fix: resolve gDRstyle linting violations

.gitignore

@@ -46,3 +46,4 @@ vignettes/*.pdf
 # support for build via github.com with access_token defined
 .github_access_token.txt
 docs
+.serena/

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.11.2
-Date: 2026-05-05
+Version: 1.11.3
+Date: 2026-05-27
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com",

NEWS.md

@@ -1,3 +1,6 @@
+## gDRutils 1.11.3 - 2026-05-27
+* apply updated gDRstyle rules
+
 ## gDRutils 1.11.2 - 2026-05-05
 * update author email address
 
@@ -127,7 +130,7 @@
 * make split_SE_components working correctly for sa assay data, modified with `avearge_biological_duplicates`
 
 ## gDRutils 1.5.4 - 2024-12-09
-* minor improvement in the logic of `average_biological_replicates` (new blacklisted column)
+* improve in the logic of `average_biological_replicates` (new blacklisted column)
 
 ## gDRutils 1.5.3 - 2024-12-02
 * refactor `set_unique_*` functions
@@ -252,7 +255,7 @@
 * release Bioc 3.18
 
 ## gDRutils 1.0.0 - 2023-10-24
-* prerelease Bioc 3.18
+* prepare prerelease for Bioc 3.18
 
 ## gDRutils 0.99.34 - 2023-10-18
 * adjust NEWS to Bioc format
@@ -267,7 +270,7 @@
 * add `wide_structure` param to `convert_mae_assay_to_dt`
 
 ## gDRutils 0.99.30 - 2023-09-08
-* updated `experimentalist` description in schema
+* update `experimentalist` description in schema
 
 ## gDRutils 0.99.29 - 2023-09-05
 * add `Replicate` as a new identifier
@@ -285,7 +288,7 @@
 * add assert for missing rownames
 
 ## gDRutils 0.99.24 - 2023-06-22
-* replaced RDS with qs
+* replace RDS with qs
 
 ## gDRutils 0.99.23 - 2023-06-20
 * fix check in R 4.3
@@ -301,7 +304,7 @@
 * switch from `aggregate` to `data.table`
 
 ## gDRutils 0.99.19 - 2023-06-06
-* replaced reshape2 functions by functions from data.table
+* replace reshape2 functions by functions from data.table
 
 ## gDRutils 0.99.18 - 2023-05-22
 * format the vignette with BiocStyle
@@ -404,7 +407,7 @@
 * add co-dilution to single-agent group
 
 ## gDRutils 0.1.3.8 - 2022-11-30
-* bugfix in validate_SE
+* fix validate_SE
 
 ## gDRutils 0.1.3.7 - 2022-10-18
 * add update_env_idfs_from_mae function
@@ -453,7 +456,7 @@
 * set r2 value to NA for invalid and 0 for constant fits
 
 ## gDRutils 0.1.0.42 - 2022-04-08
-* added identifier descriptions
+* add identifier descriptions
 
 ## gDRutils 0.1.0.41 - 2022-04-08
 * fix wrong order of elements in rownames in SE
@@ -612,10 +615,10 @@
 * add `prettify_flat_metrics` function
 
 ## gDRutils 0.0.0.41 - 2021-04-29
-* bugfix flattening data.tables
+* fix flattening data.tables
 
 ## gDRutils 0.0.0.40 - 2021-04-29
-* bugfix data.table merge in `convert_se_assay_ref_to_dt`
+* fix data.table merge in `convert_se_assay_ref_to_dt`
 
 ## gDRutils 0.0.0.39 - 2021-04-27
 * add support for flattening data.tables
@@ -653,7 +656,7 @@
 * remove positional naming dependence on assay_to_dt for - merge_metrics = TRUE argument
 
 ## gDRutils 0.0.0.28 - 2021-03-16
-* minor refactor to assay_to_dt
+* refactor to assay_to_dt
 * deprecated support for assay_to_dt- include_controls = TRUE argument - not backwards compatible
 
 ## gDRutils 0.0.0.27 - 2021-03-09
@@ -671,7 +674,7 @@
 * clean-up assay_to_dt
 
 ## gDRutils 0.0.0.23 - 2021-02-04
-* added linter
+* add linter
 
 ## gDRutils 0.0.0.22 - 2021-02-03
 * move assay_to_dt from gDR to gDRutils
@@ -712,7 +715,7 @@
 * update namespaces
 
 ## gDRutils 0.0.0.10 - 2020-10-05
-* minor refactor
+* refactor
 
 ## gDRutils 0.0.0.9 - 2020-09-14
 * add small fixes for assays with empty DataFrame
@@ -727,4 +730,4 @@
 * import pipes from magrittr
 
 ## gDRutils 0.0.0.4 - 2020-06-10
-* including the masked field to be able to remove the masked data from averages
+* including the masked field to be able to remove the masked data from averages

R/assay_names.R

@@ -22,10 +22,10 @@ ASSAY_INFO_TBL <- data.table::data.table(
 #'    will return single string instead of named vector with single element
 #'    useful when function is expected to return single element/assay only
 #' @keywords assay_names
-#'    
+#'
 #' @return charvec
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_env_assay_names()
 #'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
@@ -66,7 +66,7 @@ get_env_assay_names <-
       df <- df[df[[eval(filter)]] %in% v_filters[[filter]], ]
     }
 
-    if ((nrow(df)) == 0)  {
+    if ((NROW(df)) == 0)  {
       v_filters_str <-
         paste(names(v_filters),
               v_filters,
@@ -93,9 +93,9 @@ get_env_assay_names <-
 #'
 #' @return  charvec
 #'
-#' @examples 
+#' @examples
 #' get_assay_names()
-#' 
+#'
 #' @export
 get_assay_names <- function(se = NULL, ...) {
   if (!is.null(se) &&
@@ -116,9 +116,9 @@ get_assay_names <- function(se = NULL, ...) {
 #' @keywords assay_names
 #' @return charvec of combo assay names.
 #' @export
-#' @examples 
+#' @examples
 #' get_combo_assay_names()
-#' 
+#'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
 get_combo_assay_names <- function(se = NULL, ...) {
@@ -134,7 +134,7 @@ get_combo_assay_names <- function(se = NULL, ...) {
 #' @return  charvec
 #' @export
 #'
-#' @examples 
+#' @examples
 #' get_combo_base_assay_names()
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
@@ -151,10 +151,10 @@ get_combo_base_assay_names <- function(se = NULL, ...) {
 #' @return  charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_combo_score_assay_names()
-#' 
+#'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
 get_combo_score_assay_names <- function(se = NULL, ...) {

R/combo.R

@@ -3,14 +3,14 @@
 #' @param se \code{SummarizedExperiment} object with dose-response data
 #' @param c_assays charvec of combo assays to be used
 #' @param normalization_type charvec of normalization_types expected in the data
-#' @param prettify boolean flag indicating whether or not to prettify the colnames of the returned data 
+#' @param prettify boolean flag indicating whether or not to prettify the colnames of the returned data
 #' @keywords combination_data
-#' 
+#'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
 #' @return list of data.table(s) with combo data
 #'
-#' @examples 
+#' @examples
 #' mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 #' convert_combo_data_to_dt(mae[[1]])
 #'
@@ -38,7 +38,7 @@ convert_combo_data_to_dt <-
         }
         dt
       })
-    
+
     # TODO: discuss what should be returned: assay_name or maybe assay_type?
     names(my_l) <- as.character(c_assays)
     my_l
@@ -60,10 +60,10 @@ DATA_COMBO_INFO_TBL <- data.table::data.table(
 #' @return  charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_combo_score_assay_names()
-#' 
+#'
 get_combo_score_field_names <- function() {
   dt <- DATA_COMBO_INFO_TBL[type == "scores", c("name", "pname"), with = FALSE]
   stats::setNames(dt$pname, dt$name)
@@ -75,10 +75,10 @@ get_combo_score_field_names <- function() {
 #' @return charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_combo_excess_field_names()
-#' 
+#'
 get_combo_excess_field_names <- function() {
   dt <- DATA_COMBO_INFO_TBL[type == "excess", c("name", "pname"), with = FALSE]
   stats::setNames(dt$pname, dt$name)
@@ -93,10 +93,10 @@ get_combo_excess_field_names <- function() {
 #' @return charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' convert_combo_field_to_assay("hsa_score")
-#' 
+#'
 convert_combo_field_to_assay <- function(field) {
   checkmate::assert_string(field)
   DATA_COMBO_INFO_TBL[name == field, ][["type"]]
@@ -111,26 +111,26 @@ convert_combo_field_to_assay <- function(field) {
 #' @details
 #' \code{drug_1} is diluted along the rows as the y-axis and
 #' \code{drug_2} is diluted along the columns and will be the x-axis.
-#' 
+#'
 #' @keywords combination_data
 #' @return list with axis grid positions
-#' 
+#'
 #' @examples
 #' cl_name <- "cellline_BC"
 #' drug1_name <- "drug_001"
 #' drug2_name <- "drug_026"
-#' 
+#'
 #' se <- get_synthetic_data("combo_matrix_small")[["combination"]]
 #' dt_average <- convert_se_assay_to_dt(se, "Averaged")[normalization_type == "GR"]
-#' 
+#'
 #' ls_axes <- define_matrix_grid_positions(
 #'    dt_average[["Concentration"]], dt_average[["Concentration_2"]])
-#' 
+#'
 #' @export
 define_matrix_grid_positions <- function(conc1, conc2) {
   checkmate::assert_numeric(conc1)
   checkmate::assert_numeric(conc2)
-  
+
   .generate_gap_for_single_agent <- function(x) {
     if (NROW(x) == 1) {
       x
@@ -139,8 +139,8 @@ define_matrix_grid_positions <- function(conc1, conc2) {
     } else {
       x[2] - 0.5 # diff(log10(c(0, 10^(seq(-3, 1, 0.5))))) # nolint
     }
-  } 
-  
+  }
+
   conc_1 <- sort(unique(round_concentration(conc1)))
   pos_y <- log10conc_1 <- log10(conc_1)
   pos_y[1] <- .generate_gap_for_single_agent(log10conc_1)
@@ -149,7 +149,7 @@ define_matrix_grid_positions <- function(conc1, conc2) {
                                    pos_y = pos_y,
                                    marks_y = sprintf("%.2g", conc_1)
   )
-  
+
   conc_2 <- sort(unique(round_concentration(conc2)))
   pos_x <- log10conc_2 <- log10(conc_2)
   pos_x[1] <- .generate_gap_for_single_agent(log10conc_2)
@@ -158,16 +158,16 @@ define_matrix_grid_positions <- function(conc1, conc2) {
                                    pos_x = pos_x,
                                    marks_x = sprintf("%.2g", conc_2)
   )
-  
+
   list(axis_1 = axis_1, axis_2 = axis_2)
 }
 
 #' Round concentration to ndigit significant digits
 #'
 #' @param x value to be rounded.
 #' @param ndigit number of significant digits (default = 4).
-#' 
-#' @examples 
+#'
+#' @examples
 #' round_concentration(x = c(0.00175,0.00324,0.0091), ndigit = 1)
 #'
 #' @return rounded x
@@ -176,6 +176,6 @@ define_matrix_grid_positions <- function(conc1, conc2) {
 round_concentration <- function(x, ndigit = 3) {
   checkmate::assert_numeric(x)
   checkmate::assert_integerish(ndigit)
-  
+
   round(10 ^ (round(log10(x), ndigit)), ndigit - 1 - floor(log10(x)))
 }