-
Notifications
You must be signed in to change notification settings - Fork 114
/
add_global_p.Rd
85 lines (75 loc) · 2.89 KB
/
add_global_p.Rd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_global_p.R
\name{add_global_p}
\alias{add_global_p}
\alias{add_global_p.tbl_regression}
\alias{add_global_p.tbl_uvregression}
\title{Add the global p-values}
\usage{
add_global_p(x, ...)
\method{add_global_p}{tbl_regression}(
x,
include = everything(),
keep = FALSE,
anova_fun = global_pvalue_fun,
type = "III",
quiet,
...
)
\method{add_global_p}{tbl_uvregression}(
x,
include = everything(),
keep = FALSE,
anova_fun = global_pvalue_fun,
type = "III",
quiet,
...
)
}
\arguments{
\item{x}{(\code{tbl_regression}, \code{tbl_uvregression})\cr
Object with class \code{'tbl_regression'} or \code{'tbl_uvregression'}}
\item{...}{Additional arguments to be passed to \code{car::Anova},
\code{aod::wald.test()} or \code{anova_fun} (if specified)}
\item{include}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
Variables to calculate global p-value for. Default is \code{everything()}}
\item{keep}{(scalar \code{logical})\cr
Logical argument indicating whether to also retain the individual
p-values in the table output for each level of the categorical variable.
Default is \code{FALSE}.}
\item{anova_fun}{(\code{function})\cr
Function used to calculate global p-values.
Default is generic \code{\link[=global_pvalue_fun]{global_pvalue_fun()}}, which wraps \code{car::Anova()} for
most models. The \code{type} argument is passed to this function. See help file for details.
To pass a custom function, it must accept as its first argument is a model.
Note that anything passed in \code{...} will be passed to this function.
The function must return an object of class \code{'cards'} (see \code{cardx::ard_car_anova()} as an example),
or a tibble with columns \code{'term'} and \code{'p.value'} (e.g. \verb{\\(x, type, ...) car::Anova(x, type, ...) |> broom::tidy()}).}
\item{type}{Type argument passed to \code{anova_fun}. Default is \code{"III"}}
\item{quiet}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}}
}
\description{
This function uses \code{car::Anova()} (by default) to calculate global p-values
for model covariates.
Output from \code{tbl_regression} and \code{tbl_uvregression} objects supported.
}
\examples{
\dontshow{if (gtsummary:::is_pkg_installed(c("cardx", "broom", "car"), reference_pkg = "gtsummary")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# Example 1 ----------------------------------
lm(marker ~ age + grade, trial) |>
tbl_regression() |>
add_global_p()
# Example 2 ----------------------------------
trial[c("response", "age", "trt", "grade")] |>
tbl_uvregression(
method = glm,
y = response,
method.args = list(family = binomial),
exponentiate = TRUE
) |>
add_global_p()
\dontshow{\}) # examplesIf}
}
\author{
Daniel D. Sjoberg
}