From ab52dc80241db672589c7841145c6b6b679ec4ca Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Thu, 25 Apr 2024 10:45:35 -0400
Subject: [PATCH 01/13] adding diff function

---
 NAMESPACE                          |   1 +
 R/ard_survival_survfit_diff.R      | 115 +++++++++++++++++++++++++++++
 R/construction_helpers.R           |   5 ++
 _pkgdown.yml                       |   1 +
 man/ard_emmeans_mean_difference.Rd |   7 +-
 man/ard_stats_anova.Rd             |   7 +-
 man/ard_survival_survfit_diff.Rd   |  28 +++++++
 man/construction_helpers.Rd        |   7 +-
 8 files changed, 168 insertions(+), 3 deletions(-)
 create mode 100644 R/ard_survival_survfit_diff.R
 create mode 100644 man/ard_survival_survfit_diff.Rd

diff --git a/NAMESPACE b/NAMESPACE
index d1e1abdba..c9b4e7ed9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -40,6 +40,7 @@ export(ard_survey_svyranktest)
 export(ard_survey_svyttest)
 export(ard_survival_survdiff)
 export(ard_survival_survfit)
+export(ard_survival_survfit_diff)
 export(bt)
 export(bt_strip)
 export(construct_model)
diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
new file mode 100644
index 000000000..f18390a45
--- /dev/null
+++ b/R/ard_survival_survfit_diff.R
@@ -0,0 +1,115 @@
+#' ARD Survival Differences
+#'
+#' Calculate differences in the Kaplan-Meier estimator of survival using the
+#' results from [`survival::survfit()`].
+#'
+#' @param x (`survift`)\cr
+#'   object of class `'survfit'` typically created with [`survival::survfit()`]
+#' @inheritParams ard_survival_survfit
+#'
+#' @return an ARD data frame of class 'card'
+#' @export
+#'
+#' @examples
+#' library(survival)
+#'
+#' survfit(Surv(time, status) ~ ph.ecog, data = lung) |>
+#'   ard_survival_survfit_diff(times = c(100, 200))
+ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
+  set_cli_abort_call()
+
+  # check installed packages ---------------------------------------------------
+  check_pkg_installed(c("survival", "broom"), reference_pkg = "cardx")
+  check_not_missing(x)
+  check_not_missing(times)
+  check_class(x, "survfit")
+  if (inherits(x, "survfitms")) {
+    cli::cli_abort(
+      "Argument {.arg x} cannot be class {.cls survfitms}.",
+      call = get_cli_abort_call()
+    )
+  }
+  check_range(conf.level, range = c(0, 1))
+  check_length(
+    as.list(sf$call)[["formula"]] |> as.formula() |> stats::terms() |> attr("term.labels"),
+    length = 1L,
+    message = "The {.cls survift} object passed in argument {.arg x} must be stratified by a single variable."
+  )
+  if (length(x$strata) < 2) {
+    cli::cli_abort(
+      "The {.cls survift} object passed in argument {.arg x} must have more than 1 stratifying level.",
+      call = get_cli_abort_call()
+    )
+  }
+
+  # calculate survival at the specified times
+  summary(x, times = times) |>
+    tidy_summary.survfit() |>
+    dplyr::select(any_of(c("strata", "time", "estimate", "std.error"))) %>%
+    {dplyr::left_join(
+      dplyr::filter(., .data$strata != .data$strata[1]) |> dplyr::mutate(reference = .$strata[1]),
+      dplyr::filter(., .data$strata == .data$strata[1]) |>
+        dplyr::select(-"strata") |>
+        dplyr::rename_with(.fn = ~paste0(., "0"), .cols = -"time"),
+      by = "time"
+    )} |>
+    dplyr::mutate(
+      difference = .data$estimate0 - .data$estimate,
+      difference.std.error = sqrt(.data$std.error0^2 + .data$std.error^2),
+      statistic = difference / difference.std.error,
+      conf.low = difference - difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
+      conf.high = difference + difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
+      p.value = 2 * (1 - stats::pnorm(abs(statistic)))
+    ) |>
+    dplyr::select(
+      "strata", "reference", "time",
+      estimate = "difference",
+      std.error = "difference.std.error",
+      "statistic", "conf.low", "conf.high", "p.value"
+    ) |>
+    tidyr::separate_wider_delim("strata", "=", names = c("group1", "group1_level")) |>
+    dplyr::mutate(
+      across(-cards::all_ard_groups("names"), as.list)
+    ) |>
+    tidyr::pivot_longer(
+      cols = -c(cards::all_ard_groups(), "time"),
+      names_to = "stat_name",
+      values_to = "stat"
+    ) |>
+    dplyr::rename(variable_level = "time") |>
+    dplyr::mutate(
+      variable = "time",
+      error = list(NULL),
+      warning = list(NULL),
+      fmt_fn = list(1L),
+      stat_label =
+        dplyr::case_when(
+          .data$stat_name %in% "reference" ~ "Reference Group (ref - est)",
+          .data$stat_name %in% "estimate" ~ "Survival Difference",
+          .data$stat_name %in% "std.error" ~ "Survival Difference Standard Error",
+          .data$stat_name %in% "conf.low" ~ "CI Lower Bound",
+          .data$stat_name %in% "conf.high" ~ "CI Upper Bound",
+          .data$stat_name %in% "p.value" ~ "p-value",
+          .default = .data$stat_name
+        ),
+      context = "survival_survfit_diff",
+    ) |>
+    cards::tidy_ard_column_order() %>%
+    structure(., class = c("card", class(.)))
+}
+
+
+tidy_summary.survfit <- function(x) {
+  dplyr::tibble(
+    strata = x$strata,
+    time = x$time,
+    n.risk = x$n.risk,
+    n.event = x$n.event,
+    n.censor = x$n.censor,
+    estimate = x$surv,
+    std.error = x$std.err,
+    conf.low = x$lower,
+    conf.high = x$upper
+  )
+}
+
diff --git a/R/construction_helpers.R b/R/construction_helpers.R
index ae5873532..74e56c136 100644
--- a/R/construction_helpers.R
+++ b/R/construction_helpers.R
@@ -25,6 +25,11 @@
 #'   must be specified in the `package` argument.
 #' @param method.args (named `list`)\cr
 #'   named list of arguments that will be passed to `fn`.
+#'
+#'   Note that this list may contain non-standard evaluation components.
+#'   If you are wrapping this function in other functions, the argument
+#'   must be passed in a way that does not evaluate the list, e.g.
+#'   using rlang's  embrace opoerator `{{ . }}`.
 #' @param package (`string`)\cr
 #'   string of package name that will be temporarily loaded when function
 #'   specified in `method` is executed.
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e22a3e83d..9f9a16e28 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -41,6 +41,7 @@ reference:
       - ard_survey_svyranktest
       - ard_survey_svyttest
       - ard_survival_survdiff
+      - ard_survival_survfit_diff
 
   - subtitle: "Estimation"
   - contents:
diff --git a/man/ard_emmeans_mean_difference.Rd b/man/ard_emmeans_mean_difference.Rd
index 97466d7d6..a29b62da2 100644
--- a/man/ard_emmeans_mean_difference.Rd
+++ b/man/ard_emmeans_mean_difference.Rd
@@ -28,7 +28,12 @@ If function belongs to a library that is not attached, the package name
 must be specified in the \code{package} argument.}
 
 \item{method.args}{(named \code{list})\cr
-named list of arguments that will be passed to \code{fn}.}
+named list of arguments that will be passed to \code{fn}.
+
+Note that this list may contain non-standard evaluation components.
+If you are wrapping this function in other functions, the argument
+must be passed in a way that does not evaluate the list, e.g.
+using rlang's  embrace opoerator \code{{{ . }}}.}
 
 \item{package}{(\code{string})\cr
 string of package name that will be temporarily loaded when function
diff --git a/man/ard_stats_anova.Rd b/man/ard_stats_anova.Rd
index c2ec37b56..380e38dec 100644
--- a/man/ard_stats_anova.Rd
+++ b/man/ard_stats_anova.Rd
@@ -42,7 +42,12 @@ If function belongs to a library that is not attached, the package name
 must be specified in the \code{package} argument.}
 
 \item{method.args}{(named \code{list})\cr
-named list of arguments that will be passed to \code{fn}.}
+named list of arguments that will be passed to \code{fn}.
+
+Note that this list may contain non-standard evaluation components.
+If you are wrapping this function in other functions, the argument
+must be passed in a way that does not evaluate the list, e.g.
+using rlang's  embrace opoerator \code{{{ . }}}.}
 
 \item{package}{(\code{string})\cr
 string of package name that will be temporarily loaded when function
diff --git a/man/ard_survival_survfit_diff.Rd b/man/ard_survival_survfit_diff.Rd
new file mode 100644
index 000000000..dcc6b1b58
--- /dev/null
+++ b/man/ard_survival_survfit_diff.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ard_survival_survfit_diff.R
+\name{ard_survival_survfit_diff}
+\alias{ard_survival_survfit_diff}
+\title{ARD Survival Differences}
+\usage{
+ard_survival_survfit_diff(x, times, conf.level = 0.95)
+}
+\arguments{
+\item{x}{(\code{survift})\cr
+object of class \code{'survfit'} typically created with \code{\link[survival:survfit]{survival::survfit()}}}
+
+\item{times}{(\code{numeric})\cr
+a vector of times for which to return survival probabilities.}
+}
+\value{
+an ARD data frame of class 'card'
+}
+\description{
+Calculate differences in the Kaplan-Meier estimator of survival using the
+results from \code{\link[survival:survfit]{survival::survfit()}}.
+}
+\examples{
+library(survival)
+
+survfit(Surv(time, status) ~ ph.ecog, data = lung) |>
+  ard_survival_survfit_diff(times = c(100, 200))
+}
diff --git a/man/construction_helpers.Rd b/man/construction_helpers.Rd
index 82d5439a3..b48e22176 100644
--- a/man/construction_helpers.Rd
+++ b/man/construction_helpers.Rd
@@ -63,7 +63,12 @@ If function belongs to a library that is not attached, the package name
 must be specified in the \code{package} argument.}
 
 \item{method.args}{(named \code{list})\cr
-named list of arguments that will be passed to \code{fn}.}
+named list of arguments that will be passed to \code{fn}.
+
+Note that this list may contain non-standard evaluation components.
+If you are wrapping this function in other functions, the argument
+must be passed in a way that does not evaluate the list, e.g.
+using rlang's  embrace opoerator \code{{{ . }}}.}
 
 \item{package}{(\code{string})\cr
 string of package name that will be temporarily loaded when function

From 9a3ce4b31fe6faa34e98cec8d0e724b051dc196b Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Thu, 25 Apr 2024 10:55:37 -0400
Subject: [PATCH 02/13] updates

---
 R/ard_survival_survfit_diff.R      | 29 ++++++++++++++++-------------
 R/construction_helpers.R           |  2 +-
 inst/WORDLIST                      |  1 +
 man/ard_emmeans_mean_difference.Rd |  2 +-
 man/ard_stats_anova.Rd             |  2 +-
 man/ard_survival_survfit_diff.Rd   |  3 +++
 man/construction_helpers.Rd        |  2 +-
 7 files changed, 24 insertions(+), 17 deletions(-)

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index f18390a45..843b9f344 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -5,6 +5,8 @@
 #'
 #' @param x (`survift`)\cr
 #'   object of class `'survfit'` typically created with [`survival::survfit()`]
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @inheritParams ard_survival_survfit
 #'
 #' @return an ARD data frame of class 'card'
@@ -31,7 +33,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   }
   check_range(conf.level, range = c(0, 1))
   check_length(
-    as.list(sf$call)[["formula"]] |> as.formula() |> stats::terms() |> attr("term.labels"),
+    as.list(x$call)[["formula"]] |> stats::as.formula() |> stats::terms() |> attr("term.labels"),
     length = 1L,
     message = "The {.cls survift} object passed in argument {.arg x} must be stratified by a single variable."
   )
@@ -46,20 +48,22 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   summary(x, times = times) |>
     tidy_summary.survfit() |>
     dplyr::select(any_of(c("strata", "time", "estimate", "std.error"))) %>%
-    {dplyr::left_join(
-      dplyr::filter(., .data$strata != .data$strata[1]) |> dplyr::mutate(reference = .$strata[1]),
-      dplyr::filter(., .data$strata == .data$strata[1]) |>
-        dplyr::select(-"strata") |>
-        dplyr::rename_with(.fn = ~paste0(., "0"), .cols = -"time"),
-      by = "time"
-    )} |>
+    {
+      dplyr::left_join(
+        dplyr::filter(., .data$strata != .data$strata[1]) |> dplyr::mutate(reference = .$strata[1]),
+        dplyr::filter(., .data$strata == .data$strata[1]) |>
+          dplyr::select(-"strata") |>
+          dplyr::rename_with(.fn = ~ paste0(., "0"), .cols = -"time"),
+        by = "time"
+      )
+    } |>
     dplyr::mutate(
       difference = .data$estimate0 - .data$estimate,
       difference.std.error = sqrt(.data$std.error0^2 + .data$std.error^2),
-      statistic = difference / difference.std.error,
-      conf.low = difference - difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
-      conf.high = difference + difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
-      p.value = 2 * (1 - stats::pnorm(abs(statistic)))
+      statistic = .data$difference / .data$difference.std.error,
+      conf.low = .data$difference - .data$difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
+      conf.high = .data$difference + .data$difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
+      p.value = 2 * (1 - stats::pnorm(abs(.data$statistic)))
     ) |>
     dplyr::select(
       "strata", "reference", "time",
@@ -112,4 +116,3 @@ tidy_summary.survfit <- function(x) {
     conf.high = x$upper
   )
 }
-
diff --git a/R/construction_helpers.R b/R/construction_helpers.R
index 74e56c136..662dceab2 100644
--- a/R/construction_helpers.R
+++ b/R/construction_helpers.R
@@ -29,7 +29,7 @@
 #'   Note that this list may contain non-standard evaluation components.
 #'   If you are wrapping this function in other functions, the argument
 #'   must be passed in a way that does not evaluate the list, e.g.
-#'   using rlang's  embrace opoerator `{{ . }}`.
+#'   using rlang's  embrace operator `{{ . }}`.
 #' @param package (`string`)\cr
 #'   string of package name that will be temporarily loaded when function
 #'   specified in `method` is executed.
diff --git a/inst/WORDLIST b/inst/WORDLIST
index 073fb6ff4..c4c2c8363 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -30,6 +30,7 @@ jeffreys
 pearson
 pre
 quosures
+rlang's
 sd
 strat
 vif
diff --git a/man/ard_emmeans_mean_difference.Rd b/man/ard_emmeans_mean_difference.Rd
index a29b62da2..f34b88338 100644
--- a/man/ard_emmeans_mean_difference.Rd
+++ b/man/ard_emmeans_mean_difference.Rd
@@ -33,7 +33,7 @@ named list of arguments that will be passed to \code{fn}.
 Note that this list may contain non-standard evaluation components.
 If you are wrapping this function in other functions, the argument
 must be passed in a way that does not evaluate the list, e.g.
-using rlang's  embrace opoerator \code{{{ . }}}.}
+using rlang's  embrace operator \code{{{ . }}}.}
 
 \item{package}{(\code{string})\cr
 string of package name that will be temporarily loaded when function
diff --git a/man/ard_stats_anova.Rd b/man/ard_stats_anova.Rd
index 380e38dec..4c029a93e 100644
--- a/man/ard_stats_anova.Rd
+++ b/man/ard_stats_anova.Rd
@@ -47,7 +47,7 @@ named list of arguments that will be passed to \code{fn}.
 Note that this list may contain non-standard evaluation components.
 If you are wrapping this function in other functions, the argument
 must be passed in a way that does not evaluate the list, e.g.
-using rlang's  embrace opoerator \code{{{ . }}}.}
+using rlang's  embrace operator \code{{{ . }}}.}
 
 \item{package}{(\code{string})\cr
 string of package name that will be temporarily loaded when function
diff --git a/man/ard_survival_survfit_diff.Rd b/man/ard_survival_survfit_diff.Rd
index dcc6b1b58..15e1856f5 100644
--- a/man/ard_survival_survfit_diff.Rd
+++ b/man/ard_survival_survfit_diff.Rd
@@ -12,6 +12,9 @@ object of class \code{'survfit'} typically created with \code{\link[survival:sur
 
 \item{times}{(\code{numeric})\cr
 a vector of times for which to return survival probabilities.}
+
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
 }
 \value{
 an ARD data frame of class 'card'
diff --git a/man/construction_helpers.Rd b/man/construction_helpers.Rd
index b48e22176..e10d9603a 100644
--- a/man/construction_helpers.Rd
+++ b/man/construction_helpers.Rd
@@ -68,7 +68,7 @@ named list of arguments that will be passed to \code{fn}.
 Note that this list may contain non-standard evaluation components.
 If you are wrapping this function in other functions, the argument
 must be passed in a way that does not evaluate the list, e.g.
-using rlang's  embrace opoerator \code{{{ . }}}.}
+using rlang's  embrace operator \code{{{ . }}}.}
 
 \item{package}{(\code{string})\cr
 string of package name that will be temporarily loaded when function

From f16c3d5c7ece85c297a5b4f9df6f7181c7f89ea6 Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 26 Apr 2024 15:02:32 -0400
Subject: [PATCH 03/13] updates

---
 R/ard_survival_survfit.R      |  5 ++++-
 R/ard_survival_survfit_diff.R | 25 +++++++++++++------------
 2 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/R/ard_survival_survfit.R b/R/ard_survival_survfit.R
index 9a30adf5f..571b14f43 100644
--- a/R/ard_survival_survfit.R
+++ b/R/ard_survival_survfit.R
@@ -142,7 +142,10 @@ ard_survival_survfit <- function(x, times = NULL, probs = NULL, type = NULL) {
       dplyr::vars("conf.high", "conf.low"),
       ~ ifelse(is.na(.) & .data$std.error == 0, .data$estimate, .)
     ) %>%
-    dplyr::select(dplyr::any_of(c("time", "estimate", "conf.high", "conf.low", "strata"))) %>%
+    dplyr::select(dplyr::any_of(c(
+      "time", "estimate", "std.error", "conf.high", "conf.low",
+      "strata", "n.risk"
+    ))) %>%
     # add data for time 0
     dplyr::bind_rows(
       dplyr::group_by_at(., dplyr::vars(dplyr::any_of("strata"))) %>%
diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index 843b9f344..3f45256c0 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -48,15 +48,16 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   summary(x, times = times) |>
     tidy_summary.survfit() |>
     dplyr::select(any_of(c("strata", "time", "estimate", "std.error"))) %>%
-    {
-      dplyr::left_join(
-        dplyr::filter(., .data$strata != .data$strata[1]) |> dplyr::mutate(reference = .$strata[1]),
-        dplyr::filter(., .data$strata == .data$strata[1]) |>
-          dplyr::select(-"strata") |>
-          dplyr::rename_with(.fn = ~ paste0(., "0"), .cols = -"time"),
-        by = "time"
-      )
-    } |>
+    # styler: off
+    {dplyr::left_join(
+      dplyr::filter(., .data$strata != .data$strata[1]) |>
+        dplyr::mutate(contrast = paste(.$strata[1], "-", .data$strata)),
+      dplyr::filter(., .data$strata == .data$strata[1]) |>
+        dplyr::select(-"strata") |>
+        dplyr::rename_with(.fn = ~ paste0(., "0"), .cols = -"time"),
+      by = "time"
+    )} |>
+    # styler: on
     dplyr::mutate(
       difference = .data$estimate0 - .data$estimate,
       difference.std.error = sqrt(.data$std.error0^2 + .data$std.error^2),
@@ -66,12 +67,13 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
       p.value = 2 * (1 - stats::pnorm(abs(.data$statistic)))
     ) |>
     dplyr::select(
-      "strata", "reference", "time",
+      "strata", "contrast", "time",
       estimate = "difference",
       std.error = "difference.std.error",
       "statistic", "conf.low", "conf.high", "p.value"
     ) |>
-    tidyr::separate_wider_delim("strata", "=", names = c("group1", "group1_level")) |>
+    extract_multi_strata(x = x, df_stat = _)
+  tidyr::separate_wider_delim("strata", "=", names = c("group1", "group1_level")) |>
     dplyr::mutate(
       across(-cards::all_ard_groups("names"), as.list)
     ) |>
@@ -88,7 +90,6 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
       fmt_fn = list(1L),
       stat_label =
         dplyr::case_when(
-          .data$stat_name %in% "reference" ~ "Reference Group (ref - est)",
           .data$stat_name %in% "estimate" ~ "Survival Difference",
           .data$stat_name %in% "std.error" ~ "Survival Difference Standard Error",
           .data$stat_name %in% "conf.low" ~ "CI Lower Bound",

From 38cc3d924244b1411de82b0e077c15d644b6daba Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Tue, 30 Apr 2024 15:18:02 -0700
Subject: [PATCH 04/13] Update _pkgdown.yml

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index a1acfa498..336176a8a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -68,6 +68,7 @@ reference:
   - subtitle: "{survival} package"
   - contents:
     - ard_survival_survfit
+    - ard_survival_survfit_diff
     - ard_survival_survdiff
 
   - subtitle: "Other ARD functions"

From 2d3a972558d336354e7b76defdb34dc536c69d11 Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Thu, 23 May 2024 21:31:08 -0700
Subject: [PATCH 05/13] progress

---
 R/ard_stats_t_test_onesample.R      |  2 +-
 R/ard_stats_wilcox_test_onesample.R |  2 +-
 R/ard_survival_survfit_diff.R       | 98 ++++++++++++++---------------
 3 files changed, 50 insertions(+), 52 deletions(-)

diff --git a/R/ard_stats_t_test_onesample.R b/R/ard_stats_t_test_onesample.R
index 9eb8a79c0..1a419b21a 100644
--- a/R/ard_stats_t_test_onesample.R
+++ b/R/ard_stats_t_test_onesample.R
@@ -64,7 +64,7 @@ ard_stats_t_test_onesample <- function(data, variables, by = dplyr::group_vars(d
     ) |>
     dplyr::mutate(
       stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name),
-      context = "ard_stats_t_test_onesample",
+      context = "stats_t_test_onesample",
     ) |>
     cards::tidy_ard_row_order() |>
     cards::tidy_ard_column_order()
diff --git a/R/ard_stats_wilcox_test_onesample.R b/R/ard_stats_wilcox_test_onesample.R
index 7741c2cab..88885fd0e 100644
--- a/R/ard_stats_wilcox_test_onesample.R
+++ b/R/ard_stats_wilcox_test_onesample.R
@@ -65,7 +65,7 @@ ard_stats_wilcox_test_onesample <- function(data, variables, by = dplyr::group_v
     ) |>
     dplyr::mutate(
       stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name),
-      context = "ard_stats_wilcox_test_onesample",
+      context = "stats_wilcox_test_onesample",
     ) |>
     cards::tidy_ard_row_order() |>
     cards::tidy_ard_column_order()
diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index 3f45256c0..4d6b2e93c 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -31,7 +31,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
       call = get_cli_abort_call()
     )
   }
-  check_range(conf.level, range = c(0, 1))
+  check_scalar_range(conf.level, range = c(0, 1))
   check_length(
     as.list(x$call)[["formula"]] |> stats::as.formula() |> stats::terms() |> attr("term.labels"),
     length = 1L,
@@ -44,49 +44,61 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
     )
   }
 
-  # calculate survival at the specified times
-  summary(x, times = times) |>
-    tidy_summary.survfit() |>
-    dplyr::select(any_of(c("strata", "time", "estimate", "std.error"))) %>%
-    # styler: off
+  # calculate the survival at the specified times
+  ard_survival_survfit <-
+    ard_survival_survfit(x = x, times = times) |>
+    dplyr::filter(.data$stat_name %in% c("estimate", "std.error")) |>
+    dplyr::select(-c("stat_label", "context", "fmt_fn"))
+
+  # transform the survival ARD into a cards object with the survival difference
+  card <-
+    ard_survival_survfit %>%
     {dplyr::left_join(
-      dplyr::filter(., .data$strata != .data$strata[1]) |>
-        dplyr::mutate(contrast = paste(.$strata[1], "-", .data$strata)),
-      dplyr::filter(., .data$strata == .data$strata[1]) |>
-        dplyr::select(-"strata") |>
-        dplyr::rename_with(.fn = ~ paste0(., "0"), .cols = -"time"),
-      by = "time"
+      # remove the first group from the data frame (this is our reference group)
+      dplyr::filter(., .by = cards::all_ard_groups(), dplyr::cur_group_id() > 1L) |>
+        dplyr::rename(stat1 = "stat"),
+      # merge the reference group data
+      dplyr::filter(., .by = cards::all_ard_groups(), dplyr::cur_group_id() == 1L) |>
+        dplyr::select(stat0 = "stat", everything(), -c("group1_level", "error", "warning")),
+      by = c("group1", "variable", "variable_level", "stat_name")
     )} |>
-    # styler: on
-    dplyr::mutate(
-      difference = .data$estimate0 - .data$estimate,
-      difference.std.error = sqrt(.data$std.error0^2 + .data$std.error^2),
-      statistic = .data$difference / .data$difference.std.error,
-      conf.low = .data$difference - .data$difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
-      conf.high = .data$difference + .data$difference.std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
-      p.value = 2 * (1 - stats::pnorm(abs(.data$statistic)))
-    ) |>
-    dplyr::select(
-      "strata", "contrast", "time",
-      estimate = "difference",
-      std.error = "difference.std.error",
-      "statistic", "conf.low", "conf.high", "p.value"
+    # reshape to put the stats that need to be combined on the same row
+    tidyr::pivot_wider(
+      id_cols = c("group1", "group1_level", "variable", "variable_level"),
+      names_from = "stat_name",
+      values_from = c("stat0", "stat1"),
+      values_fn = unlist
     ) |>
-    extract_multi_strata(x = x, df_stat = _)
-  tidyr::separate_wider_delim("strata", "=", names = c("group1", "group1_level")) |>
+    # calcualte the primary statistics to return
     dplyr::mutate(
-      across(-cards::all_ard_groups("names"), as.list)
+      # reference level
+      reference_level = ard_survival_survfit[["group1_level"]][1],
+      # survival difference
+      estimate = .data$stat0_estimate - .data$stat1_estimate,
+      # survival difference standard error
+      std.error = sqrt(.data$stat0_std.error^2 + .data$stat1_std.error^2),
+      # Z test statistic
+      statistic = .data$estimate / .data$std.error,
+      # confidence limits of the survival difference
+      conf.low = .data$estimate - .data$std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
+      conf.high = .data$estimate + .data$std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
+      # p-value for test where H0: no difference
+      p.value = 2 * (1 - stats::pnorm(abs(.data$statistic))),
+      across(c("reference_level", "estimate", "std.error", "statistic", "conf.low", "conf.high", "p.value"), as.list)
     ) |>
+    # reshape into the cards structure
+    dplyr::select(-starts_with("stat0_"), -starts_with("stat1_")) |>
     tidyr::pivot_longer(
-      cols = -c(cards::all_ard_groups(), "time"),
+      cols = -c(cards::all_ard_groups(), cards::all_ard_variables()),
       names_to = "stat_name",
       values_to = "stat"
-    ) |>
-    dplyr::rename(variable_level = "time") |>
+    )
+
+  # final prepping of the cards object -----------------------------------------
+  card |>
     dplyr::mutate(
-      variable = "time",
-      error = list(NULL),
-      warning = list(NULL),
+      warning = ard_survival_survfit[["warning"]][1],
+      error = ard_survival_survfit[["error"]][1],
       fmt_fn = list(1L),
       stat_label =
         dplyr::case_when(
@@ -94,6 +106,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
           .data$stat_name %in% "std.error" ~ "Survival Difference Standard Error",
           .data$stat_name %in% "conf.low" ~ "CI Lower Bound",
           .data$stat_name %in% "conf.high" ~ "CI Upper Bound",
+          .data$stat_name %in% "statistic" ~ "z statistic",
           .data$stat_name %in% "p.value" ~ "p-value",
           .default = .data$stat_name
         ),
@@ -102,18 +115,3 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
     cards::tidy_ard_column_order() %>%
     structure(., class = c("card", class(.)))
 }
-
-
-tidy_summary.survfit <- function(x) {
-  dplyr::tibble(
-    strata = x$strata,
-    time = x$time,
-    n.risk = x$n.risk,
-    n.event = x$n.event,
-    n.censor = x$n.censor,
-    estimate = x$surv,
-    std.error = x$std.err,
-    conf.low = x$lower,
-    conf.high = x$upper
-  )
-}

From 01bb016ebe54e3a1cf5c676267379ae75b01d563 Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Thu, 23 May 2024 21:32:36 -0700
Subject: [PATCH 06/13] Update ard_survival_survfit_diff.R

---
 R/ard_survival_survfit_diff.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index 4d6b2e93c..d52ca7aa9 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -53,15 +53,15 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   # transform the survival ARD into a cards object with the survival difference
   card <-
     ard_survival_survfit %>%
-    {dplyr::left_join(
-      # remove the first group from the data frame (this is our reference group)
-      dplyr::filter(., .by = cards::all_ard_groups(), dplyr::cur_group_id() > 1L) |>
-        dplyr::rename(stat1 = "stat"),
-      # merge the reference group data
-      dplyr::filter(., .by = cards::all_ard_groups(), dplyr::cur_group_id() == 1L) |>
-        dplyr::select(stat0 = "stat", everything(), -c("group1_level", "error", "warning")),
-      by = c("group1", "variable", "variable_level", "stat_name")
-    )} |>
+    {dplyr::left_join( # styler: off
+        # remove the first group from the data frame (this is our reference group)
+        dplyr::filter(., .by = cards::all_ard_groups(), dplyr::cur_group_id() > 1L) |>
+          dplyr::rename(stat1 = "stat"),
+        # merge the reference group data
+        dplyr::filter(., .by = cards::all_ard_groups(), dplyr::cur_group_id() == 1L) |>
+          dplyr::select(stat0 = "stat", everything(), -c("group1_level", "error", "warning")),
+        by = c("group1", "variable", "variable_level", "stat_name")
+    )} |> # styler: off
     # reshape to put the stats that need to be combined on the same row
     tidyr::pivot_wider(
       id_cols = c("group1", "group1_level", "variable", "variable_level"),

From a64f53ab030f506cc387569305c95cdaaa8cf2fd Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 06:54:09 -0700
Subject: [PATCH 07/13] progress

---
 R/ard_survival_survfit_diff.R                 |  7 ++-
 .../_snaps/ard_survival_survfit_diff.md       | 27 +++++++++
 .../testthat/test-ard_survival_survfit_diff.R | 56 +++++++++++++++++++
 3 files changed, 87 insertions(+), 3 deletions(-)
 create mode 100644 tests/testthat/_snaps/ard_survival_survfit_diff.md
 create mode 100644 tests/testthat/test-ard_survival_survfit_diff.R

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index d52ca7aa9..7617c1e52 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -25,9 +25,10 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   check_not_missing(x)
   check_not_missing(times)
   check_class(x, "survfit")
-  if (inherits(x, "survfitms")) {
+
+  if (inherits(x, c("survfitms", "survfitcox"))) {
     cli::cli_abort(
-      "Argument {.arg x} cannot be class {.cls survfitms}.",
+      "Argument {.arg x} cannot be class {.cls {c('survfitms', 'survfitcox')}}.",
       call = get_cli_abort_call()
     )
   }
@@ -39,7 +40,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   )
   if (length(x$strata) < 2) {
     cli::cli_abort(
-      "The {.cls survift} object passed in argument {.arg x} must have more than 1 stratifying level.",
+      "The {.cls survift} object's stratifying variable must have 2 or more levels.",
       call = get_cli_abort_call()
     )
   }
diff --git a/tests/testthat/_snaps/ard_survival_survfit_diff.md b/tests/testthat/_snaps/ard_survival_survfit_diff.md
new file mode 100644
index 000000000..4ac19b2f4
--- /dev/null
+++ b/tests/testthat/_snaps/ard_survival_survfit_diff.md
@@ -0,0 +1,27 @@
+# ard_survival_survfit_diff() messaging
+
+    Code
+      ard_survival_survfit_diff(survfit(Surv(AVAL, 1 - CNSR) ~ SEX + TRTA, cards::ADTTE),
+      times = c(25, 50))
+    Condition
+      Error in `ard_survival_survfit_diff()`:
+      ! The <survift> object passed in argument `x` must be stratified by a single variable.
+
+---
+
+    Code
+      ard_survival_survfit_diff(survfit(Surv(AVAL, 1 - CNSR) ~ constant, dplyr::mutate(
+        cards::ADTTE, constant = 1L)), times = c(25, 50))
+    Condition
+      Error in `ard_survival_survfit_diff()`:
+      ! The <survift> object's stratifying variable must have 2 or more levels.
+
+---
+
+    Code
+      ard_survival_survfit_diff(survfit(coxph(Surv(AVAL, CNSR) ~ SEX + strata(TRTA),
+      cards::ADTTE)), times = c(25, 50))
+    Condition
+      Error in `ard_survival_survfit_diff()`:
+      ! Argument `x` cannot be class <survfitms/survfitcox>.
+
diff --git a/tests/testthat/test-ard_survival_survfit_diff.R b/tests/testthat/test-ard_survival_survfit_diff.R
new file mode 100644
index 000000000..b4977a7f1
--- /dev/null
+++ b/tests/testthat/test-ard_survival_survfit_diff.R
@@ -0,0 +1,56 @@
+test_that("ard_survival_survfit_diff() works", {
+  withr::local_package("survival")
+  sf <- survfit(Surv(AVAL, 1- CNSR) ~ SEX, cards::ADTTE)
+  expect_silent(
+    ard1 <- ard_survival_survfit_diff(sf, times = c(25, 50))
+  )
+
+  # check the survival differences are accurate
+  expect_equal(
+    ard1 |>
+      dplyr::filter(variable_level == 25, stat_name == "estimate") |>
+      dplyr::pull(stat) |>
+      unlist(),
+    summary(sf, times = 25) |>
+      getElement("surv") |>
+      reduce(`-`)
+  )
+  expect_equal(
+    ard1 |>
+      dplyr::filter(variable_level == 50, stat_name == "estimate") |>
+      dplyr::pull(stat) |>
+      unlist(),
+    summary(sf, times = 50) |>
+      getElement("surv") |>
+      reduce(`-`)
+  )
+})
+
+test_that("ard_survival_survfit_diff() messaging", {
+  withr::local_package("survival")
+
+  # we can only do one stratifying variable at a time
+  expect_snapshot(
+    error = TRUE,
+    survfit(Surv(AVAL, 1- CNSR) ~ SEX + TRTA, cards::ADTTE) |>
+      ard_survival_survfit_diff(times = c(25, 50))
+  )
+
+  # the stratifying variable must have 2 or more levels
+  expect_snapshot(
+    error = TRUE,
+    survfit(
+      Surv(AVAL, 1- CNSR) ~ constant,
+      cards::ADTTE |> dplyr::mutate(constant = 1L)
+    ) |>
+      ard_survival_survfit_diff(times = c(25, 50))
+  )
+
+  # cannot pass a multi-state model or stratified Cox
+  expect_snapshot(
+    error = TRUE,
+    coxph(Surv(AVAL, CNSR) ~ SEX + strata(TRTA), cards::ADTTE) |>
+      survfit() |>
+      ard_survival_survfit_diff(times = c(25, 50))
+  )
+})

From 9afaea80f063c39459dafb7f8a31da511374698a Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 06:59:04 -0700
Subject: [PATCH 08/13] progress

---
 R/ard_survival_survfit_diff.R                   | 4 +++-
 tests/testthat/test-ard_survival_survfit_diff.R | 5 +++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index 7617c1e52..d63342a07 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -74,6 +74,8 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
     dplyr::mutate(
       # reference level
       reference_level = ard_survival_survfit[["group1_level"]][1],
+      # short description of method
+      method = "Survival Difference (Z-test)",
       # survival difference
       estimate = .data$stat0_estimate - .data$stat1_estimate,
       # survival difference standard error
@@ -85,7 +87,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
       conf.high = .data$estimate + .data$std.error * stats::qnorm(1 - (1 - .env$conf.level) / 2),
       # p-value for test where H0: no difference
       p.value = 2 * (1 - stats::pnorm(abs(.data$statistic))),
-      across(c("reference_level", "estimate", "std.error", "statistic", "conf.low", "conf.high", "p.value"), as.list)
+      across(c("reference_level", "estimate", "std.error", "statistic", "conf.low", "conf.high", "p.value", "method"), as.list)
     ) |>
     # reshape into the cards structure
     dplyr::select(-starts_with("stat0_"), -starts_with("stat1_")) |>
diff --git a/tests/testthat/test-ard_survival_survfit_diff.R b/tests/testthat/test-ard_survival_survfit_diff.R
index b4977a7f1..990621dd0 100644
--- a/tests/testthat/test-ard_survival_survfit_diff.R
+++ b/tests/testthat/test-ard_survival_survfit_diff.R
@@ -24,6 +24,11 @@ test_that("ard_survival_survfit_diff() works", {
       getElement("surv") |>
       reduce(`-`)
   )
+
+  # check the structure of the ARD object
+  expect_silent(
+    cards::check_ard_structure(ard1)
+  )
 })
 
 test_that("ard_survival_survfit_diff() messaging", {

From 181123ea3a3e297fea1ea0d41045ca37117c114a Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 07:19:50 -0700
Subject: [PATCH 09/13] Update test-ard_survival_survfit_diff.R

---
 tests/testthat/test-ard_survival_survfit_diff.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-ard_survival_survfit_diff.R b/tests/testthat/test-ard_survival_survfit_diff.R
index 990621dd0..231150ac9 100644
--- a/tests/testthat/test-ard_survival_survfit_diff.R
+++ b/tests/testthat/test-ard_survival_survfit_diff.R
@@ -1,6 +1,6 @@
 test_that("ard_survival_survfit_diff() works", {
   withr::local_package("survival")
-  sf <- survfit(Surv(AVAL, 1- CNSR) ~ SEX, cards::ADTTE)
+  sf <- survfit(Surv(AVAL, 1 - CNSR) ~ SEX, cards::ADTTE)
   expect_silent(
     ard1 <- ard_survival_survfit_diff(sf, times = c(25, 50))
   )
@@ -37,7 +37,7 @@ test_that("ard_survival_survfit_diff() messaging", {
   # we can only do one stratifying variable at a time
   expect_snapshot(
     error = TRUE,
-    survfit(Surv(AVAL, 1- CNSR) ~ SEX + TRTA, cards::ADTTE) |>
+    survfit(Surv(AVAL, 1 - CNSR) ~ SEX + TRTA, cards::ADTTE) |>
       ard_survival_survfit_diff(times = c(25, 50))
   )
 
@@ -45,7 +45,7 @@ test_that("ard_survival_survfit_diff() messaging", {
   expect_snapshot(
     error = TRUE,
     survfit(
-      Surv(AVAL, 1- CNSR) ~ constant,
+      Surv(AVAL, 1 - CNSR) ~ constant,
       cards::ADTTE |> dplyr::mutate(constant = 1L)
     ) |>
       ard_survival_survfit_diff(times = c(25, 50))

From bfbde9aaf89fa3c998b92989baa554c49110e15e Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 07:41:17 -0700
Subject: [PATCH 10/13] progress

---
 R/ard_survival_survfit_diff.R                   | 7 ++++---
 man/ard_survival_survfit_diff.Rd                | 7 +++++--
 tests/testthat/test-ard_survival_survfit_diff.R | 2 ++
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index d63342a07..656d1c150 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -12,11 +12,12 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("survival", "ggsurvfit"), reference_pkg = "cardx"))
+#' library(ggsurvfit)
 #' library(survival)
 #'
-#' survfit(Surv(time, status) ~ ph.ecog, data = lung) |>
-#'   ard_survival_survfit_diff(times = c(100, 200))
+#' survfit(Surv_CNSR() ~ TRTA, data = cards::ADTTE) |>
+#'   ard_survival_survfit_diff(times = c(25, 50))
 ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   set_cli_abort_call()
 
diff --git a/man/ard_survival_survfit_diff.Rd b/man/ard_survival_survfit_diff.Rd
index 15e1856f5..3a7a7bd7d 100644
--- a/man/ard_survival_survfit_diff.Rd
+++ b/man/ard_survival_survfit_diff.Rd
@@ -24,8 +24,11 @@ Calculate differences in the Kaplan-Meier estimator of survival using the
 results from \code{\link[survival:survfit]{survival::survfit()}}.
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("survival", "ggsurvfit"), reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+library(ggsurvfit)
 library(survival)
 
-survfit(Surv(time, status) ~ ph.ecog, data = lung) |>
-  ard_survival_survfit_diff(times = c(100, 200))
+survfit(Surv_CNSR() ~ TRTA, data = cards::ADTTE) |>
+  ard_survival_survfit_diff(times = c(25, 50))
+\dontshow{\}) # examplesIf}
 }
diff --git a/tests/testthat/test-ard_survival_survfit_diff.R b/tests/testthat/test-ard_survival_survfit_diff.R
index 231150ac9..e1f00dd9a 100644
--- a/tests/testthat/test-ard_survival_survfit_diff.R
+++ b/tests/testthat/test-ard_survival_survfit_diff.R
@@ -1,3 +1,5 @@
+skip_if_not(is_pkg_installed(c("survival", "broom"), reference_pkg = "cardx"))
+
 test_that("ard_survival_survfit_diff() works", {
   withr::local_package("survival")
   sf <- survfit(Surv(AVAL, 1 - CNSR) ~ SEX, cards::ADTTE)

From cebbdf9fcf391c47f6e29d64a8954c63f123bea2 Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 15:45:41 -0700
Subject: [PATCH 11/13] Update R/ard_survival_survfit_diff.R

Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Signed-off-by: Daniel Sjoberg <danield.sjoberg@gmail.com>
---
 R/ard_survival_survfit_diff.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index 656d1c150..039d4731d 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -37,7 +37,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   check_length(
     as.list(x$call)[["formula"]] |> stats::as.formula() |> stats::terms() |> attr("term.labels"),
     length = 1L,
-    message = "The {.cls survift} object passed in argument {.arg x} must be stratified by a single variable."
+    message = "The {.cls survfit} object passed in argument {.arg x} must be stratified by a single variable."
   )
   if (length(x$strata) < 2) {
     cli::cli_abort(

From f5ce75a1a2e0d52804d65231b1b90f586c671b6e Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 15:45:49 -0700
Subject: [PATCH 12/13] Update R/ard_survival_survfit_diff.R

Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Signed-off-by: Daniel Sjoberg <danield.sjoberg@gmail.com>
---
 R/ard_survival_survfit_diff.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ard_survival_survfit_diff.R b/R/ard_survival_survfit_diff.R
index 039d4731d..5700c2e5c 100644
--- a/R/ard_survival_survfit_diff.R
+++ b/R/ard_survival_survfit_diff.R
@@ -41,7 +41,7 @@ ard_survival_survfit_diff <- function(x, times, conf.level = 0.95) {
   )
   if (length(x$strata) < 2) {
     cli::cli_abort(
-      "The {.cls survift} object's stratifying variable must have 2 or more levels.",
+      "The {.cls survfit} object's stratifying variable must have 2 or more levels.",
       call = get_cli_abort_call()
     )
   }

From fae6d19f558db51d4286bdcbfb33afc4004225cb Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 24 May 2024 15:53:57 -0700
Subject: [PATCH 13/13] snap updates

---
 .../testthat/_snaps/ard_attributes.survey.design.md | 13 +++++++++++++
 tests/testthat/_snaps/ard_survival_survfit_diff.md  |  4 ++--
 2 files changed, 15 insertions(+), 2 deletions(-)
 create mode 100644 tests/testthat/_snaps/ard_attributes.survey.design.md

diff --git a/tests/testthat/_snaps/ard_attributes.survey.design.md b/tests/testthat/_snaps/ard_attributes.survey.design.md
new file mode 100644
index 000000000..6c373f28f
--- /dev/null
+++ b/tests/testthat/_snaps/ard_attributes.survey.design.md
@@ -0,0 +1,13 @@
+# ard_attributes.survey.design() works
+
+    Code
+      attr(dclus1$variables$sname, "label") <- "School Name"
+      as.data.frame(ard_attributes(dclus1, variables = c(sname, dname), label = list(
+        dname = "District Name")))
+    Output
+        variable    context stat_name     stat_label          stat
+      1    sname attributes     label Variable Label   School Name
+      2    sname attributes     class Variable Class     character
+      3    dname attributes     label Variable Label District Name
+      4    dname attributes     class Variable Class     character
+
diff --git a/tests/testthat/_snaps/ard_survival_survfit_diff.md b/tests/testthat/_snaps/ard_survival_survfit_diff.md
index 4ac19b2f4..c5ffc0c7c 100644
--- a/tests/testthat/_snaps/ard_survival_survfit_diff.md
+++ b/tests/testthat/_snaps/ard_survival_survfit_diff.md
@@ -5,7 +5,7 @@
       times = c(25, 50))
     Condition
       Error in `ard_survival_survfit_diff()`:
-      ! The <survift> object passed in argument `x` must be stratified by a single variable.
+      ! The <survfit> object passed in argument `x` must be stratified by a single variable.
 
 ---
 
@@ -14,7 +14,7 @@
         cards::ADTTE, constant = 1L)), times = c(25, 50))
     Condition
       Error in `ard_survival_survfit_diff()`:
-      ! The <survift> object's stratifying variable must have 2 or more levels.
+      ! The <survfit> object's stratifying variable must have 2 or more levels.
 
 ---