Changed S7::@ to S7::prop.

R/get_analytes.R

@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_analytes <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "analytes")
+  S7::prop(.intelliframe, "analytes")
 }

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")
 }
 

R/get_expected.R

@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_expected <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "expected")
+  S7::prop(.intelliframe, "expected")
 }

R/get_metadata.R

@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_metadata <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "metadata")
+  S7::prop(.intelliframe, "metadata")
 }

R/get_recovery.R

@@ -10,5 +10,5 @@
 #' @examples
 #' 1+1
 get_recovery <- function(.intelliframe) {
-  S7::`@`(.intelliframe, "recovery")
+  S7::prop(.intelliframe, "recovery")
 }

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")
 }
 

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")
 }

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")
 }

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)

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

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)