broom.helpers (version 1.7.0)

tidy_add_reference_rows: Add references rows for categorical variables

Description

For categorical variables with a treatment contrast (stats::contr.treatment()), a SAS contrast (stats::contr.SAS()) or a sum contrast (stats::contr.sum()), add a reference row.

Usage

tidy_add_reference_rows(
  x,
  no_reference_row = NULL,
  model = tidy_get_model(x),
  quiet = FALSE
)

Arguments

x

a tidy tibble

no_reference_row

a vector indicating the name of variables for those no reference row should be added. Accepts tidyselect syntax. Default is NULL. See also all_categorical() and all_dichotomous()

model

the corresponding model, if not attached to x

quiet

logical argument whether broom.helpers should not return a message when requested output cannot be generated. Default is FALSE

Details

The added reference_row column will be equal to:

• TRUE for a reference row;

• FALSE for a normal row of a variable with a reference row;

• NA for variables without a reference row.

If the contrasts column is not yet available in x, tidy_add_contrasts() will be automatically applied.

tidy_add_reference_rows() will not populate the label of the reference term. It is therefore better to apply tidy_add_term_labels() after tidy_add_reference_rows() rather than before. Similarly, it is better to apply tidy_add_reference_rows() before tidy_add_n().

See Also

Other tidy_helpers: tidy_add_coefficients_type(), tidy_add_contrasts(), tidy_add_estimate_to_reference_rows(), tidy_add_header_rows(), tidy_add_n(), tidy_add_term_labels(), tidy_add_variable_labels(), tidy_attach_model(), tidy_disambiguate_terms(), tidy_identify_variables(), tidy_plus_plus(), tidy_remove_intercept(), tidy_select_variables()

Examples

# NOT RUN {
df <- Titanic %>%
  dplyr::as_tibble() %>%
  dplyr::mutate(Survived = factor(Survived, c("No", "Yes")))

res <- df %>%
  glm(
    Survived ~ Class + Age + Sex,
    data = ., weights = .$n, family = binomial,
    contrasts = list(Age = contr.sum, Class = "contr.SAS")
  ) %>%
  tidy_and_attach()
res %>% tidy_add_reference_rows()
res %>% tidy_add_reference_rows(no_reference_row = all_dichotomous())
res %>% tidy_add_reference_rows(no_reference_row = "Class")

glm(
  response ~ stage + grade * trt,
  gtsummary::trial,
  family = binomial,
  contrasts = list(
    stage = contr.treatment(4, base = 3),
    grade = contr.treatment(3, base = 2),
    trt = contr.treatment(2, base = 2)
  )
) %>%
  tidy_and_attach() %>%
  tidy_add_reference_rows()
# }