Merge branch 'main' into use_check_arg

easystats · Oct 19, 2024 · f968cd0 · f968cd0
2 parents 29419f3 + a7b97a5
commit f968cd0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.23.0.1
+Version: 0.23.0.2
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",

diff --git a/R/3_p_value.R b/R/3_p_value.R
@@ -56,8 +56,8 @@ p_value.default <- function(model,
     method <- "wald"
   }
 
-  # robust standard errors with backward compatibility for `robust = TRUE`
-  if (!is.null(vcov) || isTRUE(dots[["robust"]])) {
+  # robust standard errors
+  if (!is.null(vcov)) {
     method <- "robust"
   }
 

diff --git a/R/4_standard_error.R b/R/4_standard_error.R
@@ -23,7 +23,8 @@
 #'    - Bootstrap: `"BS"`, `"xy"`, `"residual"`, `"wild"`, `"mammen"`,
 #'      `"fractional"`, `"jackknife"`, `"norm"`, `"webb"`.
 #'      See `?sandwich::vcovBS`
-#'    - Other `sandwich` package functions: `"HAC"`, `"PC"`, `"vCL"`, `"PL"`.
+#'    - Other `sandwich` package functions: `"HAC"`, `"PC"`, `"CL"`, `"OPG"`,
+#'      `"PL"`.
 #' @param vcov_args List of arguments to be passed to the function identified by
 #'   the `vcov` argument. This function is typically supplied by the
 #'   **sandwich** or **clubSandwich** packages. Please refer to their
@@ -100,8 +101,8 @@ standard_error.default <- function(model,
     se <- .safe(sqrt(diag(do.call("vcov", fun_args))))
   }
 
-  # vcov: character (with backward compatibility for `robust = TRUE`)
-  if (is.character(vcov) || isTRUE(dots[["robust"]])) {
+  # vcov: character
+  if (is.character(vcov)) {
     .vcov <- insight::get_varcov(
       model,
       component = component,

diff --git a/R/extract_parameters.R b/R/extract_parameters.R
@@ -176,8 +176,7 @@
 
   # ==== test statistic - fix values for robust vcov
 
-  # deprecated argument `robust = TRUE`
-  if (!is.null(vcov) || isTRUE(dots[["robust"]])) {
+  if (!is.null(vcov)) {
     parameters$Statistic <- parameters$Estimate / parameters$SE
   } else if (!is.null(statistic)) {
     parameters <- merge(parameters, statistic, by = merge_by, sort = FALSE)

diff --git a/R/methods_nestedLogit.R b/R/methods_nestedLogit.R
@@ -103,8 +103,8 @@ standard_error.nestedLogit <- function(model,
     se <- .safe(sqrt(diag(do.call("vcov", fun_args))))
   }
 
-  # vcov: character (with backward compatibility for `robust = TRUE`)
-  if (is.character(vcov) || isTRUE(dots[["robust"]])) {
+  # vcov: character
+  if (is.character(vcov)) {
     .vcov <- insight::get_varcov(
       model,
       component = component,

diff --git a/R/p_value_kenward.R b/R/p_value_kenward.R
@@ -88,7 +88,7 @@ p_value_kenward.lmerMod <- function(model, dof = NULL) {
     if (is.null(se)) {
       se <- se_kenward(model)$SE
     }
-  } else if (!is.null(vcov) || isTRUE(list(...)[["robust"]])) {
+  } else if (!is.null(vcov)) {
     se <- standard_error(model,
       vcov = vcov,
       vcov_args = vcov_args,

diff --git a/R/standardize_info.R b/R/standardize_info.R
@@ -11,9 +11,9 @@
 #' @param ... Arguments passed to or from other methods.
 #'
 #' @return A data frame with information on each parameter (see
-#'   [parameters_type()]), and various standardization coefficients
-#'   for the post-hoc methods (see [standardize_parameters()]) for the predictor
-#'   and the response.
+#' [`parameters_type()`]), and various standardization coefficients
+#' for the post-hoc methods (see [`standardize_parameters()`]) for the predictor
+#' and the response.
 #'
 #' @family standardize
 #'

diff --git a/man/equivalence_test.lm.Rd b/man/equivalence_test.lm.Rd
diff --git a/man/model_parameters.default.Rd b/man/model_parameters.default.Rd
diff --git a/man/model_parameters.merMod.Rd b/man/model_parameters.merMod.Rd
diff --git a/man/model_parameters.mlm.Rd b/man/model_parameters.mlm.Rd
diff --git a/man/p_direction.lm.Rd b/man/p_direction.lm.Rd
diff --git a/man/p_function.Rd b/man/p_function.Rd
diff --git a/man/p_significance.lm.Rd b/man/p_significance.lm.Rd
diff --git a/man/p_value.Rd b/man/p_value.Rd
diff --git a/man/standard_error.Rd b/man/standard_error.Rd
diff --git a/tests/testthat/test-model_parameters_robust.R b/tests/testthat/test-model_parameters_robust.R
@@ -75,7 +75,6 @@ mtcars$am <- as.factor(mtcars$am)
 model <- lm(mpg ~ wt * am + cyl + gear, data = mtcars)
 
 test_that("model_parameters, robust", {
-  expect_warning(expect_warning(expect_warning(model_parameters(model, robust = TRUE))))
   params <- model_parameters(model, vcov = "HC3")
   robust_se <- unname(sqrt(diag(sandwich::vcovHC(model))))
   expect_equal(params$SE, robust_se, tolerance = 1e-3)

diff --git a/vignettes/model_parameters_robust.Rmd b/vignettes/model_parameters_robust.Rmd
@@ -68,14 +68,6 @@ The computation of robust standard errors is controlled by two arguments:
 
 ### Robust Covariance Matrix Estimation from Model Parameters
 
-There are two arguments (see
-[`?standard_error`](https://easystats.github.io/parameters/reference/standard_error.html)
-for further details) that allow for choosing different methods and options of
-robust estimation:
-
-- `vcov`
-- `vcov_args`
-
 Let us start with a simple example, which uses a heteroskedasticity-consistent
 covariance matrix estimation with estimation-type "HC3" (i.e.
 `sandwich::vcovHC(type = "HC3")`).