Merge branch 'envfit-atomic': Fixes #713

vegandevs · Nov 9, 2024 · 9522321 · 9522321
2 parents 3621a97 + dd77511
commit 9522321
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/R/envfit.default.R b/R/envfit.default.R
@@ -1,9 +1,12 @@
 `envfit.default` <-
     function (ord, env, permutations = 999, strata = NULL, choices = c(1, 2),
-             display = "sites", w = weights(ord, display), na.rm = FALSE, ...)
+             display = "sites", w, na.rm = FALSE, ...)
 {
     vectors <- NULL
     factors <- NULL
+    if (missing(w))
+        w <- if (is.atomic(ord)) attr(ord, "weights")
+             else weights(ord, display = display)
     X <- scores(ord, display = display, choices = choices, ...)
     keep <- complete.cases(X) & complete.cases(env)
     if (any(!keep)) {

diff --git a/man/envfit.Rd b/man/envfit.Rd
@@ -27,8 +27,7 @@
 
 \usage{
 \method{envfit}{default}(ord, env, permutations = 999, strata = NULL, 
-   choices=c(1,2),  display = "sites", w  = weights(ord, display),
-   na.rm = FALSE, ...)
+   choices=c(1,2),  display = "sites", w, na.rm = FALSE, ...)
 \method{envfit}{formula}(formula, data, ...)
 \method{plot}{envfit}(x, choices = c(1,2), labels, arrow.mul, at = c(0,0), 
    axis = FALSE, p.max = NULL, col = "blue", bg, add = TRUE, ...)