use lavaan_extract() internally for lavaan_cov())

NEWS.md

@@ -6,7 +6,7 @@
 * `write_lavaan()`: accepts a new argument, `threshold`, represented by the "|" operator.
 * `lavaan_ind()` renames to `lavaan_defined()` because it was not specific to indirect effects but actually extracts any user-defined parameters such as total effects and moderated slopes using the `:=` operator.
 * `lavaan_reg()` gets rid of the estimate argument, to comply with best practices of reporting both unstandardized and standardized parameters with their respective confidence intervals.
-* new function: `lavaan_extract()`, which takes a specific operator and extracts relevant information (now used internally for `lavaan_reg()`, `lavaan_defined()`)
+* new function: `lavaan_extract()`, which takes a specific operator and extracts relevant information (now used internally for `lavaan_reg()`, `lavaan_defined()`, `lavaan_cov()`)
 
 # lavaanExtra 0.1.8
 * CRAN resubmission

R/lavaan_cov.R

@@ -40,37 +40,17 @@
 #' library(lavaan)
 #' fit <- sem(HS.model, data = HolzingerSwineford1939)
 #' lavaan_cov(fit)
-#' lavaan_cov(fit, estimate = "r")
-#' lavaan_cor(fit) # same as previous
-lavaan_cov <- function(fit, estimate = "sigma", nice_table = FALSE, ...) {
-  og.names <- c("lhs", "rhs", "pvalue", "est", "ci.lower", "ci.upper")
-  new.names <- c("Variable 1", "Variable 2", "p", "sigma", "CI_lower", "CI_upper")
-  if (estimate == "sigma") {
-    x <- lavaan::parameterEstimates(fit)
-  } else if (estimate == "r") {
-    x <- lavaan::standardizedsolution(fit, level = 0.95)
-    og.names[4] <- "est.std"
-    new.names[4] <- "r"
-  } else {
-    stop("The 'estimate' argument may only be one of c('sigma', 'r').")
-  }
-  x <- x[which(x["op"] == "~~"), ]
-  diag <- which(x$lhs == x$rhs)
-  x <- x[-diag, ] # keep only off-diagonal elements
-  x <- x[og.names]
-  names(x) <- new.names
-  if (nice_table) {
-    insight::check_if_installed("rempsyc",
-      version = get_dep_version("rempsyc"),
-      reason = "for this feature."
-    )
-    x <- rempsyc::nice_table(x, ...)
-  }
-  x
+lavaan_cov <- function(fit, nice_table = FALSE, ...) {
+  lavaan_extract(fit,
+                 operator = "~~",
+                 lhs_name = "Variable 1",
+                 rhs_name = "Variable 2",
+                 diag = "exclude",
+                 nice_table = nice_table)
 }
 
 #' @export
 #' @describeIn lavaan_cov Shortcut for `lavaan_cov(fit, estimate = "r")`
 lavaan_cor <- function(fit, nice_table = FALSE, ...) {
-  lavaan_cov(fit, estimate = "r", nice_table = nice_table, ...)
+  lavaan_cov(fit, nice_table = nice_table, ...)
 }

R/lavaan_extract.R

@@ -57,6 +57,7 @@ lavaan_extract <- function(fit,
                            lhs_name = "Left-Hand Side",
                            rhs_name = "Right-Hand Side",
                            underscores_to_symbol = "\u2192",
+                           diag = NULL,
                            nice_table = FALSE,
                            ...) {
   if (missing(operator)) {
@@ -68,10 +69,18 @@ lavaan_extract <- function(fit,
 
   x <- lavaan::parameterEstimates(fit)
   x <- x[which(x["op"] == operator), ]
-  x <- x[og.names]
 
   es <- lavaan::standardizedsolution(fit, level = 0.95)
   es <- es[which(es["op"] == operator), ]
+
+  if (!is.null(diag) && diag == "exclude") {
+    diag <- which(x$lhs == x$rhs)
+    x <- x[-diag, ] # keep only off-diagonal elements
+    es <- es[-diag, ] # keep only off-diagonal elements
+    new.names[c(6, 9:11)] <- c("sigma", "r", "CI_lower_r", "CI_upper_r")
+  }
+
+  x <- x[og.names]
   es <- es[c("est.std", og.names[7:8])]
   names(es)[2:3] <- paste0(names(es)[2:3], ".std")
 

tests/testthat/test-lavaan_cov.R

@@ -35,17 +35,3 @@ test_that("nice_fit as nice_table", {
     c("nice_table", "flextable")
   )
 })
-
-test_that("nice_fit estimates", {
-  expect_s3_class(
-    lavaan_cov(fit, estimate = "sigma"),
-    c("lavaan.data.frame", "data.frame")
-  )
-  expect_s3_class(
-    lavaan_cov(fit, estimate = "r"),
-    c("lavaan.data.frame", "data.frame")
-  )
-  expect_error(
-    lavaan_cov(fit, estimate = "B"),
-  )
-})