tests/testthat/test-stat_glm.R

In aba: Automated Biomarker Analysis

test_that("complete.cases=F works", {
  data <- adnimerge %>% dplyr::filter(VISCODE == 'bl')

  expect_error(
    model <- data %>% aba_model() %>%
      set_groups(
        everyone(),
        DX_bl %in% c('MCI', 'AD')
      ) %>%
      set_outcomes(CSF_ABETA_STATUS_bl, ConvertedToAlzheimers) %>%
      set_predictors(
        PLASMA_PTAU181_bl, PLASMA_NFL_bl,
        c(PLASMA_PTAU181_bl, PLASMA_NFL_bl)
      ) %>%
      set_covariates(AGE, GENDER, EDUCATION) %>%
      set_stats(
        stat_glm(complete.cases=F, std.beta=T)
      ) %>%
      aba_fit(),
    NA
  )

  expect_error(
    ms <- model %>% aba_summary(),
    NA
  )

  expect_error(
    g <- ms %>% aba_plot_metric(),
    NA
  )

  expect_error(
    g <- ms %>% aba_plot_coef(),
    NA
  )

  expect_error(
    g <- ms %>% aba_plot_coef(coord_flip=T),
    NA
  )

  expect_error(
    g <- ms %>% aba_plot_roc(),
    NA
  )
})