add_ci() fix (#1490)

* fix

* Update add_ci.md

* snap updates

* update

* Update test-add_global_p.R

* increment version number

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result
     Tables
-Version: 1.7.0.9006
+Version: 1.7.0.9007
 Authors@R: 
     c(person(given = "Daniel D.",
              family = "Sjoberg",

NEWS.md

@@ -1,5 +1,7 @@
 # gtsummary (development version)
 
+* Bug fix when a subset of CIs are requested in `add_ci(include=)`. (#1484)
+
 * Added French translations for new marginal effects tidiers housed in {broom.helpers}. (#1417)
 
 * Added theme elements to control the default headers in `tbl_svysummary()`. (#1452)

R/add_ci.R

@@ -262,21 +262,21 @@ add_ci.tbl_summary <- function(x,
   if (inherits(x, "tbl_summary")) {
     single_ci_fn <- single_ci
   }
-  if (inherits(x, "tbl_svysummary")) {
+  else if (inherits(x, "tbl_svysummary")) {
     single_ci_fn <- single_ci_svy
   }
   x <-
     x %>%
     add_stat(
-      fns = everything() ~ purrr::partial(single_ci_fn,
+      fns = all_of(include) ~ purrr::partial(single_ci_fn,
         method = method,
         conf.level = conf.level,
         statistic = statistic,
         style_fun = style_fun,
         summary_type = summary_type,
         df = df
       ),
-      location = list(everything() ~ "label", all_categorical(FALSE) ~ "level")
+      location = list(all_of(include) ~ "label", all_categorical(FALSE) ~ "level")
     ) %>%
     # moving the CI cols to after the original stat cols (when `by=` variable present)
     # also renaming CI columns

tests/testthat/_snaps/add_ci.md

@@ -130,6 +130,22 @@
       </table>
       </div>
 
+# add_ci() works on a subset of variables
+
+    Code
+      trial %>% tbl_summary(include = c(response, age)) %>% add_ci(include = age) %>%
+        as_tibble()
+    Message
+      x `add_ci()` added mean CI for "age"; however, no mean is shown in the `tbl_summary()` table.
+    Output
+      # A tibble: 4 x 3
+        `**Characteristic**` `**N = 200**` `**95% CI**`
+        <chr>                <chr>         <chr>       
+      1 Tumor Response       61 (32%)      <NA>        
+      2 Unknown              7             <NA>        
+      3 Age                  47 (38, 57)   45, 49      
+      4 Unknown              11            <NA>        
+
 # add_ci() works with tbl_svysummary
 
     Code

tests/testthat/test-add_ci.R

@@ -80,6 +80,17 @@ test_that("add_ci() works", {
     expect_snapshot()
 })
 
+test_that("add_ci() works on a subset of variables", {
+  expect_snapshot(
+    trial %>%
+      tbl_summary(
+        include = c(response, age)
+      ) %>%
+      add_ci(include = age) %>%
+      as_tibble()
+  )
+})
+
 test_that("add_ci() throws errors with bad arguments", {
   tbl0 <-
     trial %>%

tests/testthat/test-add_global_p.R

@@ -70,7 +70,6 @@ test_that("no errors/warnings with standard use after tbl_regression with non-st
   tbl1 <- tbl_regression(mod1)
   tbl2 <- tbl_regression(mod2)
 
-  expect_snapshot(res %>% render_as_html())
   expect_equal(
     car::Anova(mod1, type = "II") %>% select(last_col()) %>% pull() %>% discard(is.na),
     tbl1 %>% add_global_p(include = everything(), type = "II") %>% pluck("table_body", "p.value") %>% discard(is.na)