refit_curves now updates all slots of intelliframe.

DESCRIPTION

@@ -32,9 +32,9 @@ Imports:
     scales,
     nplr,
     utils,
-    mathjaxr
+    mathjaxr,
+    S7
 Config/testthat/edition: 3
 Depends: 
-    R (>= 3.0),
-    S7
+    R (>= 3.0)
 LazyData: true

NAMESPACE

@@ -12,10 +12,6 @@ export(intelliframe)
 export(plot_curves)
 export(read_xmap)
 export(refit_curves)
-export(update_recovery)
-export(update_recovery_avg)
-export(update_summary_data)
-export(update_well_data)
 importFrom(S7,props)
 importFrom(rlang,.data)
 importFrom(stats,reformulate)

R/print.R

@@ -6,7 +6,7 @@
 #' @param ... Unused.
 #'
 #' @noRd
-method(print, intelliframe) <- function(x, max.level = 1, ...) {
+S7::method(print, intelliframe) <- function(x, max.level = 1, ...) {
   counts <- dplyr::summarise(get_well_data(x), .by = "Type", dplyr::n())
 
   counts <- lapply(c("Standard", "Control", "Unknown"), function(.type) {

R/refit_curves.R

@@ -131,28 +131,38 @@ refit_curves <- function(
 
   names(fits) <- names(standard_list)
 
-  prop(intelliframe_out, "well_data") <-
+  S7::prop(intelliframe_out, "well_data") <-
     update_well_data(well_data, fits, standard_list, silent)
 
-  prop(intelliframe_out, "recovery") <-
-    update_recovery(well_data)
+  S7::prop(intelliframe_out, "recovery") <-
+    update_recovery(
+      S7::prop(intelliframe_out, "well_data")
+    )
 
-  prop(intelliframe_out, "recovery_avg") <-
+  S7::prop(intelliframe_out, "recovery_avg") <-
     update_recovery_avg(
-      get_recovery(intelliframe_out),
-      get_recovery_avg(intelliframe_out),
+      S7::prop(intelliframe_out, "recovery"),
+      S7::prop(intelliframe_out, "recovery_avg"),
       use_excluded,
       excluded_wells
     )
 
-  prop(intelliframe_out, "summary_data") <-
+  S7::prop(intelliframe_out, "summary_data") <-
     update_summary_data(
-      well_data,
-      get_summary_data(intelliframe_out),
+      S7::prop(intelliframe_out, "well_data"),
+      S7::prop(intelliframe_out, "summary_data"),
       use_excluded,
       excluded_wells
     )
 
+  S7::prop(intelliframe_out, "curve_data") <-
+    update_curve_data(
+      S7::prop(intelliframe_out, "summary_data"),
+      S7::prop(intelliframe_out, "well_data"),
+      fits,
+      silent
+    )
+
   intelliframe_out
 }
 

R/update_curve_data.R

@@ -1,6 +1,18 @@
-update_well_data <- function(.summary_data, .well_data, .fits, .standard_list, .silent) {
+#' update_curve_data
+#'
+#' Update the curve_data property from an intelliframe object using a list of
+#'   model fits. Not meant to be called by the user.
+#'
+#' @param .summary_data A tibble containing the summary_data property.
+#' @param .well_data A tibble containing the well_data property.
+#' @param .fits A list of model fits returned by \code{nplr::nplr()}.
+#' @param .silent Should luminary warnings be printed?
+#'
+#' @return A tibble
+#'
+update_curve_data <- function(.summary_data, .well_data, .fits, .silent) {
 
-lapply(names(.fits), function(x) {
+new_curve_data <- lapply(names(.fits), function(x) {
 
   lloq <- dplyr::filter(
     .summary_data,
@@ -53,10 +65,6 @@ lapply(names(.fits), function(x) {
     })
   })
 
-  if(!silent) {
-    warning("LLoQ, MDD, and LoD may be calculated differently than in Belysa. See ?refit_curves for details.")
-  }
-
   if(.fits[[x]]@weightMethod == "res") {
     weight_meth <- paste0("(1/residual)^", .fits[[x]]@LPweight)
   } else if(.fits[[x]]@weightMethod == "sdw") {
@@ -93,4 +101,13 @@ lapply(names(.fits), function(x) {
     Equation    = model_eqn
   )
 }) |> dplyr::bind_rows()
+
+if(!.silent) {
+  warning(
+    "LLoQ, MDD, and LoD may be calculated differently than in Belysa. See ?refit_curves for details.",
+    call. = FALSE
+  )
+}
+
+new_curve_data
 }

R/update_recovery.R

@@ -5,10 +5,8 @@
 #'
 #' @param .well_data A tibble containing the well_data property.
 #'
-#' @return An intelliframe
-#' @export
+#' @return A tibble
 #'
-#' @noRd
 update_recovery <- function(.well_data){
   dplyr::filter(.well_data, .data[["Type"]] %in% c("Standard", "Control")) |>
 

R/update_recovery_avg.R

@@ -11,10 +11,8 @@
 #' @param .excluded_wells Logical vector indicating whether each well is
 #'   excluded.
 #'
-#' @return An intelliframe
-#' @export
+#' @return A tibble
 #'
-#' @noRd
 update_recovery_avg <- function(.recovery, .recovery_avg, .use_excluded, .excluded_wells) {
   correct_location <- dplyr::select(.recovery, -Location) |>
     dplyr::left_join(

R/update_summary_data.R

@@ -11,10 +11,8 @@
 #' @param .excluded_wells Logical vector indicating whether each well is
 #'   excluded.
 #'
-#' @return An intelliframe
-#' @export
+#' @return A tibble
 #'
-#' @noRd
 update_summary_data <- function(.well_data, .summary_data, .use_excluded, .excluded_wells) {
   correct_location <- dplyr::select(.well_data, -Location) |>
     dplyr::left_join(

R/update_well_data.R

@@ -9,10 +9,8 @@
 #' @param .silent Logical flag indicating whether warnings and messages during
 #' interpolation should be silenced.
 #'
-#' @return An intelliframe
-#' @export
+#' @return A tibble
 #'
-#' @noRd
 update_well_data <- function(.well_data, .fits, .standard_list, .silent) {
   lapply(names(.fits), function(analyte) {
 

R/zzz.R

@@ -1,6 +1,8 @@
 .onLoad <- function(libname, pkgname) {
+
   if (getRversion() < "4.3.0") {
-    suppressPackageStartupMessages(requireNamespace("S7"))
+    suppressPackageStartupMessages(require("S7"))
   }
+
   S7::methods_register()
 }