Collection of tidiers that can be utilized in gtsummary. See details below.
Usage
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, vcov = stats::vcov(x), ...)
Arguments
- x
(
model
)
Regression model object- exponentiate
(scalar
logical
)
Logical indicating whether to exponentiate the coefficient estimates. Default isFALSE
.- conf.level
(scalar
real
)
Confidence level for confidence interval/credible interval. Defaults to0.95
.- conf.int
(scalar
logical
)
Logical indicating whether or not to include a confidence interval in the output. Default isTRUE
.- ...
Arguments passed to method;
pool_and_tidy_mice()
:mice::tidy(x, ...)
tidy_standardize()
:parameters::standardize_parameters(x, ...)
tidy_bootstrap()
:parameters::bootstrap_parameters(x, ...)
tidy_robust()
:parameters::model_parameters(x, ...)
- quiet
- vcov, vcov_args
tidy_robust()
: Arguments passed toparameters::model_parameters()
. At least one of these arguments must be specified.tidy_wald_test()
:vcov
is the covariance matrix of the model with defaultstats::vcov()
.
- pool.args
(named
list
)
Named list of arguments passed tomice::pool()
inpool_and_tidy_mice()
. Default isNULL
- tidy_fun
(
function
)
Tidier function for the model. Default is to usebroom::tidy()
. If an error occurs, the tidying of the model is attempted withparameters::model_parameters()
, if installed.
Regression Model Tidiers
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 fromparameters::standardize_parameters()
, and merely takes the result and puts it inbroom::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 fromparameters::bootstrap_parameters(test = "p")
, and merely takes the result and puts it inbroom::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 fromparameters::model_parameters()
, and merely takes the result and puts it inbroom::tidy()
format. To use this function withtbl_regression()
, pass a function with the arguments fortidy_robust()
populated.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.
Other Tidiers
tidy_wald_test()
tidier to report Wald p-values, wrapping theaod::wald.test()
function. Use this tidier withadd_global_p(anova_fun = tidy_wald_test)
Examples
# 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
tbl_regression(mod, tidy_fun = \(x, ...) tidy_standardize(x, method = "posthoc", ...))
Characteristic
Beta
95% CI
Abbreviation: CI = Confidence Interval
# 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()
#>
#> iter imp variable
#> 1 1 age marker response
#> 1 2 age marker response
#> 2 1 age marker response
#> 2 2 age marker response
#> 3 1 age marker response
#> 3 2 age marker response
#> 4 1 age marker response
#> 4 2 age marker response
#> 5 1 age marker response
#> 5 2 age marker response