Release v0.7.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rifttable
 Type: Package
 Title: Results Tables to Bridge the Rift Between Epidemiologists and Their Data
-Version: 0.7.1
+Version: 0.7.2
 Authors@R:
     person(given = "Konrad H.",
            family = "Stopsack",
@@ -19,7 +19,7 @@ License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
     R (>= 4.1.0)
 Imports:

NEWS.md

@@ -1,3 +1,13 @@
+# rifttable 0.7.2
+
+* Bug fixes:
+  + `survdiff_ci()` now uses the `conf.level` argument correctly in confidence 
+    interval estimation using the MOVER approach (#8).
+* Internal:
+  + Anticipate changes in {dplyr} 1.2.0 in label handling in unit tests (thanks 
+    to @DavisVaughan, #10).
+
+
 # rifttable 0.7.1
 
 * Housekeeping for CRAN release

R/survdiff_ci.R

@@ -121,7 +121,8 @@ survdiff_ci <- function(
       formula = formula,
       data = data,
       id = .id,
-      weights = .weights
+      weights = .weights,
+      conf.int = conf.level
     ),
     time = time,
     extend = TRUE

tests/testthat/test-missing_data.R

@@ -2,9 +2,19 @@ data("breastcancer", package = "risks")
 df <- breastcancer |>
   dplyr::mutate(
     continuous = 1:dplyr::n(),
-    receptor = dplyr::if_else(dplyr::row_number() %in% 9:11, NA, receptor),
+    receptor = {
+      label <- attr(receptor, "label")
+      receptor <- dplyr::if_else(dplyr::row_number() %in% 9:11, NA, receptor)
+      attr(receptor, "label") <- label
+      receptor
+    },
     stage = dplyr::if_else(dplyr::row_number() %in% 29:31, NA, stage),
-    death = dplyr::if_else(dplyr::row_number() %in% 99:101, NA, death),
+    death = {
+      label <- attr(death, "label")
+      death <- dplyr::if_else(dplyr::row_number() %in% 99:101, NA, death)
+      attr(death, "label") <- label
+      death
+    },
     allempty = NA_real_,
     allempty_lgl = allempty == 1
   )

tests/testthat/test-table1_design.R

@@ -2,8 +2,18 @@ data("breastcancer", package = "risks")
 df <- breastcancer |>
   dplyr::mutate(
     continuous = 1:dplyr::n(),
-    receptor = dplyr::if_else(dplyr::row_number() %in% 9:11, NA, receptor),
-    death = dplyr::if_else(dplyr::row_number() %in% 99:101, NA, death),
+    receptor = {
+      label <- attr(receptor, "label")
+      receptor <- dplyr::if_else(dplyr::row_number() %in% 9:11, NA, receptor)
+      attr(receptor, "label") <- label
+      receptor
+    },
+    death = {
+      label <- attr(death, "label")
+      death <- dplyr::if_else(dplyr::row_number() %in% 99:101, NA, death)
+      attr(death, "label") <- label
+      death
+    },
     allempty = NA_integer_,
     allempty_lgl = allempty == 1
   )

tests/testthat/test-time2.R

@@ -201,6 +201,50 @@ testthat::test_that(
 )
 
 
+testthat::test_that(
+  desc = "cum inc difference does not ignore confidence level",
+  code = {
+    result <- survdiff_ci(
+      formula = survival::Surv(
+        time = time,
+        event = status
+      ) ~
+        sex,
+      data = cancer,
+      time = 365.25
+    )
+
+    result09 <- survdiff_ci(
+      formula = survival::Surv(
+        time = time,
+        event = status
+      ) ~
+        sex,
+      data = cancer,
+      time = 365.25,
+      conf.level = 0.9
+    )
+
+    expect_gt(
+      object = result09$conf.low,
+      expected = result$conf.low
+    )
+    expect_lt(
+      object = result09$conf.high,
+      expected = result$conf.high
+    )
+    expect_equal(
+      object = result09$estimate,
+      expected = result$estimate
+    )
+    expect_equal(
+      object = result09$std.error,
+      expected = result$std.error,
+      tolerance = 0.01
+    )
+  }
+)
+
 testthat::test_that(
   desc = "Invalid ID variable is found",
   code = {