From 8beebe6c1c97e4142f34c882f009a96bd326a81a Mon Sep 17 00:00:00 2001
From: Malcolm Barrett <malcolmbarrett@gmail.com>
Date: Fri, 8 Aug 2025 17:11:04 -0400
Subject: [PATCH 1/2] add air support

---
 .Rbuildignore                       |  2 +
 .github/workflows/format-check.yaml | 23 +++++++++
 .vscode/extensions.json             |  5 ++
 .vscode/settings.json               | 10 ++++
 R/plot_ess.R                        | 10 ++--
 air.toml                            |  0
 tests/testthat/test-check_ess.R     | 61 ++++++++++++++---------
 tests/testthat/test-ess.R           |  2 +-
 tests/testthat/test-plot_ess.R      | 75 +++++++++++++++++------------
 9 files changed, 129 insertions(+), 59 deletions(-)
 create mode 100644 .github/workflows/format-check.yaml
 create mode 100644 .vscode/extensions.json
 create mode 100644 .vscode/settings.json
 create mode 100644 air.toml

diff --git a/.Rbuildignore b/.Rbuildignore
index 23c85c6..2dca8b9 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,5 @@
 ^scratch$
 ^\.claude$
 CLAUDE.md
+^[.]?air[.]toml$
+^\.vscode$
diff --git a/.github/workflows/format-check.yaml b/.github/workflows/format-check.yaml
new file mode 100644
index 0000000..e29e3c4
--- /dev/null
+++ b/.github/workflows/format-check.yaml
@@ -0,0 +1,23 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: format-check.yaml
+
+permissions: read-all
+
+jobs:
+  format-check:
+    name: format-check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Check
+        run: air format . --check
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000..344f76e
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..a9f69fe
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,10 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    },
+    "[quarto]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "quarto.quarto"
+    }
+}
diff --git a/R/plot_ess.R b/R/plot_ess.R
index 4c21d3a..ca9f4c5 100644
--- a/R/plot_ess.R
+++ b/R/plot_ess.R
@@ -71,7 +71,7 @@
 #' # Using pre-computed ESS data
 #' ess_data <- check_ess(nhefs_weights, .wts = c(w_ate, w_att))
 #' plot_ess(ess_data)
-#' 
+#'
 #' # Show ESS on original scale instead of percentage
 #' plot_ess(nhefs_weights, .wts = c(w_ate, w_att), percent_scale = FALSE)
 #'
@@ -108,7 +108,7 @@ plot_ess <- function(
 
   # Determine if we have groups
   has_groups <- "group" %in% names(.data)
-  
+
   # Choose which variable to plot
   y_var <- if (percent_scale) "ess_pct" else "ess"
 
@@ -191,12 +191,14 @@ plot_ess <- function(
   p <- p +
     ggplot2::labs(
       x = "method",
-      y = if (percent_scale) "effective sample size (%)" else "effective sample size"
+      y = if (percent_scale) "effective sample size (%)" else
+        "effective sample size"
     ) +
     ggplot2::scale_y_continuous(
       limits = c(0, y_upper),
       expand = c(0, 0),
-      labels = if (percent_scale) \(x) scales::percent(x / 100) else scales::number
+      labels = if (percent_scale) \(x) scales::percent(x / 100) else
+        scales::number
     )
 
   p
diff --git a/air.toml b/air.toml
new file mode 100644
index 0000000..e69de29
diff --git a/tests/testthat/test-check_ess.R b/tests/testthat/test-check_ess.R
index 050babb..51257a1 100644
--- a/tests/testthat/test-check_ess.R
+++ b/tests/testthat/test-check_ess.R
@@ -1,6 +1,6 @@
 test_that("check_ess works with no weights", {
   result <- check_ess(nhefs_weights)
-  
+
   expect_s3_class(result, "tbl_df")
   expect_equal(nrow(result), 1)
   expect_equal(result$method, "observed")
@@ -10,7 +10,7 @@ test_that("check_ess works with no weights", {
 
 test_that("check_ess works with single weight", {
   result <- check_ess(nhefs_weights, .wts = w_ate)
-  
+
   expect_s3_class(result, "tbl_df")
   expect_equal(nrow(result), 2)
   expect_equal(result$method, c("observed", "w_ate"))
@@ -20,7 +20,7 @@ test_that("check_ess works with single weight", {
 
 test_that("check_ess works with multiple weights", {
   result <- check_ess(nhefs_weights, .wts = c(w_ate, w_att, w_atm))
-  
+
   expect_s3_class(result, "tbl_df")
   expect_equal(nrow(result), 4)
   # Methods may be returned in different order due to tidyselect
@@ -29,14 +29,14 @@ test_that("check_ess works with multiple weights", {
 
 test_that("check_ess works without observed", {
   result <- check_ess(nhefs_weights, .wts = w_ate, include_observed = FALSE)
-  
+
   expect_equal(nrow(result), 1)
   expect_equal(result$method, "w_ate")
 })
 
 test_that("check_ess works with binary groups", {
   result <- check_ess(nhefs_weights, .wts = w_ate, .group = qsmk)
-  
+
   expect_s3_class(result, "tbl_df")
   expect_true("group" %in% names(result))
   expect_equal(length(unique(result$group)), 2)
@@ -45,7 +45,7 @@ test_that("check_ess works with binary groups", {
 
 test_that("check_ess works with categorical groups", {
   result <- check_ess(nhefs_weights, .wts = w_cat_ate, .group = alcoholfreq_cat)
-  
+
   expect_s3_class(result, "tbl_df")
   expect_true("group" %in% names(result))
   expect_true(length(unique(result$group)) > 2)
@@ -53,7 +53,7 @@ test_that("check_ess works with categorical groups", {
 
 test_that("check_ess works with continuous groups", {
   result <- check_ess(nhefs_weights, .wts = w_ate, .group = age, n_tiles = 4)
-  
+
   expect_s3_class(result, "tbl_df")
   expect_true("group" %in% names(result))
   expect_equal(length(unique(result$group)), 4)
@@ -62,16 +62,24 @@ test_that("check_ess works with continuous groups", {
 
 test_that("check_ess works with custom tile labels", {
   labels <- c("Young", "Middle", "Older")
-  result <- check_ess(nhefs_weights, .wts = w_ate, .group = age, 
-                      n_tiles = 3, tile_labels = labels)
-  
+  result <- check_ess(
+    nhefs_weights,
+    .wts = w_ate,
+    .group = age,
+    n_tiles = 3,
+    tile_labels = labels
+  )
+
   expect_setequal(as.character(unique(result$group)), labels)
 })
 
 test_that("check_ess handles tidyselect syntax", {
   result1 <- check_ess(nhefs_weights, .wts = starts_with("w_a"))
-  result2 <- check_ess(nhefs_weights, .wts = c(w_ate, w_att, w_atc, w_atm, w_ato))
-  
+  result2 <- check_ess(
+    nhefs_weights,
+    .wts = c(w_ate, w_att, w_atc, w_atm, w_ato)
+  )
+
   # Should have same number of methods (plus observed)
   expect_equal(nrow(result1), nrow(result2))
 })
@@ -80,7 +88,7 @@ test_that("check_ess handles psw weight objects", {
   # Assuming psw weights are numeric vectors with special class
   # The extract_weight_data function should handle conversion
   result <- check_ess(nhefs_weights, .wts = w_ate)
-  
+
   expect_true(is.numeric(result$ess))
   expect_true(all(result$ess > 0))
 })
@@ -90,15 +98,20 @@ test_that("check_ess validates inputs", {
     check_ess("not a data frame"),
     "halfmoon_type_error"
   )
-  
+
   expect_halfmoon_error(
     check_ess(nhefs_weights, .group = "not_a_column"),
     "halfmoon_column_error"
   )
-  
+
   expect_halfmoon_error(
-    check_ess(nhefs_weights, .wts = w_ate, .group = age,
-              n_tiles = 3, tile_labels = c("Too", "Few")),
+    check_ess(
+      nhefs_weights,
+      .wts = w_ate,
+      .group = age,
+      n_tiles = 3,
+      tile_labels = c("Too", "Few")
+    ),
     "halfmoon_length_error"
   )
 })
@@ -106,12 +119,12 @@ test_that("check_ess validates inputs", {
 test_that("ESS calculation is correct", {
   # Create simple test case with known ESS
   test_df <- data.frame(
-    wts = c(1, 1, 1, 1),  # Equal weights -> ESS = n
-    wts2 = c(4, 0, 0, 0)  # All weight on one obs -> ESS = 1
+    wts = c(1, 1, 1, 1), # Equal weights -> ESS = n
+    wts2 = c(4, 0, 0, 0) # All weight on one obs -> ESS = 1
   )
-  
+
   result <- check_ess(test_df, .wts = c(wts, wts2), include_observed = FALSE)
-  
+
   expect_equal(result$ess[result$method == "wts"], 4)
   expect_equal(result$ess[result$method == "wts2"], 1)
   expect_equal(result$ess_pct[result$method == "wts"], 100)
@@ -122,10 +135,10 @@ test_that("check_ess handles NA values", {
   # Create data with NAs
   test_df <- nhefs_weights
   test_df$w_ate[1:10] <- NA
-  
+
   result <- check_ess(test_df, .wts = w_ate)
-  
+
   # Should still compute ESS on non-NA values
   expect_true(all(!is.na(result$ess)))
   expect_true(all(result$ess > 0))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-ess.R b/tests/testthat/test-ess.R
index 8e8b1e7..0b9a617 100644
--- a/tests/testthat/test-ess.R
+++ b/tests/testthat/test-ess.R
@@ -29,7 +29,7 @@ test_that("ess gives `NaN` if all weights are 0", {
 test_that("ess handles NA values", {
   # With na.rm = FALSE (default), should return NA
   expect_true(is.na(ess(c(1, 2, NA, 3))))
-  
+
   # With na.rm = TRUE, should calculate ESS on non-NA values
   expect_equal(ess(c(1, 1, NA, 1), na.rm = TRUE), 3)
   expect_true(ess(c(0.5, 2, NA, 0.1), na.rm = TRUE) < 3)
diff --git a/tests/testthat/test-plot_ess.R b/tests/testthat/test-plot_ess.R
index 609a4d6..dc19473 100644
--- a/tests/testthat/test-plot_ess.R
+++ b/tests/testthat/test-plot_ess.R
@@ -1,13 +1,13 @@
 test_that("plot_ess creates a ggplot object", {
   p <- plot_ess(nhefs_weights, .wts = w_ate)
-  
+
   expect_s3_class(p, "ggplot")
   expect_s3_class(p, "gg")
 })
 
 test_that("plot_ess works with raw data", {
   p <- plot_ess(nhefs_weights, .wts = c(w_ate, w_att))
-  
+
   expect_s3_class(p, "ggplot")
   # Check that data was computed
   expect_true("ess_pct" %in% names(p$data))
@@ -16,39 +16,42 @@ test_that("plot_ess works with raw data", {
 test_that("plot_ess works with pre-computed ESS data", {
   ess_data <- check_ess(nhefs_weights, .wts = c(w_ate, w_att))
   p <- plot_ess(ess_data)
-  
+
   expect_s3_class(p, "ggplot")
   expect_equal(nrow(p$data), nrow(ess_data))
 })
 
 test_that("plot_ess works without groups", {
   p <- plot_ess(nhefs_weights, .wts = c(w_ate, w_att))
-  
+
   # Should have single fill color (no group aesthetic)
   expect_true(!"fill" %in% names(p$mapping))
-  
+
   # Check layers
   expect_true(any(sapply(p$layers, function(l) inherits(l$geom, "GeomCol"))))
 })
 
 test_that("plot_ess works with groups", {
   p <- plot_ess(nhefs_weights, .wts = c(w_ate, w_att), .group = qsmk)
-  
+
   # Should have fill aesthetic for groups
   expect_true("fill" %in% names(p$mapping))
-  
+
   # Check for dodged position
-  col_layer <- p$layers[[which(sapply(p$layers, function(l) inherits(l$geom, "GeomCol")))]]
+  col_layer <- p$layers[[which(sapply(
+    p$layers,
+    function(l) inherits(l$geom, "GeomCol")
+  ))]]
   expect_s3_class(col_layer$position, "PositionDodge")
 })
 
 test_that("plot_ess includes reference line", {
   p <- plot_ess(nhefs_weights, .wts = w_ate)
-  
+
   # Check for horizontal line at 100
   hline_layer <- sapply(p$layers, function(l) inherits(l$geom, "GeomHline"))
   expect_true(any(hline_layer))
-  
+
   # Check that line is at 100
   hline_idx <- which(hline_layer)[1]
   expect_equal(p$layers[[hline_idx]]$data$yintercept, 100)
@@ -57,18 +60,24 @@ test_that("plot_ess includes reference line", {
 test_that("plot_ess labels work correctly", {
   p_with_labels <- plot_ess(nhefs_weights, .wts = w_ate, show_labels = TRUE)
   p_without_labels <- plot_ess(nhefs_weights, .wts = w_ate, show_labels = FALSE)
-  
+
   # Check for text layer
-  text_layer_with <- sapply(p_with_labels$layers, function(l) inherits(l$geom, "GeomText"))
-  text_layer_without <- sapply(p_without_labels$layers, function(l) inherits(l$geom, "GeomText"))
-  
+  text_layer_with <- sapply(
+    p_with_labels$layers,
+    function(l) inherits(l$geom, "GeomText")
+  )
+  text_layer_without <- sapply(
+    p_without_labels$layers,
+    function(l) inherits(l$geom, "GeomText")
+  )
+
   expect_true(any(text_layer_with))
   expect_false(any(text_layer_without))
 })
 
 test_that("plot_ess y-axis uses percent scale", {
   p <- plot_ess(nhefs_weights, .wts = w_ate)
-  
+
   # Check that y-axis has percent labels
   y_scale <- p$scales$get_scales("y")
   expect_true(is.function(y_scale$labels))
@@ -76,37 +85,43 @@ test_that("plot_ess y-axis uses percent scale", {
 
 test_that("plot_ess handles continuous groups", {
   p <- plot_ess(nhefs_weights, .wts = w_ate, .group = age, n_tiles = 4)
-  
+
   expect_s3_class(p, "ggplot")
   expect_true("fill" %in% names(p$mapping))
 })
 
 test_that("plot_ess customization works", {
   p <- plot_ess(
-    nhefs_weights, 
+    nhefs_weights,
     .wts = w_ate,
     fill_color = "red",
     alpha = 0.5,
     reference_line_color = "blue",
     reference_line_type = "solid"
   )
-  
+
   expect_s3_class(p, "ggplot")
-  
+
   # Check fill color for non-grouped plot
-  col_layer <- p$layers[[which(sapply(p$layers, function(l) inherits(l$geom, "GeomCol")))]]
+  col_layer <- p$layers[[which(sapply(
+    p$layers,
+    function(l) inherits(l$geom, "GeomCol")
+  ))]]
   expect_equal(col_layer$aes_params$fill, "red")
   expect_equal(col_layer$aes_params$alpha, 0.5)
-  
+
   # Check reference line
-  hline_layer <- p$layers[[which(sapply(p$layers, function(l) inherits(l$geom, "GeomHline")))]]
+  hline_layer <- p$layers[[which(sapply(
+    p$layers,
+    function(l) inherits(l$geom, "GeomHline")
+  ))]]
   expect_equal(hline_layer$aes_params$colour, "blue")
   expect_equal(hline_layer$aes_params$linetype, "solid")
 })
 
 test_that("plot_ess has correct labels", {
   p <- plot_ess(nhefs_weights, .wts = w_ate)
-  
+
   expect_equal(p$labels$x, "method")
   expect_equal(p$labels$y, "effective sample size (%)")
 })
@@ -114,11 +129,11 @@ test_that("plot_ess has correct labels", {
 test_that("plot_ess y-limits are appropriate", {
   # Create data with low ESS
   test_df <- data.frame(
-    wts = c(10, 0.1, 0.1, 0.1)  # Very unequal weights
+    wts = c(10, 0.1, 0.1, 0.1) # Very unequal weights
   )
-  
+
   p <- plot_ess(test_df, .wts = wts, include_observed = FALSE)
-  
+
   # Y-axis should start at 0 and go above the max value
   y_scale <- p$scales$get_scales("y")
   expect_equal(y_scale$limits[1], 0)
@@ -131,22 +146,22 @@ test_that("plot_ess snapshot tests", {
     "plot_ess_basic",
     plot_ess(nhefs_weights, .wts = c(w_ate, w_att))
   )
-  
+
   # Plot with groups
   expect_doppelganger(
     "plot_ess_groups",
     plot_ess(nhefs_weights, .wts = c(w_ate, w_att), .group = qsmk)
   )
-  
+
   # Plot without labels
   expect_doppelganger(
     "plot_ess_no_labels",
     plot_ess(nhefs_weights, .wts = c(w_ate, w_att), show_labels = FALSE)
   )
-  
+
   # Plot with continuous groups
   expect_doppelganger(
     "plot_ess_continuous",
     plot_ess(nhefs_weights, .wts = w_ate, .group = age, n_tiles = 3)
   )
-})
\ No newline at end of file
+})

From 6660a0a645c5edf07a8157d8fda5b16a44f82182 Mon Sep 17 00:00:00 2001
From: Malcolm Barrett <malcolmbarrett@gmail.com>
Date: Fri, 8 Aug 2025 17:14:13 -0400
Subject: [PATCH 2/2] update name

---
 .github/workflows/format-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/format-check.yaml b/.github/workflows/format-check.yaml
index e29e3c4..bbb1384 100644
--- a/.github/workflows/format-check.yaml
+++ b/.github/workflows/format-check.yaml
@@ -5,7 +5,7 @@ on:
     branches: [main, master]
   pull_request:
 
-name: format-check.yaml
+name: air
 
 permissions: read-all