custom_tidiers | R Documentation |
maturing Collection of tidiers that can be utilized in gtsummary. See details below.
tidy_standardize( x, exponentiate = FALSE, conf.level = 0.95, conf.int = TRUE, ..., quiet = FALSE ) tidy_bootstrap( x, exponentiate = FALSE, conf.level = 0.95, conf.int = TRUE, ..., quiet = FALSE ) tidy_robust( x, exponentiate = FALSE, conf.level = 0.95, conf.int = TRUE, vcov = NULL, vcov_args = NULL, ..., quiet = FALSE ) pool_and_tidy_mice(x, pool.args = NULL, ..., quiet = FALSE) tidy_gam(x, conf.int = FALSE, exponentiate = FALSE, conf.level = 0.95, ...) tidy_wald_test(x, tidy_fun = NULL, ...)
x |
a regression model object |
exponentiate |
Logical indicating whether or not to exponentiate the
the coefficient estimates. This is typical for logistic and multinomial
regressions, but a bad idea if there is no log or logit link. Defaults
to |
conf.level |
The confidence level to use for the confidence interval
if |
conf.int |
Logical indicating whether or not to include a confidence
interval in the tidied output. Defaults to |
... |
arguments passed to method;
|
quiet |
Logical indicating whether to print messages in console. Default is
|
vcov, vcov_args |
arguments passed to
|
pool.args |
named list of arguments passed to |
tidy_fun |
Option to specify a particular tidier function for the
model. Default is to use |
These tidiers are passed to tbl_regression()
and tbl_uvregression()
to
obtain modified results.
tidy_standardize()
tidier to report standardized coefficients. The
parameters
package includes a wonderful function to estimate standardized coefficients.
The tidier uses the output from parameters::standardize_parameters()
, and
merely takes the result and puts it in broom::tidy()
format.
tidy_bootstrap()
tidier to report bootstrapped coefficients. The
parameters
package includes a wonderful function to estimate bootstrapped coefficients.
The tidier uses the output from parameters::bootstrap_parameters(test = "p")
, and
merely takes the result and puts it in broom::tidy()
format.
tidy_robust()
tidier to report robust standard errors, confidence intervals,
and p-values. The parameters
package includes a wonderful function to calculate robust standard errors, confidence intervals, and p-values
The tidier uses the output from parameters::model_parameters()
, and
merely takes the result and puts it in broom::tidy()
format. To use this
function with tbl_regression()
, pass a function with the arguments for
tidy_robust()
populated. This is easily done using purrr::partial()
e.g.
tbl_regression(tidy_fun = partial(tidy_robust, vcov = "CL"))
pool_and_tidy_mice()
tidier to report models resulting from multiply imputed data
using the mice package. Pass the mice model object before the model results
have been pooled. See example.
tidy_wald_test()
tidier to report Wald p-values, wrapping the
aod::wald.test()
function.
Use this tidier with add_global_p(anova_fun = tidy_wald_test)
Example 1
Example 2
Example 3
# Example 1 ---------------------------------- mod <- lm(age ~ marker + grade, trial) tbl_stnd <- tbl_regression(mod, tidy_fun = tidy_standardize) tbl <- tbl_regression(mod) tidy_standardize_ex1 <- tbl_merge( list(tbl_stnd, tbl), tab_spanner = c("**Standardized Model**", "**Original Model**") ) # Example 2 ---------------------------------- # use "posthoc" method for coef calculation tidy_standardize_ex2 <- tbl_regression(mod, tidy_fun = purrr::partial(tidy_standardize, method = "posthoc")) # Example 3 ---------------------------------- # Multiple Imputation using the mice package set.seed(1123) pool_and_tidy_mice_ex3 <- suppressWarnings(mice::mice(trial, m = 2)) %>% with(lm(age ~ marker + grade)) %>% tbl_regression()
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