modified ace( method = ...)

[ape.git] / R / ace.R

diff --git a/R/ace.R b/R/ace.R
index 2b9230ec7c9d43e7063ea9add8f24e8cb87a88e3..b751c697d63e116b24a972517b294715dbd4fb65 100644 (file)
--- a/R/ace.R
+++ b/R/ace.R
@@ -1,4 +1,4 @@
-## ace.R (2013-01-31)
+## ace.R (2013-03-18)
 
 ##   Ancestral Character Estimation
 
@@ -19,10 +19,12 @@
     se
 }
 
-ace <- function(x, phy, type = "continuous", method = "ML", CI = TRUE,
-                model = if (type == "continuous") "BM" else "ER",
-                scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1,
-                use.expm = FALSE)
+ace <-
+  function(x, phy, type = "continuous",
+           method = if (type == "continuous") "REML" else "ML",
+           CI = TRUE, model = if (type == "continuous") "BM" else "ER",
+           scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1,
+           use.expm = FALSE)
 {
     if (!inherits(phy, "phylo"))
         stop('object "phy" is not of class "phylo"')