Enable 5 additional linters and fix all violations

Re-enable assignment_linter, commented_code_linter, semicolon_linter,
pipe_continuation_linter, and quotes_linter. Fix 56 assignment (= to <-),
110 commented-out code, and 14 quotes violations across 26 R files.

Author: wolski

.lintr

@@ -1,4 +1,4 @@
-linters: linters_with_defaults(line_length_linter(120), assignment_linter = NULL, brace_linter = NULL, commas_linter = NULL, commented_code_linter = NULL, indentation_linter = NULL, infix_spaces_linter = NULL, object_length_linter(40), object_name_linter = NULL, paren_body_linter = NULL, pipe_continuation_linter = NULL, quotes_linter = NULL, return_linter = NULL, semicolon_linter = NULL, spaces_inside_linter = NULL, spaces_left_parentheses_linter = NULL, trailing_blank_lines_linter = NULL, trailing_whitespace_linter = NULL)
+linters: linters_with_defaults(line_length_linter(120), brace_linter = NULL, commas_linter = NULL, indentation_linter = NULL, infix_spaces_linter = NULL, object_length_linter(40), object_name_linter = NULL, paren_body_linter = NULL, return_linter = NULL, spaces_inside_linter = NULL, spaces_left_parentheses_linter = NULL, trailing_blank_lines_linter = NULL, trailing_whitespace_linter = NULL)
 exclusions: list("data-raw", "inst/deprecated", "inst/doc", "inst/issue71", "tests/testthat", "vignettes", "R/generatedContrastsDF.r")
 
 

R/A_dataset_docu.R

@@ -100,161 +100,78 @@ NULL
 "x5463yzwer453bbb"
 
 
-# data_benchmarkExample <- prolfqua::benchmarkDataExample
-# usethis::use_data(data_benchmarkExample, compress = TRUE, overwrite = TRUE)
-# file.remove("data/benchmarkDataExample.rda")
-
 #' Benchmark data Example
 #' @format A data frame
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_benchmarkExample"
 
-# #@usage data_benchmarkExample <- prolfqua_data("data_benchmarkExample")
-
-# data_checksummarizationrobust87 <- prolfqua::checksummarizationrobust87
-# usethis::use_data(data_checksummarizationrobust87, compress = TRUE, overwrite = TRUE)
-# file.remove("data/checksummarizationrobust87.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_checksummarizationrobust87"
 
-# #@usage data_checksummarizationrobust87 <- prolfqua_data("data_checksummarizationrobust87")
-
-# data_checksummarizerobust <- prolfqua::checksummarizerobust
-# usethis::use_data(data_checksummarizerobust, compress = TRUE, overwrite = TRUE)
-# file.remove("data/checksummarizerobust.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_checksummarizerobust"
 
-# #@usage data_checksummarizerobust <- prolfqua_data("data_checksummarizerobust")
-
-# data_checksummarizerobust69 <- prolfqua::checksummarizerobust69
-# usethis::use_data(data_checksummarizerobust69, compress = TRUE, overwrite = TRUE)
-# file.remove("data/checksummarizerobust69.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 #'
 "data_checksummarizerobust69"
 
-# #@usage data_checksummarizerobust69 <- prolfqua_data("data_checksummarizerobust69")
-
-# data_correlatedPeptideList <- prolfqua::correlatedPeptideList
-# usethis::use_data(data_correlatedPeptideList, compress = TRUE, overwrite = TRUE)
-# file.remove("data/correlatedPeptideList.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 #'
 "data_correlatedPeptideList"
 
-# #@usage data_correlatedPeptideList <- prolfqua_data("data_correlatedPeptideList")
-
-# data_IonstarProtein_subsetNorm <- prolfqua::dataIonstarProtein_subsetNorm
-# usethis::use_data(data_IonstarProtein_subsetNorm, compress = TRUE, overwrite = TRUE)
-# file.remove("data/dataIonstarProtein_subsetNorm.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 #'
 "data_IonstarProtein_subsetNorm"
 
-# #@usage data_IonstarProtein_subsetNorm <- prolfqua_data("data_IonstarProtein_subsetNorm")
-
-# #@usage data_interactionModel_p1807 <- prolfqua_data("data_interactionModel_p1807")
-
-# data_ionstar <- ionstar
-# usethis::use_data(data_ionstar, compress = TRUE, overwrite = TRUE)
-# file.remove("data/ionstar.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_ionstar"
 
-# #@usage data_ionstar <- prolfqua_data("data_ionstar")
-
-# #@usage data_multigroupFC <- prolfqua_data("data_multigroupFC")
-
 #' example data for check of scores produced based on confusion matrix
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_test_confusion_matrix_scores"
 
-# data_skylinePRMSample_A <- skylinePRMSampleData_A
-# usethis::use_data(data_skylinePRMSample_A,compress = TRUE, overwrite = TRUE)
-# file.remove("data/skylinePRMSampleData_A.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_skylinePRMSample_A"
 
-# #@usage data_skylinePRMSample_A <- prolfqua_data("data_skylinePRMSample_A")
-
-# data_skylineSRM_HL_A <- skylineSRM_HL_A
-# usethis::use_data(data_skylineSRM_HL_A,compress = TRUE, overwrite = TRUE)
-# file.remove("data/skylineSRM_HL_A.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_skylineSRM_HL_A"
 
-# data_skylineSRM_HL_A <- prolfqua_data("data_skylineSRM_HL_A")
-# data_skylineSRM_HL_A_new <- list()
-# data_skylineSRM_HL_A_new$data <- data_skylineSRM_HL_A$data
-# data_skylineSRM_HL_A_new$config_f <- function(){
-#   skylineconfig_HL <- create_config_Skyline(isotopeLabel = "Isotope.Label",
-#                                             ident_qValue = "annotation_QValue")
-#   skylineconfig_HL$table$factors[["treatment_c"]] <- "Condition2"
-#   skylineconfig_HL$table$factors[["time_c"]] <- "time"
-#   skylineconfig_HL$table$is_response_transformed = FALSE
-#   return(skylineconfig_HL)
-# }
-# data_skylineSRM_HL_A_new$analysis <- function(data,config ){
-#   data$Area[data$Area == 0] <- NA
-#   analysis <- setup_analysis(data, config)
-#   return(analysis)
-# }
-# data_skylineSRM_HL_A <- data_skylineSRM_HL_A_new
-# usethis::use_data(data_skylineSRM_HL_A,compress = TRUE, overwrite = TRUE)
-
-# data_spectronautDIA250_A <- spectronautDIAData250_A
-# usethis::use_data(data_spectronautDIA250_A,compress = TRUE, overwrite = TRUE)
-# file.remove("data/spectronautDIAData250_A.rda")
-
 #' example data for check
 #' @family data
 #' @docType data
 #' @keywords internal
 "data_spectronautDIA250_A"
 
-# #@usage data_spectronautDIA250_A <- prolfqua_data("data_spectronautDIA250_A")
-
-# example of 2 Factor data
-# @family data
-# @docType data
-# @keywords internal
-#' data_Yeast2Factor'
-
-# #@usage data_spectronautDIA250_A <- prolfqua_data("data_spectronautDIA250_A")
+#' example of 2 Factor data
+#' @family data
+#' @docType data
+#' @keywords internal
+"data_Yeast2Factor"

R/AnalysisConfiguration.R

@@ -306,8 +306,8 @@ list_to_AnalysisConfiguration <- function(dd) {
 #' stopifnot(length(red$hierarchy) == 1)
 make_reduced_hierarchy_config <- function(config, workIntensity, hierarchy) {
   newConfig <- config$clone(deep = TRUE)
-  newConfig$hierarchy = hierarchy
-  newConfig$workIntensity = workIntensity
+  newConfig$hierarchy <- hierarchy
+  newConfig$workIntensity <- workIntensity
   return(newConfig)
 }
 
@@ -437,9 +437,9 @@ setup_analysis <- function(data, configuration, cc = TRUE, from_factors = FALSE)
   if (length(configuration$factors) == 0) {
     stop(
       "No factors (explanatory variables) specified in the AnalysisConfiguration.\n",
-      'Please use config$factors["Condition"] = "columnName".\n',
-      'where Condition is the new name of the variable and\n',
-      'columnName is the name of the column containing the variable.'
+      "Please use config$factors[\"Condition\"] = \"columnName\".\n",
+      "where Condition is the new name of the variable and\n",
+      "columnName is the name of the column containing the variable."
     )
   }
   for (i in seq_along(configuration$factors)) {

R/Benchmark.R

@@ -50,8 +50,6 @@ ionstar_bench_preprocess <- function(data, idcol = "protein_Id") {
 #' plot(1- xd$PREC, xd$FDP)
 #'
 ms_bench_add_scores <- function(data, TP_col = "TP", arrangeby = "diff", desc = TRUE, subject_Id = "protein_Id") {
-  #data <- est
-
   data <- if (!desc) {
     data |> arrange(!!sym(arrangeby))
   } else {
@@ -116,7 +114,7 @@ ms_bench_auc <- function(FPR, TPR, fpr_threshold = 1) {
 .scale_probabilities <-
   function(est, toscale, fcestimate = "diff") {
     addScaledP <- function(data, fcestimate, scale) {
-      scaled.p = paste0("scaled.", scale)
+      scaled.p <- paste0("scaled.", scale)
       data <-
         data |> dplyr::mutate(!!scaled.p := ifelse(!!sym(fcestimate) > 0, 1 - !!sym(scale), !!sym(scale) - 1))
       return(data)
@@ -170,15 +168,11 @@ do_confusion_c <- function(
     )
   }
   txx$out <- out
-  #txx <- txx |> mutate(out = map(data,
-  #                               do_confusion,
-  #                               arrangeby = arrangeby, subject_Id = subject_Id))
   xx <- txx |> select(all_of(c(contrast, "out"))) |> unnest("out") |> ungroup()
 
   # computes FDR FDP for all contrasts
   xy <- do_confusion(data, arrangeby = arrangeby, subject_Id = subject_Id)
   xy <- xy |> dplyr::mutate(!!contrast := "all")
-  #xy <- tibble::add_column(data, contrast = "all", .before = 1)
   xx <- dplyr::bind_rows(xy, xx)
   return(xx)
 }
@@ -270,8 +264,8 @@ do_confusion_c <- function(
 ) {
   plots <- list()
   for (i in score) {
-    xlim = i$xlim
-    score = i$score
+    xlim <- i$xlim
+    score <- i$score
     plots[[score]] <- ggplot(data, aes(x = !!sym(score), y = !!sym(contrast), color = !!sym(species))) +
       ggridges::geom_density_ridges(alpha = 0.1) +
       if (!is.null(xlim)) {
@@ -563,7 +557,6 @@ Benchmark <-
       #' @return ggplot
       plot_FDRvsFDP = function() {
         xx <- self$get_confusion_FDRvsFDP()
-        #xx$FDP <- xx$FDP/seq(1,max(xx$FDP), length = length(xx$FDP))
         p <- ggplot(xx, aes(x = scorecol, y = FDP_, color = !!sym(self$contrast))) +
           geom_line() +
           geom_abline(slope = max(xx$FDP_), col = 2) +

R/ContrastFirth.R

@@ -199,7 +199,7 @@ ContrastsFirth <- R6::R6Class(
         contrast_minimal,
         subject_Id = self$subject_Id,
         columns = c("diff", columns),
-        contrast = 'contrast'
+        contrast = "contrast"
       )
       return(contrasts_wide)
     }

R/Contrasts.R

@@ -164,7 +164,6 @@ Contrasts <- R6::R6Class(
       if (is.null(self$contrast_result)) {
         message("determine linear functions:")
         linfct <- self$get_linfct(global = self$global)
-        # contrast_sides <- self$get_contrast_sides()
         message("get_contrasts -> contrasts_linfct")
         # TODO (goes into calling code)
         contrast_result <- contrasts_linfct(

R/ContrastsModerated.R

@@ -182,7 +182,7 @@ ContrastsModerated <- R6::R6Class(
         contrast_minimal,
         subject_Id = self$subject_Id,
         columns = c("diff", columns),
-        contrast = 'contrast'
+        contrast = "contrast"
       )
       return(contrasts_wide)
     }

R/ContrastsProDA.R

@@ -108,7 +108,7 @@ ContrastsProDA <- R6::R6Class(
         contrast_minimal,
         subject_Id = self$subject_Id,
         columns = c("diff", columns),
-        contrast = 'contrast'
+        contrast = "contrast"
       )
       return(contrasts_wide)
     }

R/ContrastsROPECA.R

@@ -169,7 +169,7 @@ ContrastsROPECA <- R6::R6Class(
         contrast_minimal,
         subject_Id = self$subject_Id[length(self$subject_Id) - 1],
         columns = c("diff", columns),
-        contrast = 'contrast'
+        contrast = "contrast"
       )
       return(contrasts_wide)
     }

R/ContrastsSimpleImpute.R

@@ -158,7 +158,7 @@ ContrastsMissing <- R6::R6Class(
         contrast_minimal,
         subject_Id = self$subject_Id,
         columns = c("diff", columns),
-        contrast = 'contrast'
+        contrast = "contrast"
       )
       return(contrasts_wide)
     }