tidy up tidy fun

NEWS.md

@@ -1,5 +1,7 @@
 # beeca 0.1.4
 
+- Add `tidy_beeca()` function
+
 # beeca 0.1.3
 
 - Preparation for CRAN submission

R/beeca-package.R

@@ -5,3 +5,6 @@
 #' @importFrom lifecycle deprecated
 ## usethis namespace: end
 NULL
+
+## declare global variables
+utils::globalVariables(c("estimate", "std.error", "statistic"))

R/tidy_beeca.R

@@ -45,7 +45,7 @@
 #' broom::tidy(fit1, conf.int = TRUE)
 #' tidy_beeca(fit1, conf.int = TRUE)
 #'
-tidy_beeca <- function(x, conf.int = FALSE, conf.level = 0.95, ...) {
+tidy_beeca <- function(x, conf.int = FALSE, conf.level = 0.95) {
 
   results <- NULL
 
@@ -56,11 +56,16 @@ tidy_beeca <- function(x, conf.int = FALSE, conf.level = 0.95, ...) {
     stop("x must be a 'beeca' object")
   }
 
-  results <- broom::tidy(x)
-
-  ## Extract results
+  # extract results
   marginal_results <- x$marginal_results
 
+  # Validate that marginal_results has the necessary columns
+  required_cols <- c("TRTVAR", "STAT", "TRTVAL", "STATVAL")
+  if (!all(required_cols %in% names(marginal_results))) {
+    stop("marginal_results must contain the required columns: ", paste(required_cols, collapse = ", "))
+  }
+
+  # tidy inputs  ---------------------------------------------------------------
 
   # define a tidy tibble
   result <- tibble::tibble(
@@ -69,19 +74,21 @@ tidy_beeca <- function(x, conf.int = FALSE, conf.level = 0.95, ...) {
     estimate = marginal_results[marginal_results$STAT == "diff", "STATVAL"][[1]],
     std.error = marginal_results[marginal_results$STAT == "diff_se", "STATVAL"][[1]],
     statistic = estimate / std.error,        # z-score
-    p.value = 2 * (1 - pnorm(abs(statistic)))   # 2-sided p-value
+    p.value = 2 * (1 - stats::pnorm(abs(statistic)))   # 2-sided p-value
   )
 
   ## add confidence interval if specified
   if (conf.int) {
 
     result <- result |>
       dplyr::mutate(
-        conf.low = estimate - qnorm(1 - conf.level / 2) * std.error,
-        conf.high = estimate + qnorm(1 - conf.level / 2) * std.error
+        conf.low = estimate - stats::qnorm(1 - conf.level / 2) * std.error,
+        conf.high = estimate + stats::qnorm(1 - conf.level / 2) * std.error
       )
   }
 
   # return tidy tibble
   return(result)
 }
+
+

tests/testthat/test-tidy_beeca.R

@@ -43,22 +43,16 @@ test_that("tidy_beeca returns correct values", {
   expect_equal(result$term, "trtp")
   expect_equal(result$estimate, fit$marginal_results$STATVAL[fit$marginal_results$STAT == "diff"])
   expect_equal(result$std.error, fit$marginal_results$STATVAL[fit$marginal_results$STAT == "diff_se"])
-  expect_equal(result$statistic, NA)
-  expect_equal(result$p.value, NA)
-})
+  })
 
 test_that("tidy_beeca returns correct values with confidence intervals", {
   result <- tidy_beeca(fit, conf.int = TRUE)
   expect_equal(result$term, "trtp")
   expect_equal(result$estimate, fit$marginal_results$STATVAL[fit$marginal_results$STAT == "diff"])
   expect_equal(result$std.error, fit$marginal_results$STATVAL[fit$marginal_results$STAT == "diff_se"])
-  expect_equal(result$statistic, NA)
-  expect_equal(result$p.value, NA)
   conf.low <- result$estimate - qnorm(1 - 0.95 / 2) * result$std.error
   conf.high <- result$estimate + qnorm(1 - 0.95 / 2) * result$std.error
   expect_equal(result$conf.low, conf.low, tolerance = 1e-8)
   expect_equal(result$conf.high, conf.high, tolerance = 1e-8)
 })
 
-
-