some modifs for ape 3.0-8

[ape.git] / man / ace.Rd

diff --git a/man/ace.Rd b/man/ace.Rd
index 15bd38758e42de2c7ede2fb709125350ced28b62..101aebf2c4bb61aa863c1bffe9d8fcc1aa4964bc 100644 (file)
--- a/man/ace.Rd
+++ b/man/ace.Rd
@@ -25,7 +25,8 @@
 \usage{
 ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     model = if (type == "continuous") "BM" else "ER",
-    scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1)
+    scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1,
+    use.expm = FALSE)
 \method{print}{ace}(x, digits = 4, ...)
 \method{logLik}{ace}(object, ...)
 \method{deviance}{ace}(object, ...)
@@ -56,6 +57,10 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
     structure to be used (this also gives the assumed model).}
   \item{ip}{the initial value(s) used for the ML estimation procedure
     when \code{type == "discrete"} (possibly recycled).}
+  \item{use.expm}{a logical specifying whether to use the package
+    \pkg{expm} to compute the matrix exponential (relevant only if
+    \code{type = "d"}). The default is to use the function
+    \code{matexpo} from \pkg{ape} (see details).}
   \item{digits}{the number of digits to be printed.}
   \item{object}{an object of class \code{"ace"}.}
   \item{k}{a numeric value giving the penalty per estimated parameter;
@@ -108,6 +113,14 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
   \code{"SYM"} is a symmetrical model (e.g., \code{matrix(c(0, 1, 2, 1,
     0, 3, 2, 3, 0), 3)}). If a short-cut is used, the number of states
   is determined from the data.
+
+  With discrete characters it is necessary to compute the exponential of
+  the rate matrix. By default (and the only possible choice until
+  \pkg{ape} 3.0-7) the function \code{\link{matexpo}} in \pkg{ape} is
+  used. If \code{use.expm = TRUE}, the function
+  \code{\link[expm]{expm}}, in the package of the same name, is
+  used. \code{matexpo} is faster but quite inaccurate for large and/or
+  asymmetric matrices. In case of doubt, use the latter.
 }
 \value{
   an object of class \code{"ace"} with the following elements: