## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library("vimp") library("SuperLearner") ## ----load-vrc01-data---------------------------------------------------------- # read in the data data("vrc01") # subset to the columns of interest for this analysis library("dplyr") library("tidyselect") # retain only the columns of interest for this analysis y <- vrc01$ic50.censored X <- vrc01 %>% select(starts_with("geog"), starts_with("subtype"), starts_with("length")) learners <- "SL.glm" ## ----est-subtype-01AE-cond, warning = FALSE----------------------------------- # note the use of a small V and a small number of SL folds, for illustration only set.seed(1234) V <- 2 sl_cvcontrol <- list(V = 2) subtype_01_AE_cond <- vimp_auc(Y = y, X = X, indx = 5, SL.library = learners, na.rm = TRUE, V = V, cvControl = sl_cvcontrol) ## ----est-subtype-01AE-marg, warning = FALSE----------------------------------- # note the use of a small V and a small number of SL folds, for illustration only set.seed(5678) subtype_01_AE_marg <- vimp_auc(Y = y, X = X[, 5, drop = FALSE], indx = 1, SL.library = learners, na.rm = TRUE, V = V, cvControl = sl_cvcontrol) ## ----est-famhist-spvim, warning = FALSE--------------------------------------- set.seed(91011) all_vim_spvim <- sp_vim(Y = y, X = X, type = "auc", SL.library = learners, na.rm = TRUE, V = V, cvControl = sl_cvcontrol, env = environment()) ## ----show-ests---------------------------------------------------------------- subtype_01_AE_cond subtype_01_AE_marg # note: need to look at row for s = 5 all_vim_spvim