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Adds ard_regression_basic().
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@rparmm
rparmm committed Feb 26, 2024
1 parent e694331 commit 67ada66
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -11,6 +11,7 @@ export(ard_paired_ttest)
export(ard_paired_wilcoxtest)
export(ard_proportion_ci)
export(ard_regression)
export(ard_regression_basic)
export(ard_ttest)
export(ard_wilcoxtest)
export(contains)
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40 changes: 40 additions & 0 deletions R/ard_regression.R
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Expand Up @@ -79,3 +79,43 @@ ard_regression.default <- function(x, tidy_fun = broom.helpers::tidy_with_broom_
cards::tidy_ard_column_order() %>%
{structure(., class = c("card", class(.)))} # styler: off
}

#' ard_regression_basic
#'
#' @description
#' A function that takes a regression model and provides basic statistics in an
#' ARD structure.
#'
#'
#' @param x regression model object
#' @param tidy_fun(`function`)\cr
#' a tidier. Default is [`broom.helpers::tidy_with_broom_or_parameters`]
#' @param ... Arguments passed to `broom.helpers::tidy_plus_plus()`
#'
#' @return data frame
#' @name ard_regression_basic
#' @export
#'
#' @examples
#' lm(AGE ~ ARM, data = cards::ADSL) |>
#' ard_regression_basic()
#'
ard_regression_basic <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or_parameters, ...) {
# check installed packages ---------------------------------------------------
cards::check_pkg_installed("broom.helpers", reference_pkg = "cards")

# check inputs ---------------------------------------------------------------
check_not_missing(x, "model")

args <-
list(
add_reference_rows = FALSE,
add_estimate_to_reference_rows = FALSE,
add_n = FALSE,
intercept = FALSE
) |>
utils::modifyList(val = rlang::dots_list(...))

rlang::inject(ard_regression(x = x, tidy_fun = tidy_fun, !!!args)) |>
dplyr::filter(!.data$stat_name %in% c("term", "var_type", "var_label", "var_class", "label"))
}
31 changes: 31 additions & 0 deletions man/ard_regression_basic.Rd
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44 changes: 44 additions & 0 deletions tests/testthat/_snaps/ard_regression.md
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Expand Up @@ -54,3 +54,47 @@
Message
i 1 more variable: statistic_fmt_fn

# ard_regression_basic() works

Code
as.data.frame(ard_regression_basic(lm(AGE ~ ARM, data = cards::ADSL)))
Output
variable variable_level context stat_name stat_label
1 ARM Xanomeline High Dose regression var_nlevels N Levels
2 ARM Xanomeline High Dose regression contrasts contrasts
3 ARM Xanomeline High Dose regression contrasts_type Contrast Type
4 ARM Xanomeline High Dose regression estimate Coefficient
5 ARM Xanomeline High Dose regression std.error Standard Error
6 ARM Xanomeline High Dose regression statistic statistic
7 ARM Xanomeline High Dose regression p.value p-value
8 ARM Xanomeline High Dose regression conf.low CI Lower Bound
9 ARM Xanomeline High Dose regression conf.high CI Upper Bound
10 ARM Xanomeline Low Dose regression var_nlevels N Levels
11 ARM Xanomeline Low Dose regression contrasts contrasts
12 ARM Xanomeline Low Dose regression contrasts_type Contrast Type
13 ARM Xanomeline Low Dose regression estimate Coefficient
14 ARM Xanomeline Low Dose regression std.error Standard Error
15 ARM Xanomeline Low Dose regression statistic statistic
16 ARM Xanomeline Low Dose regression p.value p-value
17 ARM Xanomeline Low Dose regression conf.low CI Lower Bound
18 ARM Xanomeline Low Dose regression conf.high CI Upper Bound
statistic statistic_fmt_fn
1 3 0
2 contr.treatment NULL
3 treatment NULL
4 -0.8283499 1
5 1.267394 1
6 -0.653585 1
7 0.5139775 1
8 -3.324433 1
9 1.667733 1
10 3 0
11 contr.treatment NULL
12 treatment NULL
13 0.4573643 1
14 1.267394 1
15 0.3608698 1
16 0.7185003 1
17 -2.038718 1
18 2.953447 1

144 changes: 144 additions & 0 deletions tests/testthat/_snaps/ard_regression.new.md
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@@ -0,0 +1,144 @@
# ard_regression() works

Code
print(dplyr::mutate(ard_regression(lm(AGE ~ ARM, data = cards::ADSL),
add_estimate_to_reference_rows = TRUE), statistic = lapply(statistic, function(
x) ifelse(is.numeric(x), cards::round5(x, 3), x))), n = Inf)
Message
{cards} data frame: 43 x 7
Output
variable variable_level stat_name stat_label statistic
1 ARM Placebo term term ARMPlacebo
2 ARM Placebo var_label Label Description of Planned Arm
3 ARM Placebo var_class Class character
4 ARM Placebo var_type Type categorical
5 ARM Placebo var_nlevels N Levels 3
6 ARM Placebo contrasts contrasts contr.treatment
7 ARM Placebo contrasts_type Contrast… treatment
8 ARM Placebo reference_row referenc… TRUE
9 ARM Placebo label Level La… Placebo
10 ARM Placebo n_obs N Obs. 86
11 ARM Placebo estimate Coeffici… 0
12 ARM Xanomeli… term term ARMXanomeline High Dose
13 ARM Xanomeli… var_label Label Description of Planned Arm
14 ARM Xanomeli… var_class Class character
15 ARM Xanomeli… var_type Type categorical
16 ARM Xanomeli… var_nlevels N Levels 3
17 ARM Xanomeli… contrasts contrasts contr.treatment
18 ARM Xanomeli… contrasts_type Contrast… treatment
19 ARM Xanomeli… reference_row referenc… FALSE
20 ARM Xanomeli… label Level La… Xanomeline High Dose
21 ARM Xanomeli… n_obs N Obs. 84
22 ARM Xanomeli… estimate Coeffici… -0.828
23 ARM Xanomeli… std.error Standard… 1.267
24 ARM Xanomeli… statistic statistic -0.654
25 ARM Xanomeli… p.value p-value 0.514
26 ARM Xanomeli… conf.low CI Lower… -3.324
27 ARM Xanomeli… conf.high CI Upper… 1.668
28 ARM Xanomeli… term term ARMXanomeline Low Dose
29 ARM Xanomeli… var_label Label Description of Planned Arm
30 ARM Xanomeli… var_class Class character
31 ARM Xanomeli… var_type Type categorical
32 ARM Xanomeli… var_nlevels N Levels 3
33 ARM Xanomeli… contrasts contrasts contr.treatment
34 ARM Xanomeli… contrasts_type Contrast… treatment
35 ARM Xanomeli… reference_row referenc… FALSE
36 ARM Xanomeli… label Level La… Xanomeline Low Dose
37 ARM Xanomeli… n_obs N Obs. 84
38 ARM Xanomeli… estimate Coeffici… 0.457
39 ARM Xanomeli… std.error Standard… 1.267
40 ARM Xanomeli… statistic statistic 0.361
41 ARM Xanomeli… p.value p-value 0.719
42 ARM Xanomeli… conf.low CI Lower… -2.039
43 ARM Xanomeli… conf.high CI Upper… 2.953
statistic_fmt_fn
1 NULL
2 NULL
3 NULL
4 NULL
5 0
6 NULL
7 NULL
8 NULL
9 NULL
10 1
11 1
12 NULL
13 NULL
14 NULL
15 NULL
16 0
17 NULL
18 NULL
19 NULL
20 NULL
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 NULL
29 NULL
30 NULL
31 NULL
32 0
33 NULL
34 NULL
35 NULL
36 NULL
37 1
38 1
39 1
40 1
41 1
42 1
43 1
Message
i 1 more variable: context

# ard_regression_basic() works

Code
as.data.frame(ard_regression_basic(lm(AGE ~ ARM, data = cards::ADSL)))
Output
variable variable_level context stat_name stat_label
1 ARM Xanomeline High Dose regression var_nlevels N Levels
2 ARM Xanomeline High Dose regression contrasts contrasts
3 ARM Xanomeline High Dose regression contrasts_type Contrast Type
4 ARM Xanomeline High Dose regression estimate Coefficient
5 ARM Xanomeline High Dose regression std.error Standard Error
6 ARM Xanomeline High Dose regression statistic statistic
7 ARM Xanomeline High Dose regression p.value p-value
8 ARM Xanomeline High Dose regression conf.low CI Lower Bound
9 ARM Xanomeline High Dose regression conf.high CI Upper Bound
10 ARM Xanomeline Low Dose regression var_nlevels N Levels
11 ARM Xanomeline Low Dose regression contrasts contrasts
12 ARM Xanomeline Low Dose regression contrasts_type Contrast Type
13 ARM Xanomeline Low Dose regression estimate Coefficient
14 ARM Xanomeline Low Dose regression std.error Standard Error
15 ARM Xanomeline Low Dose regression statistic statistic
16 ARM Xanomeline Low Dose regression p.value p-value
17 ARM Xanomeline Low Dose regression conf.low CI Lower Bound
18 ARM Xanomeline Low Dose regression conf.high CI Upper Bound
statistic statistic_fmt_fn
1 3 0
2 contr.treatment NULL
3 treatment NULL
4 -0.8283499 1
5 1.267394 1
6 -0.653585 1
7 0.5139775 1
8 -3.324433 1
9 1.667733 1
10 3 0
11 contr.treatment NULL
12 treatment NULL
13 0.4573643 1
14 1.267394 1
15 0.3608698 1
16 0.7185003 1
17 -2.038718 1
18 2.953447 1

14 changes: 14 additions & 0 deletions tests/testthat/test-ard_regression.R
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Expand Up @@ -8,3 +8,17 @@ test_that("ard_regression() works", {
print(n = Inf)
)
})

test_that("ard_regression_basic() works",{
expect_error(
lm(AGE ~ ARM, data = cards::ADSL) |>
ard_regression_basic(),
NA
)

expect_snapshot(
lm(AGE ~ ARM, data = cards::ADSL) |>
ard_regression_basic() |>
as.data.frame()
)
})

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