[deprecate]: functionality for Report.sso from convert_output()

DESCRIPTION

@@ -42,6 +42,7 @@ Imports:
     ggplot2 (>= 4.0.0),
     glue,
     gt,
+    lifecycle,
     purrr,
     rlang,
     scales,
@@ -61,9 +62,10 @@ Suggests:
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
-Config/roxygen2/version: 8.1.0
+Config/roxygen2/version: 8.1.1
 Config/testthat/edition: 3
 Config/testthat/parallel: false
 Encoding: UTF-8
 Language: en-US
 LazyData: true
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(calculate_reference_point)
 export(convert_output)
 export(create_latex_table)
 export(create_rda)
@@ -35,3 +36,4 @@ export(table_projections)
 export(table_total_catch)
 export(theme_noaa)
 export(theme_table)
+importFrom(lifecycle,deprecated)

R/convert_output.R

@@ -3,7 +3,7 @@
 #' Format stock assessment output file to a standardized tibble.
 #'
 #' @param file Path. Assessment model output file path. Currently accepts SS3
-#' Report.sso file, BAM .rda file, Rceattle model object, and FIMS model object.
+#' `r4ss::ss_output()` or Report.sso file (being deprecated), BAM .rda file, Rceattle model object, and FIMS model object.
 #' @param model String. Assessment model used in evaluation
 #'
 #' Default: NULL
@@ -48,6 +48,18 @@ convert_output <- function(
   fleet_names = NULL,
   save_dir = NULL
 ) {
+
+  if (grepl("Report.sso", file)) {
+    lifecycle::deprecate_warn(
+      when = "2.8.0", 
+      what = I("convert_output(file = 'Report.sso')"), 
+      details = c(
+        i = "Please use the returned object from `r4ss::ss_output()`",
+        i = "File will be compatible until Oct. 1, 2027"
+      )
+    )
+  }
+
   # check if entered save_dir exists so doesn't waste user time finding this out at the end
   if (!is.null(save_dir)) {
     if (!grepl(".rda", save_dir)) {

R/stockplotr-package.R

@@ -2,6 +2,7 @@
 "_PACKAGE"
 
 ## usethis namespace: start
+#' @importFrom lifecycle deprecated
 ## usethis namespace: end
 NULL
 

R/utils_plot.R

@@ -875,8 +875,13 @@ get_id <- function(dat) {
 
 #------------------------------------------------------------------------------
 
-# Calculate reference value point
-
+#' Calculate reference value point
+#'
+#' @inheritParams plot_spawning_biomass dat lbs
+#' @param reference_name String. Name of the reference point (e.g. "spawning biomass msy")
+#'
+#' @returns the value of the reference point name found in the dat file.
+#' @export
 calculate_reference_point <- function(
   dat,
   reference_name,