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| branches: [main, master] | ||
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| name: R-CMD-check | ||
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| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
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| - main | ||
| push: | ||
| branches: | ||
| - main | ||
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| Package: cardx | ||
| Title: Extra Analysis Results Data Utilities | ||
| Version: 0.1.0.9008 | ||
| Version: 0.1.0.9021 | ||
| Authors@R: c( | ||
| person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")), | ||
| person("Abinaya", "Yogasekaram", , "[email protected]", role = "aut"), | ||
| person("Emily", "de la Rua", , "[email protected]", role = "aut"), | ||
| person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")) | ||
| ) | ||
| Description: Create extra Analysis Results Data (ARD) summary objects. | ||
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@@ -17,23 +18,28 @@ BugReports: https://github.com/insightsengineering/cardx/issues | |
| Depends: | ||
| R (>= 4.1) | ||
| Imports: | ||
| cards (>= 0.1.0.9002), | ||
| cards (>= 0.1.0.9014), | ||
| cli (>= 3.6.1), | ||
| dplyr (>= 1.1.2), | ||
| glue (>= 1.6.2), | ||
| rlang (>= 1.1.1), | ||
| tidyr (>= 1.3.0) | ||
| Suggests: | ||
| aod (>= 1.3.3), | ||
| broom (>= 1.0.5), | ||
| broom.helpers (>= 1.13.0), | ||
| broom.helpers (>= 1.15.0), | ||
| car (>= 3.0-11), | ||
| effectsize (>= 0.6.0), | ||
| geepack (>= 1.3.2), | ||
| ggsurvfit (>= 1.0.0), | ||
| lme4 (>= 1.1-31), | ||
| parameters (>= 0.20.2), | ||
| smd (>= 0.6.6), | ||
| spelling, | ||
| survey (>= 4.1), | ||
| survival (>= 3.2-11), | ||
| testthat (>= 3.2.0), | ||
| withr | ||
| withr (>= 2.5.0) | ||
| Remotes: | ||
| insightsengineering/cards | ||
| Config/Needs/website: insightsengineering/nesttemplate | ||
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| #' ARD Wald Test | ||
| #' | ||
| #' @description | ||
| #' Function takes a regression model object and calculates Wald | ||
| #' statistical test using [`aod::wald.test()`]. | ||
| #' | ||
| #' @param x regression model object | ||
| #' @param ... arguments passed to `aod::wald.test(...)` | ||
| #' | ||
| #' @return data frame | ||
| #' @export | ||
| #' | ||
| #' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "aod", reference_pkg = "cardx")) | ||
| #' lm(AGE ~ ARM, data = cards::ADSL) |> | ||
| #' ard_aod_wald_test() | ||
| ard_aod_wald_test <- function(x, ...) { | ||
| set_cli_abort_call() | ||
| # check installed packages --------------------------------------------------- | ||
| check_pkg_installed("aod", reference_pkg = "cardx") | ||
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| # check inputs --------------------------------------------------------------- | ||
| check_not_missing(x) | ||
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| # run regression() ----------------------------------------------------------- | ||
| reg_model <- cards::eval_capture_conditions( | ||
| ard_regression_basic(x, intercept = TRUE, stats_to_remove = c( | ||
| "var_type", | ||
| "var_label", | ||
| "var_class", "label", | ||
| "contrasts_type", "contrasts", "var_nlevels", "std.error", | ||
| "conf.low", "conf.high", "statistic", "p.value", "estimate" | ||
| )) | ||
| ) | ||
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| if (!is.null(reg_model[["error"]])) { | ||
| cli::cli_abort( | ||
| c("Unable to identify underlying variable names in regression model.", | ||
| i = "Is this model type supported by {.fun broom.helpers::tidy_plus_plus}, which is the function used to identify variable names?" | ||
| ), | ||
| call = get_cli_abort_call() | ||
| ) | ||
| } | ||
| aod <- | ||
| reg_model[["result"]] %>% | ||
| dplyr::select(c( | ||
| variable = "variable", | ||
| model_terms = "stat" | ||
| )) %>% | ||
| dplyr::mutate(term_id = dplyr::row_number()) %>% | ||
| tidyr::nest(data = -"variable") %>% | ||
| dplyr::rowwise() %>% | ||
| dplyr::mutate( | ||
| model_terms = unlist(.data$data[["model_terms"]]) %>% list(), | ||
| model_terms_id = rlang::set_names(.data$data[["term_id"]]) %>% list() | ||
| ) | ||
| # run wald.test() ----------------------------------------------------------- | ||
| wald_test <- | ||
| cards::eval_capture_conditions(lapply(seq_len(length(aod$model_terms_id)), function(terms_id) { | ||
| aod::wald.test( | ||
| Sigma = stats::vcov(x), | ||
| b = stats::coef(x), Terms = aod$model_terms_id[[terms_id]] | ||
| ) | ||
| })) | ||
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| df_list <- do.call(rbind, lapply(wald_test$result, .extract_wald_results)) | ||
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| cbind(aod$variable, df_list) %>% | ||
| tidyr::pivot_longer( | ||
| cols = !"aod$variable", | ||
| names_to = "stat_name", | ||
| values_to = "stat" | ||
| ) %>% | ||
| dplyr::rename( | ||
| "variable" = "aod$variable" | ||
| ) |> | ||
| dplyr::mutate( | ||
| stat = as.list(.data$stat), | ||
| stat_label = | ||
| dplyr::case_when( | ||
| .data$stat_name %in% "statistic" ~ "Statistic", | ||
| .data$stat_name %in% "df" ~ "Degrees of Freedom", | ||
| .data$stat_name %in% "p.value" ~ "p-value", | ||
| TRUE ~ .data$stat_name | ||
| ), | ||
| fmt_fn = | ||
| map( | ||
| .data$stat, | ||
| function(.x) { | ||
| # styler: off | ||
| if (is.integer(.x)) return(0L) | ||
| if (is.numeric(.x)) return(1L) | ||
| # styler: on | ||
| NULL | ||
| } | ||
| ), | ||
| context = "aod_wald_test", | ||
| warning = wald_test["warning"], | ||
| error = wald_test["error"] | ||
| ) |> | ||
| cards::tidy_ard_column_order() %>% | ||
| {structure(., class = c("card", class(.)))} # styler: off | ||
| } | ||
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| #' Extract data from wald.test object | ||
| #' | ||
| #' @param wald_test (`data.frame`)\cr wald test object object from `aod::wald.test()` | ||
| #' | ||
| #' @return a data frame containing the wald test results. | ||
| #' @keywords internal | ||
| .extract_wald_results <- function(wald_test) { | ||
| df <- wald_test$result$chi2[("df")] | ||
| statistic <- wald_test$result$chi2[("chi2")] | ||
| p.value <- wald_test$result$chi2[("P")] | ||
| data.frame(df, statistic, p.value) | ||
| } |
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