Fix "vce" bug with length 1 "variables" argument (#113)

* Fix vce = "simulation" when variables has length of 1 * Fix vce = "bootstrap" when variables has length of 1 * Add name to DESCRIPTION * Update NEWS.md
leeper · Dec 23, 2019 · f4054c59bbff7c1e312441577ad776583fc1fbb8 · f4054c5
1 parent b9ad25f
commit f4054c59bbff7c1e312441577ad776583fc1fbb8
Unified Split

Showing with 30 additions and 4 deletions.

+2 −3 NEWS.md

+14 −1 R/get_effect_variances.R

+14 −0 tests/testthat/tests-edge-cases.R
diff --git a/NEWS.md b/NEWS.md
@@ -2,8 +2,8 @@
 
 * Setup a `cplot.default()` method and modified documentation of `cplot()`, `image()`, and `persp()` methods slightly. (#84, h/t Luke Sonnet)
 * Improve the documentation the behavior of `cplot()` for generalized linear models, which can generate unexpected confidence intervals (albeit ones consistent with base R's behavior). (#92)
-* Models fit using the `lme4` package can now have variance estimation via 
-bootstrap and simulation (#105).
+* Fix bug that caused spurious `NA`s and errors in `margins()` when `vce` was `"bootstrap"` or `"simulation"` and `variables` had a length of 1. (#112)
+* Models fit using the `lme4` package can now have variance estimation via bootstrap and simulation (#105).
 
 # margins 0.3.24
 
@@ -44,7 +44,6 @@ bootstrap and simulation (#105).
 * Updated examples in `README.Rmd`. (#83)
 
 # margins 0.3.16
->>>>>>> master
 
 * Fixed a bug in `cplot()` when `xvar` was of class "ordered". (#77, h/t Francisco Llaneras)
 * Fixed a bug in `plot.margins()` when `at` contained only one variable. (#78, h/t @cyberbryce)

diff --git a/R/get_effect_variances.R b/R/get_effect_variances.R
@@ -123,6 +123,13 @@ function(data,
             }
             return(means)
         })
+        # When length(variables) == 1, effectmat is a vector
+        if (!is.matrix(effectmat)) {
+            # Coerce to 1 row matrix
+            effectmat <- matrix(effectmat, nrow = 1)
+            # Rownames are lost in these cases
+            rownames(effectmat) <- paste0("dydx_", variables)
+        }
         # calculate the variance of the simulated AMEs
         vc <- var(t(effectmat))
         variances <- diag(vc)
@@ -164,7 +171,13 @@ function(data,
             means
         }
         # bootstrap the data and take the variance of bootstrapped AMEs
-        vc <- var(t(replicate(iterations, bootfun())))
+        vc <- if (length(variables) > 1) {
+            var(t(replicate(iterations, bootfun())))
+        } else { # Take the variance of the vector
+            # Need to coerce to 1 x 1 matrix with appropriate dimnames
+            matrix(var(replicate(iterations, bootfun())), nrow = 1L, 
+                   dimnames = list(nms <- paste0("dydx_", variables), nms))
+        }
         variances <- diag(vc)
         jacobian <- NULL
     }

diff --git a/tests/testthat/tests-edge-cases.R b/tests/testthat/tests-edge-cases.R
@@ -35,3 +35,17 @@ test_that("margins() errors correctly when there are no RHS variables", {
     expect_error(marginal_effects(x))
     expect_error(margins(x))
 })
+
+test_that("vce = 'bootstrap' works with one variable as variables argument", {
+    x <- lm(mpg ~ wt + hp * cyl, data = mtcars)
+    suppressWarnings(m <- margins(x, vce = "bootstrap", variables = "hp"))
+    expect_true(inherits(m, "data.frame"))
+    expect_true(nrow(summary(m)) == 1L)
+})
+
+test_that("vce = 'simulation' works with one variable as variables argument", {
+    x <- lm(mpg ~ wt + hp * cyl, data = mtcars)
+    suppressWarnings(m <- margins(x, vce = "simulation", variables = "hp"))
+    expect_true(inherits(m, "data.frame"))
+    expect_true(nrow(summary(m)) == 1L)
+})