tests/testthat/fixtures/predict.R

In SchlossLab/mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines

library(dplyr)
devtools::load_all()

results_mtx <- readRDS(testthat::test_path("fixtures", "results_mtx.Rds"))
get_sensspec_seed <- function(colnum) {
  result <- results_mtx[, colnum]
  trained_model <- result$trained_model
  test_data <- result$test_data
  seed <- result$performance$seed
  method <- result$trained_model$method
  sensspec <- calc_model_sensspec(
    trained_model,
    test_data,
    "dx", "cancer"
  ) %>%
    mutate(seed = seed, method = method)
  return(sensspec)
}
sensspec_dat <- purrr::map_dfr(
  seq(1, dim(results_mtx)[2]),
  get_sensspec_seed
)
saveRDS(sensspec_dat, testthat::test_path("fixtures", "sensspec_dat.Rds"))
saveRDS(calc_mean_prc(sensspec_dat), testthat::test_path("fixtures", "sensspec_prc.Rds"))
saveRDS(calc_mean_roc(sensspec_dat), testthat::test_path("fixtures", "sensspec_roc.Rds"))

saveRDS(
  calc_model_sensspec(
    otu_mini_bin_results_glmnet$trained_model,
    otu_mini_bin_results_glmnet$test_data,
    "dx",
    "cancer"
  ),
  testthat::test_path("fixtures", "otu_mini_bin_results_glmnet_sensspec.Rds")
)