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mlsurvlrnrs

CRAN checks Dependencies R build status R build status R build status

The goal of mlsurvlrnrs is to enhance the mlexperiments R package with survival learners.

Currently implemented learners are:

Name Based on Description / Tasks
LearnerSurvCoxPHCox survival::coxph Cox Proportional Hazards Regression
LearnerSurvGlmnetCox glmnet::glmnet Regularized Cox Regression
LearnerSurvRangerCox ranger::ranger Random Survival Forest with right-censored data
LearnerSurvRpartCox rpart::rpart Random Survival Forest with right-censored data
LearnerSurvXgboostCox xgboost::xgb.train Cox Regression with right-censored data
LearnerSurvXgboostAft xgboost::xgb.train Accelerated failure time models with right-censored data

For a short introduction on how to use the learners together with the mlexperiments R package, please visit the wiki page.

Installation

To install the development version, run

install.packages("remotes")
remotes::install_github("kapsner/mlsurvlrnrs")

mlsurvlrnrs's People

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mlsurvlrnrs's Issues

Prepare CRAN initial submission

  • reduce unit-test runtime
  • make vignettes static
  • move survival-svm to experimental branch
  • update github wiki
  • run spell-tests and fix errors devtools::spell_check()
  • run rcmdcheck::rcmdcheck(args = "--as-cran") and fix errors
  • run rhub cran tests
  • prepare cran-comments.md usethis::use_cran_comments()
  • initial submission

coxph: cat_vars not working, when specifying via `set_data`

cat_vars are not respected when specifying via set_data:

coxph_validator <- mlexperiments::MLCrossValidation$new(
  learner = mlsurvlrnrs::LearnerSurvCoxPHCox$new(),
  fold_list = validation_fold_list,
  seed = seed,
  ncores = n_cores,
  return_models = TRUE
)
coxph_validator$performance_metric <- mlsurvlrnrs::c_index
coxph_validator$set_data(
  x = train_x[, which(colnames(train_x) %in% cox_feature_cols)],
  y = train_y,
  cat_vars = ml_cat_vars[which(ml_cat_vars %in% cox_feature_cols)]
)
res_coxph <- coxph_validator$execute()

However, when setting them with learner_args, everything works fine:

coxph_validator$learner_args <- list(cat_vars = ml_cat_vars[which(ml_cat_vars %in% cox_feature_cols)])

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