Merge pull request #160 from gdrplatform/GDR-2558.2

refactor: utilize calc_sd function

DESCRIPTION

@@ -2,8 +2,8 @@ Type: Package
 Package: gDRcore
 Title: Processing functions and interface to process and analyze drug
     dose-response data
-Version: 1.3.9
-Date: 2024-08-09
+Version: 1.3.10
+Date: 2024-08-19
 Authors@R: c(
     person("Bartosz", "Czech", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-9908-3007")),
@@ -29,7 +29,7 @@ Imports:
     BiocParallel,
     checkmate,
     futile.logger,
-    gDRutils (>= 1.1.14),
+    gDRutils (>= 1.3.9),
     MultiAssayExperiment,
     purrr,
     stringr,    

NEWS.md

@@ -1,3 +1,6 @@
+## gDRcore 1.3.10 - 2024-08-19
+* utilize `calc_sd` function
+
 ## gDRcore 1.3.9 - 2024-08-09
 * fix issue with wrong mapping of Day0 data
 

R/average_SE.R

@@ -92,7 +92,7 @@ average_FUN <- function(x,
     unmasked <- x[!masked, , drop = FALSE]
     agg_df <- unmasked[, list(mean(x, na.rm = TRUE),
                               # set sd = 1 for single values
-                    ifelse(length(x) == 1, 0, sd(x, na.rm = TRUE))),
+                    gDRutils::calc_sd(x)),
              by = c("normalization_type", series_identifiers)]
     data.table::setorderv(agg_df, c(series_identifiers, "normalization_type"))
     data.table::setnames(agg_df, c("V1", "V2"), c("x", "x_std"))

rplatform/dependencies.yaml

@@ -1,6 +1,6 @@
 pkgs:
   gDRutils:
-    ver: '>= 1.1.14'
+    ver: '>= 1.3.9'
     url: gdrplatform/gDRutils
     ref: main
     subdir: ~