regr.glm, regr.glmboost, regr.IBk, regr.ksvm, regr.liblinear, regr.lightgbm, regr.lmer, regr.M5Rules, regr.mars, regr.mob, regr.priority_lasso, regr.randomForest, regr.rfsrc, regr.rpart, regr.rsm, regr.rvm, surv.akritas, surv.aorsf, surv.blackboost, surv.cforest, surv.coxboost, surv.coxph, surv.coxtime, surv.ctree, surv.cv_coxboost, surv.cv_glmnet, surv.deephit, surv.deepsurv, surv.dnnsurv, surv.flexible, surv.gamboost, surv.gbm, surv.glmboost, surv.glmnet, surv.kaplan, surv.loghaz, surv.mboost, surv.nelson, surv.obliqueRSF, surv.parametric, surv.pchazard, surv.penalized, surv.priority_lasso, surv.ranger, surv.rfsrc, surv.rpart, surv.svm, surv.xgboost

I tried this to install BART model install_learners("surv.bart")

But got an error: Error: Element with key 'surv.bart' not found in DictionaryLearner! Did you mean 'surv.parametric' / 'surv.rpart'?

I tried this code chunk but no success

library(mlr3) library(mlr3proba) library(distr6)

Attaching package: ‘distr6’

The following object is masked from ‘package:stats’:

qqplot

The following object is masked from ‘package:base’:

truncate

library(BART) Loading required package: nlme Loading required package: nnet Loading required package: survival learner = mlr3::lrn("surv.bart") Error: Element with key 'surv.bart' not found in DictionaryLearner! Did you mean 'surv.rpart'?

sessionInfo() R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/Denver tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BART_2.9.6 survival_3.5-8 nnet_7.3-19 nlme_3.1-164
[5] distr6_1.8.4 mlr3proba_0.6.0-9000 mlr3_0.18.0 mlr3pipelines_0.5.0-2
[9] mlr3extralearners_0.7.1 librarian_1.8.1

loaded via a namespace (and not attached): [1] Matrix_1.6-5 gtable_0.3.4 dplyr_1.1.4 compiler_4.3.3 param6_0.2.4
[6] crayon_1.5.2 tidyselect_1.2.1 Rcpp_1.0.12 parallel_4.3.3 splines_4.3.3
[11] globals_0.16.3 scales_1.3.0 uuid_1.2-0 RhpcBLASctl_0.23-42 lattice_0.22-5
[16] ggplot2_3.5.0 R6_2.5.1 generics_0.1.3 ooplah_0.2.0 palmerpenguins_0.1.1 [21] backports_1.4.1 checkmate_2.3.1 future_1.33.1 tibble_3.2.1 mlr3viz_0.8.0
[26] set6_0.2.6 munsell_0.5.0 paradox_0.11.1 pillar_1.9.0 rlang_1.1.3
[31] utf8_1.2.4 lgr_0.4.4 mlr3misc_0.14.0 cli_3.6.2 withr_3.0.0
[36] magrittr_2.0.3 dictionar6_0.1.3 digest_0.6.35 grid_4.3.3 rstudioapi_0.15.0
[41] lifecycle_1.0.4 vctrs_0.6.5 glue_1.7.0 data.table_1.15.2 listenv_0.9.1
[46] codetools_0.2-19 fansi_1.0.6 parallelly_1.37.1 colorspace_2.1-0 pkgconfig_2.0.3
[51] tools_4.3.3

sebffischer commented 6 months ago

Please run the code below and then try again.

remotes::install_github("mlr-org/mlr3extralearners")
Kuroshiwo commented 6 months ago

Thank you very much @sebffischer . It worked.

Although I got another error in BART. I will chase that through BART.