From 3ee96e5af9801eff13e2e0df77db9f0bef8421aa Mon Sep 17 00:00:00 2001
From: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Date: Fri, 6 Sep 2024 17:32:43 -0400
Subject: [PATCH] Use `group_var` argument to `control_lineplot_vars` instead
 of deprecated `strata` (#1223)

Fixes #1222
---
 DESCRIPTION                            | 2 +-
 NEWS.md                                | 1 +
 R/tm_g_lineplot.R                      | 3 ++-
 README.md                              | 2 +-
 man/template_g_lineplot.Rd             | 2 +-
 man/tm_g_lineplot.Rd                   | 2 +-
 tests/testthat/_snaps/tm_g_lineplot.md | 4 ++--
 7 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 942c7b1baa..5797e64be2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -60,7 +60,7 @@ Imports:
     teal.logger (>= 0.2.0.9004),
     teal.reporter (>= 0.2.1),
     teal.widgets (>= 0.4.0),
-    tern.gee (>= 0.1.4),
+    tern.gee (>= 0.1.5),
     tern.mmrm (>= 0.3.1),
     utils,
     vistime (>= 1.2.3)
diff --git a/NEWS.md b/NEWS.md
index c965d13d9e..22622e69ef 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -14,6 +14,7 @@
 * Clarified the documentation specifying whether multiple values can be selected in the `arm_var` argument for each module.
 * Replaced use of the `rtables::add_colcounts()` function with the `show_colcounts` argument to `basic_table()`.
 * Began deprecation cycle for the `show_labels` argument of `template_summary` which has no effect on the `tm_t_summary` module.
+* Replaced instances of deprecated `strata` argument to `tern::control_lineplot_vars()` with `group_var`.
 
 # teal.modules.clinical 0.9.1
 
diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
index 533b3a8075..fc0d58eb02 100644
--- a/R/tm_g_lineplot.R
+++ b/R/tm_g_lineplot.R
@@ -5,6 +5,7 @@
 #' @inheritParams tern::g_lineplot
 #' @inheritParams tern::control_lineplot_vars
 #' @inheritParams template_arguments
+#' @param strata (`string` or `NA`)\cr group variable name.
 #' @param param (`character`)\cr parameter to filter the data by.
 #' @param incl_screen (`logical`)\cr whether the screening visit should be included.
 #' @param ggplot2_args (`ggplot2_args`) optional\cr object created by [teal.widgets::ggplot2_args()] with settings
@@ -94,7 +95,7 @@ template_g_lineplot <- function(dataname = "ANL",
   )
 
   z$variables <- substitute(
-    expr = variables <- control_lineplot_vars(x = x, y = y, strata = arm, paramcd = paramcd, y_unit = y_unit),
+    expr = variables <- control_lineplot_vars(x = x, y = y, group_var = arm, paramcd = paramcd, y_unit = y_unit),
     env = list(x = x, y = y, arm = strata, paramcd = paramcd, y_unit = y_unit)
   )
 
diff --git a/README.md b/README.md
index 378f153fad..d502cce440 100644
--- a/README.md
+++ b/README.md
@@ -64,7 +64,7 @@ install.packages('teal.modules.clinical')
 pak::pak("insightsengineering/teal.modules.clinical@*release")
 ```
 
-Alternatively, you might want to use the development version available on [r-universe](https://r-universe.dev/).
+Alternatively, you might want to use the development version available on [r-universe](https://r-universe.dev/search).
 
 ```r
 # beta versions
diff --git a/man/template_g_lineplot.Rd b/man/template_g_lineplot.Rd
index 70cf2a02a8..f60c8b1bf8 100644
--- a/man/template_g_lineplot.Rd
+++ b/man/template_g_lineplot.Rd
@@ -29,7 +29,7 @@ template_g_lineplot(
 \arguments{
 \item{dataname}{(\code{character})\cr analysis data used in teal module.}
 
-\item{strata}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} use the \code{group_var} parameter instead.}
+\item{strata}{(\code{string} or \code{NA})\cr group variable name.}
 
 \item{x}{(\code{string})\cr x-variable name.}
 
diff --git a/man/tm_g_lineplot.Rd b/man/tm_g_lineplot.Rd
index 3fe9f92700..5831b28a52 100644
--- a/man/tm_g_lineplot.Rd
+++ b/man/tm_g_lineplot.Rd
@@ -44,7 +44,7 @@ tm_g_lineplot(
 
 \item{parentname}{(\code{character})\cr parent analysis data used in teal module, usually this refers to \code{ADSL}.}
 
-\item{strata}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} use the \code{group_var} parameter instead.}
+\item{strata}{(\code{string} or \code{NA})\cr group variable name.}
 
 \item{x}{(\code{string})\cr x-variable name.}
 
diff --git a/tests/testthat/_snaps/tm_g_lineplot.md b/tests/testthat/_snaps/tm_g_lineplot.md
index 28d5b3ca9f..82e7977b32 100644
--- a/tests/testthat/_snaps/tm_g_lineplot.md
+++ b/tests/testthat/_snaps/tm_g_lineplot.md
@@ -10,7 +10,7 @@
       
       $variables
       variables <- control_lineplot_vars(x = "AVISIT", y = "AVAL", 
-          strata = "ARM", paramcd = "PARAMCD", y_unit = "AVALU")
+          group_var = "ARM", paramcd = "PARAMCD", y_unit = "AVALU")
       
       $graph
       {
@@ -40,7 +40,7 @@
       }
       
       $variables
-      variables <- control_lineplot_vars(x = "AVISIT", y = "CHG", strata = "ARMCD", 
+      variables <- control_lineplot_vars(x = "AVISIT", y = "CHG", group_var = "ARMCD", 
           paramcd = "PARAMCD", y_unit = "AVALU")
       
       $graph