various changes to DNAbin functions + new labels.DNAbin()

[ape.git] / R / compar.gee.R

diff --git a/R/compar.gee.R b/R/compar.gee.R
index 9c52460198409835b7aea9042664b3132d2048b7..488379c4b00d52775651515b4c3cba090790ba30 100644 (file)
--- a/R/compar.gee.R
+++ b/R/compar.gee.R
@@ -20,10 +20,9 @@ do not match: the former were ignored in the analysis.")
     effect.assign <- attr(model.matrix(formula, data = data), "assign")
     for (i in all.vars(formula)) {
         if (any(is.na(eval(parse(text = i), envir = data))))
-          stop("the present method cannot (yet) be used directly with missing data: you may consider removing the species with missing data from your tree with the function `drop.tip'.")
+          stop("the present method cannot (yet) be used directly with missing data: you may consider removing the species with missing data from your tree with the function 'drop.tip'.")
     }
-    if (is.null(phy$edge.length))
-      stop("the tree has no branch lengths.")
+    if (is.null(phy$edge.length)) stop("the tree has no branch lengths.")
     R <- vcv.phylo(phy, cor = TRUE)
     id <- rep(1, dim(R)[1])
     geemod <- do.call("gee", list(formula, id, data = data, family = family, R = R,
@@ -31,9 +30,9 @@ do not match: the former were ignored in the analysis.")
                                   scale.value = scale.value))
     W <- geemod$naive.variance
     fname <-
-        if is.function(family) deparse(substitute(family)) else family
+        if (is.function(family)) deparse(substitute(family)) else family
     if (fname == "binomial")
-      W <- summary(glm(formula, family = quasibinomial, data = data))$cov.scaled
+        W <- summary(glm(formula, family = quasibinomial, data = data))$cov.scaled
     N <- geemod$nobs
     dfP <- sum(phy$edge.length)*N / sum(diag(vcv.phylo(phy)))
     obj <- list(call = geemod$call,