replace "silent" argument with "quiet"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.18.4
+Version: 0.18.4.9000
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7213-9392"))

NEWS.md

@@ -3,6 +3,7 @@
 * Object type checks more consistent
 * Updated `plot_sample_curves()` to have better options
 * Added `correct_gradient_pos_density()` to adjust WAD values of sample data based on the gradient position
+* Replace the *silent* argument with `get_all_by_isotope()` with *quiet* to fit better with other functions
 
 # qSIP2 0.17
 

R/get_all_by_isotope.R

@@ -2,13 +2,21 @@
 #'
 #' @param qsip_data_object (*qsip_data or qsip_source_data*) A qsip object with source data
 #' @param isotopes (*string(s)*) Isotopes used to pull source_mat_ids. Can be a standard isotope name (e.g. `12C`) or special terms `labeled` or `unlabeled`
-#' @param silent (*boolean*) If `TRUE`, suppresses messages about missing isotope hits and doesn't fail
+#' @param quiet (*boolean*) If `TRUE`, suppresses messages about missing isotope hits and doesn't fail
 #'
 #' @returns A vector of source_mat_ids. It may also print some messages.
 #'
 #' @export
 
-get_all_by_isotope <- function(qsip_data_object, isotopes, silent = FALSE) {
+get_all_by_isotope <- function(qsip_data_object,
+                               isotopes,
+                               quiet = FALSE,
+                               silent = lifecycle::deprecated()) {
+
+  if (lifecycle::is_present(silent)) {
+    lifecycle::deprecate_warn("0.18.4.9000", "get_all_by_isotope(silent)")
+  }
+
   if (inherits(qsip_data_object, qsip_data)) {
     source_data <- qsip_data_object@source_data@data
   } else if (inherits(qsip_data_object, qsip_source_data)) {
@@ -36,7 +44,7 @@ get_all_by_isotope <- function(qsip_data_object, isotopes, silent = FALSE) {
     dplyr::select(source_mat_id, isotope)
 
   # error if no source_mat_ids are found that match the criteria
-  if (isFALSE(silent)) {
+  if (isFALSE(quiet)) {
 
     if (nrow(source_mat_ids) == 0) {
       i <- paste(isotopes, collapse = ", ")

R/plot_resampling_convergence.R

@@ -25,14 +25,14 @@ plot_resampling_convergence = function(qsip_data_object) {
   )
 
   dplyr::bind_rows(k) |>
-    ggplot(aes(x = unlabeled_resamples, y = mean_resampled_EAF)) +
-      geom_point() +
-      facet_wrap(~feature_id, scales = "free_y") +
-      scale_x_log10() +
-      geom_smooth(color = "#037bcf",
+      ggplot2::ggplot(ggplot2::aes(x = unlabeled_resamples, y = mean_resampled_EAF)) +
+      ggplot2::geom_point() +
+      ggplot2::facet_wrap(~feature_id, scales = "free_y") +
+      ggplot2::scale_x_log10() +
+      ggplot2::geom_smooth(color = "#037bcf",
                   formula = 'y ~ x',
                   method = 'loess') +
       #geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.1) +
-      geom_hline(aes(yintercept = observed_EAF), color = "red") +
-      geom_boxplot(aes(group = unlabeled_resamples))
+      ggplot2::geom_hline(aes(yintercept = observed_EAF), color = "red") +
+      ggplot2::geom_boxplot(ggplot2::aes(group = unlabeled_resamples))
 }

R/run_comparison_groups.R

@@ -53,18 +53,18 @@ run_comparison_groups <- function(groups,
   groups = groups |>
     dplyr::mutate(unlabeled = dplyr::case_match(
       unlabeled,
-      "unlabeled" ~ paste(get_all_by_isotope(qsip_data_object, "unlabeled", silent = TRUE), collapse = ","),
-      "12C" ~ paste(get_all_by_isotope(qsip_data_object, "12C", silent = TRUE), collapse = ","),
-      "14N" ~ paste(get_all_by_isotope(qsip_data_object, "14N", silent = TRUE), collapse = ","),
-      "16O" ~ paste(get_all_by_isotope(qsip_data_object, "16O", silent = TRUE), collapse = ","),
+      "unlabeled" ~ paste(get_all_by_isotope(qsip_data_object, "unlabeled", quiet = TRUE), collapse = ","),
+      "12C" ~ paste(get_all_by_isotope(qsip_data_object, "12C", quiet = TRUE), collapse = ","),
+      "14N" ~ paste(get_all_by_isotope(qsip_data_object, "14N", quiet = TRUE), collapse = ","),
+      "16O" ~ paste(get_all_by_isotope(qsip_data_object, "16O", quiet = TRUE), collapse = ","),
       .default = unlabeled
     ))  |>
     dplyr::mutate(labeled = dplyr::case_match(
       labeled,
-      "labeled" ~ paste(get_all_by_isotope(qsip_data_object, "labeled", silent = TRUE), collapse = ","),
-      "13C" ~ paste(get_all_by_isotope(qsip_data_object, "13C", silent = TRUE), collapse = ","),
-      "15N" ~ paste(get_all_by_isotope(qsip_data_object, "15N", silent = TRUE), collapse = ","),
-      "18O" ~ paste(get_all_by_isotope(qsip_data_object, "18O", silent = TRUE), collapse = ","),
+      "labeled" ~ paste(get_all_by_isotope(qsip_data_object, "labeled", quiet = TRUE), collapse = ","),
+      "13C" ~ paste(get_all_by_isotope(qsip_data_object, "13C", quiet = TRUE), collapse = ","),
+      "15N" ~ paste(get_all_by_isotope(qsip_data_object, "15N", quiet = TRUE), collapse = ","),
+      "18O" ~ paste(get_all_by_isotope(qsip_data_object, "18O", quiet = TRUE), collapse = ","),
       .default = labeled
     ))
 

qSIP2.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 84eb367f-bac8-4c00-a392-89c277624d1a
 
 RestoreWorkspace: No
 SaveWorkspace: No