Paired test ordering (#1560)

* ordering fix for paired test

* increment version number

* Update NEWS.md

* cleanup

* Update test-vetted_models-clogit.R

* Update DESCRIPTION

* Update add_difference.md

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result
     Tables
-Version: 1.7.2.9000
+Version: 1.7.2.9001
 Authors@R: 
     c(person(given = "Daniel D.",
              family = "Sjoberg",
@@ -75,12 +75,12 @@ Depends:
     R (>= 3.4)
 Imports: 
     broom (>= 1.0.1),
-    broom.helpers (>= 1.13.0),
+    broom.helpers (>= 1.14.0),
     cli (>= 3.1.1),
     dplyr (>= 1.1.1),
     forcats (>= 1.0.0),
     glue (>= 1.6.2),
-    gt (>= 0.9.0),
+    gt (>= 0.10.0),
     knitr (>= 1.37),
     lifecycle (>= 1.0.1),
     purrr (>= 1.0.1),

NEWS.md

@@ -1,5 +1,7 @@
 # gtsummary (development version)
 
+* Fix in `add_difference()` for pair t-tests. Previously, the sign of the reported difference depended on which group appeared first in the source data. Function has been updated to consistently report the difference as the first group mean minus the second group mean. (#1557)
+
 # gtsummary 1.7.2
 
 * Removed messaging about the former auto-removal of the `tbl_summary(group)` variable from the table: a change that occurred 3+ years ago in gtsummary v1.3.1

R/utils-add_p_tests.R

@@ -141,7 +141,7 @@ add_p_tbl_summary_paired.t.test <- function(data, variable, by, group,
 
   # reshaping data
   data_wide <-
-    tidyr::pivot_wider(data,
+    tidyr::pivot_wider(dplyr::arrange(data, .data[[by]]),
       id_cols = all_of(group),
       names_from = all_of(by),
       values_from = all_of(variable)
@@ -245,7 +245,7 @@ add_p_tbl_summary_paired.wilcox.test <- function(data, variable, by, group,
 
   # reshaping data
   data_wide <-
-    tidyr::pivot_wider(data,
+    tidyr::pivot_wider(dplyr::arrange(data, .data[[by]]),
       id_cols = all_of(group),
       names_from = all_of(by),
       values_from = all_of(variable)

tests/testthat/_snaps/add_difference.md

@@ -135,3 +135,33 @@
       1                   -0.42  -4.5, 3.7         0.8
       2                   -4.7% -18%, 8.4%         0.5
 
+# ordering in add_difference() with paired tests
+
+    Code
+      mtcars %>% mutate(.by = am, id = row_number(), am = factor(am, levels = c(0, 1))) %>%
+        tbl_summary(by = am, include = mpg) %>% add_difference(test = ~
+        "paired.t.test", group = id) %>% as_kable()
+    Message
+      Note for variable 'mpg': Some observations included in the calculation of summary statistics were omitted from the p-value calculation due to unbalanced missingness within group.
+    Output
+      
+      
+      |**Characteristic** |   **0**, N = 19   |   **1**, N = 13   | **Difference** | **95% CI** | **p-value** |
+      |:------------------|:-----------------:|:-----------------:|:--------------:|:----------:|:-----------:|
+      |mpg                | 17.3 (15.0, 19.2) | 22.8 (21.0, 30.4) |      -7.0      | -10, -3.6  |   <0.001    |
+
+---
+
+    Code
+      mtcars %>% mutate(.by = am, id = row_number(), am = factor(am, levels = c(1, 0))) %>%
+        tbl_summary(by = am, include = mpg) %>% add_difference(test = ~
+        "paired.t.test", group = id) %>% as_kable()
+    Message
+      Note for variable 'mpg': Some observations included in the calculation of summary statistics were omitted from the p-value calculation due to unbalanced missingness within group.
+    Output
+      
+      
+      |**Characteristic** |   **1**, N = 13   |   **0**, N = 19   | **Difference** | **95% CI** | **p-value** |
+      |:------------------|:-----------------:|:-----------------:|:--------------:|:----------:|:-----------:|
+      |mpg                | 22.8 (21.0, 30.4) | 17.3 (15.0, 19.2) |      7.0       |  3.6, 10   |   <0.001    |
+

tests/testthat/test-add_difference.R

@@ -342,3 +342,35 @@ test_that("add_difference() with emmeans()", {
     NA
   )
 })
+
+
+test_that("ordering in add_difference() with paired tests", {
+  expect_snapshot(
+    mtcars %>%
+      mutate(
+        .by = am,
+        id = row_number(),
+        am = factor(am, levels = c(0, 1))
+      ) %>%
+      tbl_summary(
+        by = am,
+        include = mpg
+      ) %>%
+      add_difference(test = ~"paired.t.test", group = id) %>%
+      as_kable()
+  )
+  expect_snapshot(
+    mtcars %>%
+      mutate(
+        .by = am,
+        id = row_number(),
+        am = factor(am, levels = c(1, 0))
+      ) %>%
+      tbl_summary(
+        by = am,
+        include = mpg
+      ) %>%
+      add_difference(test = ~"paired.t.test", group = id) %>%
+      as_kable()
+  )
+})

tests/testthat/test-vetted_models-clogit.R

@@ -25,7 +25,6 @@ skip_on_cran()
 skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
 library(survival)
 
 # clogit() ---------------------------------------------------------------------

tests/testthat/test-vetted_models-coxph.R

@@ -25,14 +25,12 @@ skip_on_cran()
 skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
-library(survival)
 
 # coxph() ----------------------------------------------------------------------
 test_that("vetted_models coxph()", {
   # building models to check
-  mod_coxph_lin <- coxph(Surv(ttdeath, death) ~ age + trt + grade, data = trial)
-  mod_coxph_int <- coxph(Surv(ttdeath, death) ~ age + trt * grade, data = trial)
+  mod_coxph_lin <- survival::coxph(survival::Surv(ttdeath, death) ~ age + trt + grade, data = trial)
+  mod_coxph_int <- survival::coxph(survival::Surv(ttdeath, death) ~ age + trt * grade, data = trial)
   # 1.  Runs as expected with standard use
   #       - without errors, warnings, messages
   expect_error(
@@ -157,8 +155,8 @@ test_that("vetted_models coxph()", {
   expect_error(
     trial %>%
       tbl_uvregression(
-        y = Surv(ttdeath, death),
-        method = coxph
+        y = survival::Surv(ttdeath, death),
+        method = survival::coxph
       ) %>%
       add_global_p() %>%
       add_q(),
@@ -167,8 +165,8 @@ test_that("vetted_models coxph()", {
   expect_warning(
     trial %>%
       tbl_uvregression(
-        y = Surv(ttdeath, death),
-        method = coxph
+        y = survival::Surv(ttdeath, death),
+        method = survival::coxph
       ) %>%
       add_nevent() %>%
       add_global_p() %>%

tests/testthat/test-vetted_models-geeglm.R

@@ -26,7 +26,6 @@ skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("geepack", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
 
 # geeglm() --------------------------------------------------------------------
 test_that("vetted_models geeglm()", {

tests/testthat/test-vetted_models-glm.R

@@ -26,7 +26,6 @@ skip_on_cran()
 skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
 
 # glm() ------------------------------------------------------------------------
 test_that("vetted_models glm()", {

tests/testthat/test-vetted_models-glmer.R

@@ -26,7 +26,6 @@ skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("lme4", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
 
 # glmer() --------------------------------------------------------------------
 test_that("vetted_models glmer()", {

tests/testthat/test-vetted_models-lm.R

@@ -25,7 +25,6 @@ skip_on_cran()
 testthat::skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
 
 # lm() ------------------------------------------------------------------------
 test_that("vetted_models lm()", {

tests/testthat/test-vetted_models-lmer.R

@@ -26,7 +26,6 @@ skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("lme4", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
 
 # lmer() -----------------------------------------------------------------------
 test_that("vetted_models lmer()", {

tests/testthat/test-vetted_models-survreg.R

@@ -35,15 +35,13 @@ skip_if(!isTRUE(as.logical(Sys.getenv("CI"))))
 skip_if_not(broom.helpers::.assert_package("car", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("lme4", pkg_search = "gtsummary", boolean = TRUE))
 skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
-library(dplyr)
-library(survival)
 
 
 # survreg() --------------------------------------------------------------------
 test_that("vetted_models survreg()", {
   # building models to check
-  mod_survreg_lin <- survreg(Surv(ttdeath, death) ~ age + trt + grade, data = trial)
-  mod_survreg_int <- survreg(Surv(ttdeath, death) ~ age + trt * grade, data = trial)
+  mod_survreg_lin <- survival::survreg(survival::Surv(ttdeath, death) ~ age + trt + grade, data = trial)
+  mod_survreg_int <- survival::survreg(survival::Surv(ttdeath, death) ~ age + trt * grade, data = trial)
   # 1.  Runs as expected with standard use
   #       - without errors, warnings, messages
   expect_error(
@@ -82,15 +80,15 @@ test_that("vetted_models survreg()", {
   #       - labels are correct
   expect_equal(
     tbl_survreg_lin$table_body %>%
-      filter(row_type == "label") %>%
-      pull(label),
+      dplyr::filter(row_type == "label") %>%
+      dplyr::pull(label),
     c("Age", "Chemotherapy Treatment", "Grade"),
     ignore_attr = TRUE
   )
   expect_equal(
     tbl_survreg_int$table_body %>%
-      filter(row_type == "label") %>%
-      pull(label),
+      dplyr::filter(row_type == "label") %>%
+      dplyr::pull(label),
     c("Age", "Chemotherapy Treatment", "Grade", "Chemotherapy Treatment * Grade"),
     ignore_attr = TRUE
   )
@@ -99,8 +97,8 @@ test_that("vetted_models survreg()", {
   #       - interaction labels are correct
   expect_equal(
     tbl_survreg_int$table_body %>%
-      filter(var_type == "interaction") %>%
-      pull(label),
+      dplyr::filter(var_type == "interaction") %>%
+      dplyr::pull(label),
     c("Chemotherapy Treatment * Grade", "Drug B * II", "Drug B * III"),
     ignore_attr = TRUE
   )
@@ -127,7 +125,7 @@ test_that("vetted_models survreg()", {
   #       - numbers in table are correct
   expect_equal(
     tbl_survreg_lin2$table_body %>%
-      pull(p.value) %>%
+      dplyr::pull(p.value) %>%
       na.omit() %>%
       as.vector(),
     car::Anova(mod_survreg_lin, type = "III") %>%
@@ -137,16 +135,16 @@ test_that("vetted_models survreg()", {
   )
   expect_equal(
     tbl_survreg_int2$table_body %>%
-      pull(p.value) %>%
+      dplyr::pull(p.value) %>%
       na.omit() %>%
       as.vector(),
     car::Anova(mod_survreg_int, type = "III") %>%
       as.data.frame() %>%
-      pull(`Pr(>Chisq)`),
+      dplyr::pull(`Pr(>Chisq)`),
     ignore_attr = TRUE
   )
   expect_equal(
-    tbl_survreg_lin3$table_body %>% filter(variable == "trt") %>% pull(p.value),
+    tbl_survreg_lin3$table_body %>% dplyr::filter(variable == "trt") %>% pull(p.value),
     car::Anova(mod_survreg_lin, type = "III") %>%
       as.data.frame() %>%
       tibble::rownames_to_column() %>%
@@ -160,8 +158,8 @@ test_that("vetted_models survreg()", {
   expect_error(
     trial %>%
       tbl_uvregression(
-        y = Surv(ttdeath, death),
-        method = survreg
+        y = survival::Surv(ttdeath, death),
+        method = survival::survreg
       ) %>%
       add_global_p() %>%
       add_q(),