fix .cdl & .all error;fix lme4 note

Author: jluchman

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: domir
 Title: Tools to Support Relative Importance Analysis
-Version: 1.1.0
-Date: 2023-9-2
+Version: 1.1.1
+Date: 2023-10-1
 Authors@R: 
     person(given = "Joseph",
            family = "Luchman",
@@ -25,6 +25,7 @@ Suggests:
     Formula,
     ggplot2,
     knitr,
+    lme4,
     parameters,
     performance,
     pscl,

NEWS.md

@@ -1,6 +1,14 @@
+# domir 1.1.1
+
+## bug fixes
+
+-   `domir()` produced error when `.cdl = FALSE` was combined with `.all`
+-   *lme4* added to suggested list due to reference in documentation and CRAN warning
+
 # domir 1.1.0
 
 ## visible
+
 -   `formula_list` method implemented
     - merger of planned `list` and `Formula::Formula` methods
     - `fmllst2Fml` can be used to translate `formula_list`s to `Formula::Formula`s
@@ -123,11 +131,7 @@
 
 ## bug fixes
 
-<<<<<<< HEAD
--   `Ensemble_Coordinator` that submitted factor #'s instead of text in R versions \< 4
-=======
 -   `Ensemble_Coordinator` that submitted factor numbers instead of text in R versions \< 4.0
->>>>>>> 1.0
 
 # domir 0.0.0
 

R/dominance_internals.r

@@ -231,11 +231,11 @@ dominance_scalar <-
       # if there is an '.adj' and/or '.all' model, adjust models with 1 name
       # for that value; other models adjust automatically given increment
       if (result_adjustment > 0)
-        uniq_cmb_count <-
+        value_vector <-
           replace(
-            uniq_cmb_count,
-            uniq_cmb_count - result_adjustment,
-            combo_count_by_subset == 1
+            value_vector,
+            combo_count_by_subset == 1,
+            value_vector[combo_count_by_subset == 1] - result_adjustment
           )
       # generates number of 'unique' combinations the focal name has at
       # specific number of value generating names not considering self; note

cran-comments.md

@@ -1,9 +1,18 @@
-## Minor version update: 1.1.0
+## Patch version update: 1.1.1
 
-This minor update has added a new S3 method the the primary `domir()` function
-that parses a list of formulas by RHS~LHS name pairs. This update has also
-begun an extensive code linting process to improve its readability and 
-complexity.
+This patch update fixed a bug in the computation of a returned matrix when an 
+infrequently used optional argument is non-`NULL` and added the *lme4* package 
+to this package's list of suggested packages given its reference in 
+documentation and a warning from CRAN checks.
+
+## CRAN check results
+
+    Check: Rd cross-references
+    Result: NOTE
+        Undeclared package ‘lme4’ in Rd xrefs
+    Flavor: r-devel-linux-x86_64-fedora-clang
+    
+Comment: `lme4`has been added to this package's list of suggested packages.
 
 ## Test environments
 
@@ -29,9 +38,8 @@ Comment: DOI: 10.1002/asmb.446 links reliably to Lipovetsky's and Conklin's 2001
 Windows Server 2022, R-devel, 64 bit: 3 NOTES
 
     * checking HTML version of manual ... NOTE
-    Skipping checking math rendering: package 'V8' unavailable
 
-Comment: Assume the note stems from a temporary issue with package `{V8}` on the RHub platform and is not reproducible in many other platforms.
+Comment: Previously, this issue arose with the package `{V8}` on the RHub platform and was not reproducible on the win-builder, macOS-builder, or my local checks.
 
     * checking for non-standard things in the check directory ... NOTE
     Found the following files/directories:
@@ -51,7 +59,15 @@ Fedora Linux, R-devel, clang, gfortran and Ubuntu Linux 20.04.1 LTS, R-release,
     Skipping checking HTML validation: no command 'tidy' found
     Skipping checking math rendering: package 'V8' unavailable
 
-Comment: Assume the note stems from an issue with package `{V8}` and `{broom}` on the RHub platform and is not reproducible in many other platforms.
+Comment: This is a similar issue to Rhub's Windows check in that the `{V8}` package seems unavailable and is throwing a NOTE. Again, not an issue that occured with win-builder, macOS-builder, or my local checks.
+
+Ubuntu Linux 20.04.1 LTS, R-release, GCC (rhub): 1 NOTE
+
+    * checking HTML version of manual ... NOTE
+    Skipping checking HTML validation: no command 'tidy' found
+    Skipping checking math rendering: package 'V8' unavailable
+    
+Comment: Consistent with the Fedora-based check, the Ubuntu check is throwing a NOTE given the `{V8}` package is seems unavailable. Again, not an issue that occured with win-builder, macOS-builder, or my local checks.
 
 ## Downstream dependencies