From d3e1d78418b55c86929dc3503a60357f12d9d0fe Mon Sep 17 00:00:00 2001
From: bailliem <bailliem@gmail.com>
Date: Fri, 26 Jul 2024 20:12:41 +0200
Subject: [PATCH] tidy up tidy fun

---
 NEWS.md                          |  2 ++
 R/beeca-package.R                |  3 +++
 R/tidy_beeca.R                   | 21 ++++++++++++++-------
 man/tidy_beeca.Rd                | 12 ++++++++----
 tests/testthat/test-tidy_beeca.R |  8 +-------
 5 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 9c90526..fcfb1b2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
 # beeca 0.1.4
 
+- Add `tidy_beeca()` function
+
 # beeca 0.1.3
 
 - Preparation for CRAN submission
diff --git a/R/beeca-package.R b/R/beeca-package.R
index 94b926a..10a8b0c 100644
--- a/R/beeca-package.R
+++ b/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"))
diff --git a/R/tidy_beeca.R b/R/tidy_beeca.R
index 7818901..fac676e 100644
--- a/R/tidy_beeca.R
+++ b/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(
@@ -69,7 +74,7 @@ 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
@@ -77,11 +82,13 @@ tidy_beeca <- function(x, conf.int = FALSE, conf.level = 0.95, ...) {
 
     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)
 }
+
+
diff --git a/man/tidy_beeca.Rd b/man/tidy_beeca.Rd
index f30d335..a28f6f3 100644
--- a/man/tidy_beeca.Rd
+++ b/man/tidy_beeca.Rd
@@ -4,7 +4,7 @@
 \alias{tidy_beeca}
 \title{Tidy a beeca/glm object}
 \usage{
-tidy_beeca(x, conf.int = FALSE, conf.level = 0.95, ...)
+tidy_beeca(x, conf.int = FALSE, conf.level = 0.95)
 }
 \arguments{
 \item{x}{a 'glm' object created with \code{get_marginal_effect()}}
@@ -15,7 +15,7 @@ tidy_beeca(x, conf.int = FALSE, conf.level = 0.95, ...)
 }
 \value{
 a tibble
-the default values returned are the following
+The default values returned are the following
 \tabular{ll}{
 term      \tab treatment variable \cr
 contrast  \tab the contrast used to estimate the marginal effect \cr
@@ -23,14 +23,18 @@ estimate  \tab the average treatment effect \cr
 std.error \tab the standard error based on the Ge or Ye method \cr
 statistic \tab the z-score of the estimate divided by the standard error \cr
 p.value   \tab 2-sided p-value \cr
+conf.low  \tab lower bound of the confidence interval (if specified) \cr
+conf.high \tab upper bound of the confidence interval (if specified) \cr
 }
 }
 \description{
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}\cr
+}
+\details{
 The broom package exports a tidier for \code{"glm"} objects.
 This function adds on top of that and returns more information
 that is stored from g-computation.
-}
-\details{
+
 The function also utilizes additional information stored when the
 glm object is created with \code{get_marginal_effect()}.
 It's recommended to always use this function with \code{get_marginal_effect()}.
diff --git a/tests/testthat/test-tidy_beeca.R b/tests/testthat/test-tidy_beeca.R
index 8c47781..1cbd2eb 100644
--- a/tests/testthat/test-tidy_beeca.R
+++ b/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)
 })
 
-
-