Don't return the intercept when include_response = FALSE (#1185)

* Update standardize_parameters.R

* fix test

* Update R/standardize_parameters.R

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Update tests/testthat/test-standardize_parameters.R

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* air

* version bump + news

* remove p etc from unstantdardized intercept

* Update standardize_parameters.R

* always NA inferential stats for NA std coef

* Update NEWS.md

* fix tests

* air

* fix and add tests

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel <mail@danielluedecke.de>

Author: 3 people

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.28.3.2
+Version: 0.28.3.3
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",

NEWS.md

@@ -2,6 +2,12 @@
 
 ## Changes
 
+* `standardize_parameters()` (and by extension `model_parameters()`) with any of
+  the _post-hoc_ standardization methods no longer standardizes the
+  `"(Intercept)"` parameter - instead setting it to `NA`.
+* `standardize_parameters()` with any of the _post-hoc_ standardization methods
+  sets all inferential statistics (z, p, etc...) for the `"(Intercept)"` and any
+  other `NA` parameters to `NA`.
 * `model_parameters()` now supports objects from the *lavaan.mi* package.
 
 ## Bug fixes

R/extract_parameters.R

@@ -306,6 +306,8 @@
       parameters$CI_high <- std_parms$CI_high
     }
 
+    parameters <- .NA_inferential_cols(parameters)
+
     coef_col <- "Std_Coefficient"
   }
 
@@ -648,6 +650,7 @@
 
   # Std Coefficients for other methods than "refit"
   if (!is.null(standardize)) {
+    # give minimal attributes required for standardization
     temp_pars <- parameters
     class(temp_pars) <- c("parameters_model", class(temp_pars))
     attr(temp_pars, "ci") <- ci
@@ -662,6 +665,8 @@
       parameters$CI_high <- std_parms$CI_high
     }
 
+    parameters <- .NA_inferential_cols(parameters)
+
     coef_col <- "Std_Coefficient"
   }
 
@@ -1048,3 +1053,17 @@
   }
   p
 }
+
+.NA_inferential_cols <- function(pr) {
+  # For models where the response is NOT standardized, the (Intercept) is set
+  # to NA and so we also need to set all inferential statistics to NA
+  rows_to_NA <- pr$Parameter %in% "(Intercept)" | is.na(pr$Std_Coefficient)
+  if (any(rows_to_NA)) {
+    # fmt: skip
+    cols_not_to_NA <- c(".id", "Parameter", "Component", "Response", "Effects", "Group",
+                        "CI", "Std_Coefficient")
+    cols_to_NA <- setdiff(colnames(pr), cols_not_to_NA)
+    pr[rows_to_NA, cols_to_NA] <- NA
+  }
+  pr
+}