BayesERtools (version 0.2.0)

edit_spec_coveff: Customize specifications for covariate effect simulations/visualizations

Description

• build_spec_coveff_one_variable() is a helper function to create a new specification for a single variable. This is useful when you want to customize the specification for a single variable.

• replace_spec_coveff() is used to replace the specification for some (or all) variables in the original specification data frame. If you want to replace multiple variables, you can just stack the specifications together.

Usage

build_spec_coveff_one_variable(
  var_name,
  values_vec,
  qi_width_cov = 0.9,
  n_sigfig = 3,
  use_seps = TRUE,
  drop_trailing_dec_mark = TRUE,
  show_ref_value = TRUE
)
replace_spec_coveff(spec_orig, spec_new, replace_ref_value = FALSE)

Value

See build_spec_coveff() for the structure of the return object. build_spec_coveff_one_variable() returns a data frame corresponding to the specification for a single variable, which can be used as an input to replace_spec_coveff().

Arguments

var_name

The name of the variable for which a new spec is to be created.

values_vec

The vector of the values for creating a new spec.

qi_width_cov

the width of the quantile interval for continuous covariates in the forest plot. Default is 0.9 (i.e. visualize effect of covariate effect at their 5th and 95th percentile values).

n_sigfig

Number of significant figures to form value_label of continuous variables. See gt::vec_fmt_number() for details.

use_seps

Whether to use separators for thousands in printing numbers. See gt::vec_fmt_number() for details.

drop_trailing_dec_mark

Whether to drop the trailing decimal mark (".") in value_label of continuous variables. See gt::vec_fmt_number() for details.

show_ref_value

Whether to show the reference value in the plot and table. Setting this results in the show_ref_value column in the specification data frame.

spec_orig

Original specification data frame.

spec_new

New specification data frame. It can be generated by build_spec_coveff_one_variable() or manually crafting with the following variables: var_name, var_label, value_order, value_annot, value_label, value_cont or value_cat, is_ref_value, show_ref_value. You can have multiple variables stacked together.

replace_ref_value

Whether to replace the reference values from the original specification data frame. Default is FALSE; in this case, show_ref_value is set to FALSE as it can be confusing. If you set replace_ref_value to TRUE, the reference calculation for the forest plot is also done with the one in spec_new.

Examples

set.seed(1234)
data(d_sim_binom_cov_hgly2)

ermod_bin <- suppressWarnings(dev_ermod_bin(
  data = d_sim_binom_cov_hgly2, var_resp = "AEFLAG",
  var_exposure = "AUCss_1000", var_cov = c("BGLUC", "RACE"),
  verbosity_level = 0,
  # Below option to make the example run fast
  chains = 2, iter = 1000
))

spec_coveff <- build_spec_coveff(ermod_bin)
spec_new_bgluc <- build_spec_coveff_one_variable(
  "BGLUC", seq(4, 8, by = 0.1),
  qi_width_cov = 0.8, show_ref_value = FALSE
)
spec_coveff_new <- replace_spec_coveff(spec_coveff, spec_new_bgluc)
plot_coveff(ermod_bin, spec_coveff = spec_coveff_new)