Release candidate 6.5.0

DESCRIPTION

@@ -12,10 +12,10 @@ Authors@R: c(
            family = "Scheidel",
            role = "cre",
            email = "calebjscheidel@gmail.com"),    
-    person(given = "Standard BioTools, Inc.", role = c("cph", "fnd"))
+    person(given = "SomaLogic Operating Co., Inc.", role = c("cph", "fnd"))
     )
 Description: Load and export 'SomaScan' data via the
-    'Standard BioTools, Inc.' structured text file
+    'SomaLogic Operating Co., Inc.' structured text file
     called an ADAT ('*.adat'). For file format see
     <https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md>.
     The package also exports auxiliary functions for
@@ -49,7 +49,7 @@ Suggests:
     withr
 VignetteBuilder: 
     knitr
-Copyright: Standard BioTools, Inc. 2025
+Copyright: SomaLogic Operating Co., Inc. 2026
 Encoding: UTF-8
 Language: en-US
 LazyData: true

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2025
-COPYRIGHT HOLDER: Standard BioTools, Inc.
+YEAR: 2026
+COPYRIGHT HOLDER: SomaLogic Operating Co., Inc.

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright © 2025 Standard BioTools, Inc.
+Copyright © 2026 SomaLogic Operating Co., Inc.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -1,12 +1,28 @@
-# SomaDataIO (development version)
+# SomaDataIO (6.4.0.9000)
 
-### Backward Compatibility
+### Function and Object Improvements
 
-* Added backward compatibility for `filter.qc` parameter in `preProcessAdat()`
-  - `filter.qc` parameter has been renamed to `filter.rowcheck` 
-  - For backward compatibility, `filter.qc` is still accepted but will generate
+* Updated `preProcessAdat()` to improve clarity
+  - `filter.qc` parameter has been renamed to `filter.rowcheck`
+  - for backward compatibility, `filter.qc` is still accepted but will generate
     a deprecation warning and will be removed in a future version
-  - Users should update their code to use `filter.rowcheck` instead
+  - removed language that discusses implication of `ColCheck` SeqIds not 
+    being removed from `preProcessAdat()` output
+* Updated `read_annotations()` function and `ver_dict` object to 
+  recognize latest menu annotations files from Q3 2025
+
+### Documentation Updates
+
+* updated statistical analysis workflow articles with clearer
+  messaging comments around `preProcessAdat()`
+* updated two-group and three-group analysis workflow articles to
+  set `center.scale = FALSE` in `preProcessAdat()` to align with guidance
+  to users for univariate analysis
+
+### Internal :construction:
+
+* Updated `dplyr` verb tests to no longer explicitly test
+  for ordering of attributes (#165)
 
 # SomaDataIO (6.4.0)
 

R/adat2eSet.R

@@ -64,10 +64,10 @@ adat2eSet <- function(adat) {
 
   experimentData       <- Biobase::experimentData(eset)
   experimentData@name  <- if ("AssayType" %in% names(lst$header)) lst$header$AssayType else ""
-  experimentData@lab   <- "Standard BioTools, Inc."
+  experimentData@lab   <- "SomaLogic Operating Co., Inc."
   experimentData@contact <- "2945 Wilderness Place, Boulder, Colorado, 80301."
   experimentData@title <- if ("Title" %in% names(lst$header)) lst$header$Title else ""
-  experimentData@url   <- "www.standardbio.com"
+  experimentData@url   <- "www.somalogic.com"
   experimentData@other <- c(list(R.version  = R.version$version.string,
                                  R.platform = R.version$platform,
                                  R.arch     = R.version$arch),

R/data.R

@@ -72,7 +72,7 @@
 #' }
 #'
 #' @source \url{https://github.com/SomaLogic/SomaLogic-Data}
-#' @source Standard BioTools, Inc.
+#' @source SomaLogic Operating Co., Inc.
 #' @keywords datasets
 #' @examples
 #' # S3 print method

R/read-annotations.R

@@ -2,7 +2,7 @@
 #'
 #' @param file A path to an annotations file location.
 #'   This is a sanctioned, versioned file provided by
-#'   Standard BioTools, Inc. and should be an _unmodified_
+#'   SomaLogic Operating Co., Inc. and should be an _unmodified_
 #'   `*.xlsx` file.
 #' @return A `tibble` containing analyte-specific annotations and
 #'   related (e.g. lift/bridging) information, keyed on SomaLogic

R/zzz.R

@@ -37,14 +37,14 @@ create_legal <- function() {
     paste(
       "SomaDataIO\u2122
 
-      Copyright \u00A9 2025 Standard BioTools, Inc.
+      Copyright \u00A9 2026 SomaLogic Operating Co., Inc.
 
       The `SomaDataIO` package is licensed under the MIT license
       (`LICENSE.md`) and is intended solely for research use
       only (\"RUO\") purposes. The code contained herein may *not*
       be used for diagnostic, clinical, therapeutic, or other
       commercial purposes. Further, \"SomaDataIO\" and \"SomaLogic\"
-      are trademarks owned by Standard BioTools, Inc. No license
+      are trademarks owned by SomaLogic Operating Co., Inc. No license
       is hereby granted to these trademarks other than for purposes
       of identifying the origin or source of the Software. The above
       copyright notice and this permission notice shall be included

README.Rmd

@@ -39,7 +39,7 @@ ver <- paste0("https://img.shields.io/badge/Version-", desc$Version,
 
 
 The `SomaDataIO` R package loads and exports 'SomaScan' data via the
-Standard BioTools, Inc. structured text file called an ADAT (`*.adat`).
+SomaLogic Operating Co., Inc. structured text file called an ADAT (`*.adat`).
 The package also exports auxiliary functions for manipulating, wrangling,
 and extracting relevant information from an ADAT object once in memory.
 Basic familiarity with the R environment is assumed, as is the ability to install
@@ -317,6 +317,6 @@ are not included with the installed package.
   - [https://www.tldrlegal.com/license/mit-license/](https://www.tldrlegal.com/license/mit-license)
 * Further:
   - "SomaDataIO" and "SomaLogic" are trademarks owned by
-    Standard BioTools, Inc. No license is hereby granted to
+    SomaLogic Operating Co., Inc. No license is hereby granted to
     these trademarks other than for purposes of identifying the origin or
     source of this Software.

README.md

@@ -20,12 +20,12 @@ MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://choosealicense.
 <!-- badges: end -->
 
 The `SomaDataIO` R package loads and exports ‘SomaScan’ data via the
-Standard BioTools, Inc. structured text file called an ADAT (`*.adat`).
-The package also exports auxiliary functions for manipulating,
-wrangling, and extracting relevant information from an ADAT object once
-in memory. Basic familiarity with the R environment is assumed, as is
-the ability to install contributed packages from the Comprehensive R
-Archive Network (CRAN).
+SomaLogic Operating Co., Inc. structured text file called an ADAT
+(`*.adat`). The package also exports auxiliary functions for
+manipulating, wrangling, and extracting relevant information from an
+ADAT object once in memory. Basic familiarity with the R environment is
+assumed, as is the ability to install contributed packages from the
+Comprehensive R Archive Network (CRAN).
 
 If you run into any issues/problems with `SomaDataIO` full documentation
 of the most recent
@@ -253,14 +253,14 @@ the most popular [dplyr](https://dplyr.tidyverse.org) and
 ``` r
 # see full complement of `soma_adat` methods
 methods(class = "soma_adat")
-#>  [1] $              $<-            ==             Math           Ops           
-#>  [6] Summary        [              [<-            [[             [[<-          
-#> [11] anti_join      arrange        count          filter         full_join     
-#> [16] getAdatVersion getAnalytes    getMeta        group_by       inner_join    
-#> [21] is_seqFormat   left_join      median         merge          mutate        
-#> [26] print          rename         right_join     row.names<-    sample_frac   
-#> [31] sample_n       semi_join      separate       slice          slice_sample  
-#> [36] summary        transform      ungroup        unite         
+#>  [1] [              [[             [[<-           [<-            ==            
+#>  [6] $              $<-            anti_join      arrange        count         
+#> [11] filter         full_join      getAdatVersion getAnalytes    getMeta       
+#> [16] group_by       inner_join     is_seqFormat   left_join      Math          
+#> [21] median         merge          mutate         Ops            print         
+#> [26] rename         right_join     row.names<-    sample_frac    sample_n      
+#> [31] semi_join      separate       slice_sample   slice          summary       
+#> [36] Summary        transform      ungroup        unite         
 #> see '?methods' for accessing help and source code
 ```
 
@@ -360,7 +360,7 @@ articles and workflows are only accessible via the `SomaDataIO`
   - <https://choosealicense.com/licenses/mit/>
   - [https://www.tldrlegal.com/license/mit-license/](https://www.tldrlegal.com/license/mit-license)
 - Further:
-  - “SomaDataIO” and “SomaLogic” are trademarks owned by Standard
-    BioTools, Inc. No license is hereby granted to these trademarks
+  - “SomaDataIO” and “SomaLogic” are trademarks owned by SomaLogic
+    Operating Co., Inc. No license is hereby granted to these trademarks
     other than for purposes of identifying the origin or source of this
     Software.

_pkgdown.yml

@@ -8,8 +8,8 @@ authors:
     href: https://github.com/stufield
   Caleb Scheidel:
     href: https://github.com/scheidec
-  Standard BioTools, Inc.:
-    href: http://www.standardbio.com
+  SomaLogic Operating Co., Inc.:
+    href: http://www.somalogic.com
   footer:
     roles: [fnd]
     text: "was developed by the Bioinformatics Dept. at"

cran-comments.md

@@ -1,9 +1,9 @@
 
-# Submission 6.4.0
+# Submission 6.5.0
 
 - This is a submission to an existing CRAN package.
 
-- It contains new functionality, minor updates to existing functions and
+- It contains minor updates to existing functions and
   improved documentation in vignettes.
 
 
@@ -35,35 +35,35 @@
 
 ```
 name	              user	system	elapsed
-Col.Meta	          0.19	0.05	0.23	
-SeqId	              0.04	0.00	0.05	
-SomaDataIO-package	0.09	0.00	0.09	
-SomaScanObjects	    0.23	0.00	0.23	
-adat-helpers      	0.05	0.00	0.04	
-adat2eSet	          0.40	0.02	0.42	
-addClass	          0	    0	    0	
-calcOutlierMap	    3.46	0.15	3.61	
+Col.Meta	          0.28	0.09	0.38	
+SeqId	              0.05	0.01	0.06	
+SomaDataIO-package	0.16	0.00	0.16	
+SomaScanObjects	    0.42	0.00	0.42	
+adat-helpers	      0.10	0.00	0.09	
+adat2eSet	          0.52	0.01	0.54	
+addClass	          0.00	0.00	0.00	
+calcOutlierMap	    4.52	0.48	5.03	
 calc_eLOD	          0.03	0.00	0.03	
-cleanNames	        0	    0	    0	
-diffAdats	          0.36	0.01	0.37	
-getAnalyteInfo	    0.13	0.02	0.14	
-getAnalytes	        0.02	0.00	0.01	
-getOutlierIds	      1.51	0.06	1.58	
-groupGenerics	      0.29	0.02	0.30	
-is_intact_attr	    0	    0	    0	
-is_seqFormat	      0	    0	    0	
-lift_adat	          0.28	0.00	0.28	
-loadAdatsAsList	    1.3	  0.0	  1.3	
-merge_clin	        0.08	0.00	0.08	
-parseHeader	        0.08	0.00	0.08	
-pivotExpressionSet	0.07	0.00	0.08	
-plot.Map	          1.07	0.08	1.16	
-preProcessAdat	    1.14	0.01	1.15	
-read_adat	          1.16	0.03	1.19	
-read_annotations	  0	    0	    0	
-rownames	          0.01	0.00	0.01	
-soma_adat	          0.2	  0.0	  0.2	
-transform	          0	    0	    0	
-updateColMeta	      0	    0	    0	
-write_adat	        0.20	0.02	0.22	
+cleanNames	        0.00	0.00	0.00	
+diffAdats	          0.49	0.00	0.50	
+getAnalyteInfo	    0.19	0.05	0.30	
+getAnalytes	        0.03	0.00	0.03	
+getOutlierIds	      1.82	0.14	2.01	
+groupGenerics	      0.43	0.01	0.47	
+is_intact_attr	    0.01	0.00	0.01	
+is_seqFormat	      0.00	0.00	0.00	
+lift_adat	          0.41	0.00	0.47	
+loadAdatsAsList	    1.70	0.02	1.75	
+merge_clin	        0.11	0.00	0.11	
+parseHeader	        0.13	0.00	0.12	
+pivotExpressionSet	0.07	0.02	0.08	
+plot.Map	          2.00	0.09	2.17	
+preProcessAdat	    2.06	0.08	2.16	
+read_adat	          1.59	0.00	1.63	
+read_annotations	  0.00	0.00	0.00	
+rownames	          0.00	0.01	0.02	
+soma_adat	          0.36	0.02	0.38	
+transform	          0.00	0.00	0.00	
+updateColMeta	      0.00	0.00	0.00	
+write_adat	        0.48	0.01	0.50	
 ```

inst/cli/merge/merge_clin.R

@@ -12,7 +12,7 @@
 #      to use for the *.adat (`key1`) and *.csv (`key2`) respectively
 #
 # Copyright:
-#   Copyright (c) 2025 Standard BioTools, Inc.
+#   Copyright (c) 2026 SomaLogic Operating Co., Inc.
 # Author:
 #   Stu Field
 #

tests/testthat/test-adat2eSet.R

@@ -13,9 +13,9 @@ test_that("`adat2eSet()` converts `soma_adt` -> eSet correctly", {
   expect_true(is.matrix(eSet@assayData$exprs))
   expect_equal(dim(eSet@assayData$exprs), c(3L, 10L))
   expect_type(eSet@experimentData@other, "list")
-  expect_equal(eSet@experimentData@url, "www.standardbio.com")
+  expect_equal(eSet@experimentData@url, "www.somalogic.com")
   expect_equal(eSet@experimentData@title, "Example Adat Set001, Example Adat Set002")
-  expect_equal(eSet@experimentData@lab, "Standard BioTools, Inc.")
+  expect_equal(eSet@experimentData@lab, "SomaLogic Operating Co., Inc.")
   expect_equal(eSet@experimentData@other$Version, "1.2")
   expect_equal(eSet@experimentData@other$ExpDate, "2020-06-18, 2020-07-20")
   expect_equal(eSet@experimentData@other$AssaySite, "SW")

vignettes/SomaDataIO.Rmd

@@ -19,7 +19,7 @@ knitr::opts_chunk$set(
 
 
 This document accompanies the `SomaDataIO` R package, which loads
-and exports 'SomaScan' data via the Standard BioTools, Inc.
+and exports 'SomaScan' data via the SomaLogic Operating Co., Inc.
 structured text file called an ADAT (`*.adat`).
 For file format see
 [here](https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md).
@@ -86,7 +86,7 @@ are not included with the installed package.
 
 SomaDataIO™
 
-Copyright © 2025 Standard BioTools, Inc.
+Copyright © 2026 SomaLogic Operating Co., Inc.
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of the SomaDataIO software and associated documentation files
@@ -95,7 +95,7 @@ including without limitation the rights to use, copy, modify, merge,
 publish, distribute, sub-license, and/or sell copies of the Software,
 and to permit persons to whom the Software is furnished to do so,
 subject to the following conditions outlined below.  Further,
-SomaDataIO and SomaLogic are trademarks owned by Standard BioTools, Inc.
+SomaDataIO and SomaLogic are trademarks owned by SomaLogic Operating Co., Inc.
 No license is hereby granted to these trademarks other than for purposes
 of identifying the origin or source of the Software.
 

vignettes/articles/cli-merge-tool.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Command Line Merge Tool"
-author: "Stu Field, Standard BioTools, Inc."
+author: "Stu Field, SomaLogic Operating Co., Inc."
 description: >
   A convenient CLI merge tool to add new clinical data
   to 'SomaScan' data.

vignettes/articles/lifting-and-bridging.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Lifting and Bridging SomaScan"
-author: "Stu Field, Standard BioTools, Inc."
+author: "Stu Field, SomaLogic Operating Co., Inc."
 description: >
   A primer on lifting and bridging 'SomaScan' data.
 output:

vignettes/articles/stat-binary-classification.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Binary Classification"
-author: "Stu Field, Standard BioTools, Inc."
+author: "Stu Field, SomaLogic Operating Co., Inc."
 description: >
   Typical binary classification of 'SomaScan' data.
 output:

vignettes/articles/stat-linear-regression.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Linear Regression"
-author: "Stu Field, Standard BioTools, Inc."
+author: "Stu Field, SomaLogic Operating Co., Inc."
 description: >
   Typical linear regression of continuous 'SomaScan' data.
 output:

vignettes/articles/stat-three-group-analysis-anova.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "ANOVA Three-Group Analysis"
-author: "Stu Field, Standard BioTools, Inc."
+author: "Stu Field, SomaLogic Operating Co., Inc."
 description: >
   Typical > 2-group comparison of 'SomaScan' data.
 output: