edit_spec_coveff {BayesERtools} | R Documentation |
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,
var_label = NULL,
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)
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. |
var_label |
The label of the variable to be used for plot. If NULL
(default), it is set to |
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 |
use_seps |
Whether to use separators for thousands in printing numbers.
See |
drop_trailing_dec_mark |
Whether to drop the trailing decimal mark
(".") in value_label of continuous variables. See |
show_ref_value |
Whether to show the reference value in the plot and
table. Setting this results in the |
spec_orig |
Original specification data frame. |
spec_new |
New specification data frame. It can be generated by
|
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. |
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()
.
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),
var_label = "Baseline Glucose (mmol/L)",
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)