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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: cardx | ||
| Title: Extra Analysis Results Data Utilities | ||
| Version: 0.1.0.9042 | ||
| Version: 0.1.0.9043 | ||
| Authors@R: c( | ||
| person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")), | ||
| person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"), | ||
|
|
@@ -18,7 +18,7 @@ BugReports: https://github.com/insightsengineering/cardx/issues | |
| Depends: | ||
| R (>= 4.1) | ||
| Imports: | ||
| cards (>= 0.1.0.9014), | ||
| cards (>= 0.1.0.9026), | ||
| cli (>= 3.6.1), | ||
| dplyr (>= 1.1.2), | ||
| glue (>= 1.6.2), | ||
|
|
@@ -33,13 +33,13 @@ Suggests: | |
| effectsize (>= 0.6.0), | ||
| emmeans (>= 1.7.3), | ||
| geepack (>= 1.3.2), | ||
| ggsurvfit (>= 1.0.0), | ||
| ggsurvfit (>= 1.1.0), | ||
| lme4 (>= 1.1-31), | ||
| parameters (>= 0.20.2), | ||
| smd (>= 0.6.6), | ||
| spelling, | ||
| survey (>= 4.1), | ||
| survival (>= 3.2-11), | ||
| survival (>= 3.6-4), | ||
| testthat (>= 3.2.0), | ||
| withr (>= 2.5.0) | ||
| Remotes: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| #' ARD Attributes | ||
| #' | ||
| #' @description | ||
| #' Add variable attributes to an ARD data frame. | ||
| #' - The `label` attribute will be added for all columns, and when no label | ||
| #' is specified and no label has been set for a column using the `label=` argument, | ||
| #' the column name will be placed in the label statistic. | ||
| #' - The `class` attribute will also be returned for all columns. | ||
| #' - Any other attribute returned by `attributes()` will also be added, e.g. factor levels. | ||
| #' | ||
| #' @rdname ard_attributes | ||
| #' @param data (`survey.design`)\cr | ||
| #' a design object often created with [`survey::svydesign()`]. | ||
| #' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr | ||
| #' variables to include | ||
| #' @param label (named `list`)\cr | ||
| #' named list of variable labels, e.g. `list(cyl = "No. Cylinders")`. | ||
| #' Default is `NULL` | ||
| #' @inheritParams rlang::args_dots_empty | ||
| #' | ||
| #' @return an ARD data frame of class 'card' | ||
| #' @export | ||
| #' | ||
| #' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey", reference_pkg = "cardx")) | ||
| #' data(api, package = "survey") | ||
| #' dclus1 <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) | ||
| #' | ||
| #' ard_attributes( | ||
| #' data = dclus1, | ||
| #' variables = c(sname, dname), | ||
| #' label = list(sname = "School Name", dname = "District Name") | ||
| #' ) | ||
| ard_attributes.survey.design <- function(data, variables = everything(), label = NULL, ...) { | ||
| set_cli_abort_call() | ||
|
|
||
| cards::ard_attributes(data = data[["variables"]], variables = {{ variables }}, label = label, ...) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| #' ARD one-sample t-test | ||
| #' | ||
| #' @description | ||
| #' Analysis results data for one-sample t-tests. | ||
| #' Result may be stratified by including the `by` argument. | ||
| #' | ||
| #' @param data (`data.frame`)\cr | ||
| #' a data frame. See below for details. | ||
| #' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr | ||
| #' column names to be analyzed. Independent t-tests will be computed for | ||
| #' each variable. | ||
| #' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr | ||
| #' optional column name to stratify results by. | ||
| #' @inheritParams ard_stats_t_test | ||
| #' | ||
| #' @return ARD data frame | ||
| #' @export | ||
| #' | ||
| #' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx")) | ||
| #' cards::ADSL |> | ||
| #' ard_stats_t_test_onesample(by = ARM, variables = AGE) | ||
| ard_stats_t_test_onesample <- function(data, variables, by = dplyr::group_vars(data), conf.level = 0.95, ...) { | ||
| set_cli_abort_call() | ||
|
|
||
| # check installed packages --------------------------------------------------- | ||
| check_pkg_installed("broom", reference_pkg = "cardx") | ||
|
|
||
| # check/process inputs ------------------------------------------------------- | ||
| check_not_missing(data) | ||
| check_not_missing(variables) | ||
| check_data_frame(data) | ||
| data <- dplyr::ungroup(data) | ||
| cards::process_selectors(data, by = {{ by }}, variables = {{ variables }}) | ||
| check_scalar_range(conf.level, range = c(0, 1)) | ||
|
|
||
| # if no variables selected, return empty tibble ------------------------------ | ||
| if (is_empty(variables)) { | ||
| return(dplyr::tibble()) | ||
| } | ||
|
|
||
| cards::ard_continuous( | ||
| data = data, | ||
| variables = all_of(variables), | ||
| by = all_of(by), | ||
| statistic = all_of(variables) ~ list(t_test_onesample = \(x) stats::t.test(x = x, conf.level = conf.level, ...) |> broom::tidy()) | ||
| ) |> | ||
| cards::bind_ard( | ||
| cards::ard_continuous( | ||
| data = data, | ||
| variables = all_of(variables), | ||
| by = all_of(by), | ||
| statistic = | ||
| all_of(variables) ~ | ||
| list(conf.level = \(x) { | ||
| formals(asNamespace("stats")[["t.test.default"]])["mu"] |> | ||
| utils::modifyList(list(conf.level = conf.level, ...)) | ||
| }) | ||
| ) | ||
| ) |> | ||
| dplyr::select(-"stat_label") |> | ||
| dplyr::left_join( | ||
| .df_ttest_stat_labels(by = NULL), | ||
| by = "stat_name" | ||
| ) |> | ||
| dplyr::mutate( | ||
| stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name), | ||
| context = "ard_stats_t_test_onesample", | ||
| ) |> | ||
| cards::tidy_ard_row_order() |> | ||
| cards::tidy_ard_column_order() | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| #' ARD one-sample Wilcox Rank-sum | ||
| #' | ||
| #' @description | ||
| #' Analysis results data for one-sample Wilcox Rank-sum. | ||
| #' Result may be stratified by including the `by` argument. | ||
| #' | ||
| #' @param data (`data.frame`)\cr | ||
| #' a data frame. See below for details. | ||
| #' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr | ||
| #' column names to be analyzed. Independent Wilcox Rank-sum tests will be computed for | ||
| #' each variable. | ||
| #' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr | ||
| #' optional column name to stratify results by. | ||
| #' @inheritParams ard_stats_wilcox_test | ||
| #' | ||
| #' @return ARD data frame | ||
| #' @export | ||
| #' | ||
| #' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx")) | ||
| #' cards::ADSL |> | ||
| #' ard_stats_wilcox_test_onesample(by = ARM, variables = AGE) | ||
| ard_stats_wilcox_test_onesample <- function(data, variables, by = dplyr::group_vars(data), conf.level = 0.95, ...) { | ||
| set_cli_abort_call() | ||
|
|
||
| # check installed packages --------------------------------------------------- | ||
| check_pkg_installed("broom", reference_pkg = "cardx") | ||
|
|
||
| # check/process inputs ------------------------------------------------------- | ||
| check_not_missing(data) | ||
| check_not_missing(variables) | ||
| check_data_frame(data) | ||
| data <- dplyr::ungroup(data) | ||
| cards::process_selectors(data, by = {{ by }}, variables = {{ variables }}) | ||
| check_scalar_range(conf.level, range = c(0, 1)) | ||
|
|
||
| # if no variables selected, return empty tibble ------------------------------ | ||
| if (is_empty(variables)) { | ||
| return(dplyr::tibble()) | ||
| } | ||
|
|
||
| cards::ard_continuous( | ||
| data = data, | ||
| variables = all_of(variables), | ||
| by = all_of(by), | ||
| statistic = all_of(variables) ~ list(t_test_onesample = \(x) stats::wilcox.test(x = x, conf.level = conf.level, ...) |> broom::tidy()) | ||
| ) |> | ||
| cards::bind_ard( | ||
| cards::ard_continuous( | ||
| data = data, | ||
| variables = all_of(variables), | ||
| by = all_of(by), | ||
| statistic = | ||
| all_of(variables) ~ | ||
| list(conf.level = \(x) { | ||
| formals(asNamespace("stats")[["wilcox.test.default"]])[c("mu", "exact", "conf.int", "tol.root", "digits.rank")] |> | ||
| utils::modifyList(list(conf.level = conf.level, ...)) |> | ||
| compact() | ||
| }) | ||
| ) | ||
| ) |> | ||
| dplyr::select(-"stat_label") |> | ||
| dplyr::left_join( | ||
| .df_ttest_stat_labels(by = NULL), | ||
| by = "stat_name" | ||
| ) |> | ||
| dplyr::mutate( | ||
| stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name), | ||
| context = "ard_stats_wilcox_test_onesample", | ||
| ) |> | ||
| cards::tidy_ard_row_order() |> | ||
| cards::tidy_ard_column_order() | ||
| } |
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