From 7f57d8b63e5b8d217689b2faeab3a25836a9565e Mon Sep 17 00:00:00 2001
From: u061745 <hefin.rhys@ucb.com>
Date: Wed, 17 Apr 2024 14:43:20 +0100
Subject: [PATCH] Changed S7::`@` to S7::prop.

---
 R/get_analytes.R           |  2 +-
 R/get_curve_data.R         |  2 +-
 R/get_expected.R           |  2 +-
 R/get_metadata.R           |  2 +-
 R/get_recovery.R           |  2 +-
 R/get_recovery_avg.R       |  2 +-
 R/get_summary_data.R       |  2 +-
 R/get_well_data.R          |  2 +-
 R/plot_curves.R            |  6 +++---
 R/update_curve_data.R      |  1 +
 man/update_curve_data.Rd   |  2 +-
 scratch/workflow example.r | 28 ++++++++++++++++++++++++++++
 12 files changed, 41 insertions(+), 12 deletions(-)
 create mode 100644 scratch/workflow example.r

diff --git a/R/get_analytes.R b/R/get_analytes.R
index 99f3e46..d54cf23 100644
--- a/R/get_analytes.R
+++ b/R/get_analytes.R
@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_analytes <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "analytes")
+  S7::prop(.intelliframe, "analytes")
 }
diff --git a/R/get_curve_data.R b/R/get_curve_data.R
index d90ca46..90795f2 100644
--- a/R/get_curve_data.R
+++ b/R/get_curve_data.R
@@ -10,6 +10,6 @@
 #' @examples
 #' 1+1
 get_curve_data <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "curve_data")
+  S7::prop(.intelliframe, "curve_data")
 }
 
diff --git a/R/get_expected.R b/R/get_expected.R
index ac40f06..54ab519 100644
--- a/R/get_expected.R
+++ b/R/get_expected.R
@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_expected <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "expected")
+  S7::prop(.intelliframe, "expected")
 }
diff --git a/R/get_metadata.R b/R/get_metadata.R
index 135db87..ab5ab00 100644
--- a/R/get_metadata.R
+++ b/R/get_metadata.R
@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_metadata <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "metadata")
+  S7::prop(.intelliframe, "metadata")
 }
diff --git a/R/get_recovery.R b/R/get_recovery.R
index 6e1def8..4198516 100644
--- a/R/get_recovery.R
+++ b/R/get_recovery.R
@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_recovery <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "recovery")
+  S7::prop(.intelliframe, "recovery")
 }
diff --git a/R/get_recovery_avg.R b/R/get_recovery_avg.R
index 60dd84b..e8975d9 100644
--- a/R/get_recovery_avg.R
+++ b/R/get_recovery_avg.R
@@ -10,6 +10,6 @@
 #' @examples
 #' 1+1
 get_recovery_avg <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "recovery_avg")
+  S7::prop(.intelliframe, "recovery_avg")
 }
 
diff --git a/R/get_summary_data.R b/R/get_summary_data.R
index a4395b4..cacaf71 100644
--- a/R/get_summary_data.R
+++ b/R/get_summary_data.R
@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_summary_data <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "summary_data")
+  S7::prop(.intelliframe, "summary_data")
 }
diff --git a/R/get_well_data.R b/R/get_well_data.R
index 48128a8..0ed34bc 100644
--- a/R/get_well_data.R
+++ b/R/get_well_data.R
@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_well_data <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "well_data")
+  S7::prop(.intelliframe, "well_data")
 }
diff --git a/R/plot_curves.R b/R/plot_curves.R
index 75af336..ce756d3 100644
--- a/R/plot_curves.R
+++ b/R/plot_curves.R
@@ -27,9 +27,9 @@ plot_curves <- function(.intelliframe, analytes = NULL, type = "individual", int
   stopifnot("data argument must be an intelliframe object" = S7::S7_inherits(.intelliframe, intelliframe))
 
   if(type == "individual") {
-    dat <- S7::`@`(.intelliframe, "well_data")
+    dat <- S7::prop(.intelliframe, "well_data")
   } else if(type == "summary") {
-    dat <- S7::`@`(.intelliframe, "summary_data") |>
+    dat <- S7::prop(.intelliframe, "summary_data") |>
       dplyr::rename("MFI" = "MFI_Avg", "Result" = "Result_Avg")
   } else stop(paste0('Argument type should be "individual" or "summary", not "', type, '".'))
 
@@ -42,7 +42,7 @@ plot_curves <- function(.intelliframe, analytes = NULL, type = "individual", int
   experimental_data <- dplyr::filter(dat, .data[["Type"]] != "Standard") |>
     dplyr::arrange(dplyr::desc(.data[["Type"]]))
 
-  curve_data <- S7::`@`(.intelliframe, "curve_data")
+  curve_data <- S7::prop(.intelliframe, "curve_data")
 
   if(!is.null(analytes)) {
     curve_data <- dplyr::filter(curve_data, .data[["Analyte"]] %in% analytes)
diff --git a/R/update_curve_data.R b/R/update_curve_data.R
index 16856d3..590474f 100644
--- a/R/update_curve_data.R
+++ b/R/update_curve_data.R
@@ -103,6 +103,7 @@ new_curve_data <- lapply(names(.fits), function(x) {
 }) |> dplyr::bind_rows()
 
 if(!.silent) {
+  message()
   warning(
     "LLoQ, MDD, and LoD may be calculated differently than in Belysa. See ?refit_curves for details.",
     call. = FALSE
diff --git a/man/update_curve_data.Rd b/man/update_curve_data.Rd
index 7373f2e..6c0481f 100644
--- a/man/update_curve_data.Rd
+++ b/man/update_curve_data.Rd
@@ -7,7 +7,7 @@
 update_curve_data(.summary_data, .well_data, .fits, .silent)
 }
 \arguments{
-\item{.summary_data}{A tibble containing the curve_data property.}
+\item{.summary_data}{A tibble containing the summary_data property.}
 
 \item{.well_data}{A tibble containing the well_data property.}
 
diff --git a/scratch/workflow example.r b/scratch/workflow example.r
new file mode 100644
index 0000000..f3bf43f
--- /dev/null
+++ b/scratch/workflow example.r	
@@ -0,0 +1,28 @@
+# load package
+# library(luminary)
+
+# load example dataset
+data(u5plex)
+
+# display object
+u5plex
+
+# extract elements
+get_well_data(u5plex)    |> View()
+get_summary_data(u5plex) |> View()
+get_analytes(u5plex)     |> View()
+get_metadata(u5plex)     |> View()
+get_curve_data(u5plex)   |> View()
+
+# plot curves
+plot_curves(u5plex)
+plot_curves(u5plex, facet_scales = "free")
+plot_curves(
+    u5plex, 
+    interactive = TRUE, 
+    rug = FALSE, 
+    analytes = c("AFM", "EPCR")
+)
+
+# refit curves
+refit_u5plex <- refit_curves(u5plex)