a few changes....

[ape.git] / man / dist.dna.Rd

diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd
index 2cee8e2f95898bd5fb8df0ee86b5c81f6bd5d894..3a5e3e027cb27d599bac0fd9d4b7ba04894e5b93 100644 (file)
--- a/man/dist.dna.Rd
+++ b/man/dist.dna.Rd
@@ -7,7 +7,9 @@ dist.dna(x, model = "K80", variance = FALSE,
          base.freq = NULL, as.matrix = FALSE)
 }
 \arguments{
-  \item{x}{a matrix or a list containing the DNA sequences.}
+  \item{x}{a matrix or a list containing the DNA sequences; this must be
+    of class \code{"DNAbin"} (use \code{\link{as.DNAbin}} is they are
+    stored as character).}
   \item{model}{a character string specifying the evlutionary model to be
     used; must be one of \code{"raw"}, \code{"N"}, \code{"JC69"},
     \code{"K80"} (the default), \code{"F81"}, \code{"K81"},
@@ -40,6 +42,7 @@ dist.dna(x, model = "K80", variance = FALSE,
   brief description is given below; more details can be found in the
   References.
 
+\itemize{
   \item{``raw'', ``N''}{This is simply the proportion or the number of
     sites that differ between each pair of sequences. This may be useful
     to draw ``saturation plots''. The options \code{variance} and
@@ -106,11 +109,15 @@ dist.dna(x, model = "K80", variance = FALSE,
     transitons and transversions.}
 
   \item{``logdet''}{The Log-Det distance, developed by Lockhart et
-    al. (1994), is related to BH87. However, this distance is symmetric.}
+    al. (1994), is related to BH87. However, this distance is
+    symmetric. Formulae from Gu and Li (1996) are used.
+    \code{dist.logdet} in \pkg{phangorn} uses a different
+    implementation that gives substantially different distances for
+    low-diverging sequences.}
 
   \item{``paralin''}{Lake (1994) developed the paralinear distance which
     can be viewed as another variant of the Barry--Hartigan distance.}
-}
+}}
 \value{
   an object of class \link[stats]{dist} (by default), or a numeric
   matrix if \code{as.matrix = TRUE}. If \code{model = "BH87"}, a numeric
@@ -136,6 +143,11 @@ dist.dna(x, model = "K80", variance = FALSE,
   sequences of unequal base compositions. \emph{Proceedings of the
     National Academy of Sciences USA}, \bold{92}, 11317--11321.
 
+  Gu, X. and Li, W.-H. (1996) Bias-corrected paralinear and LogDet
+  distances and tests of molecular clocks and phylogenies under
+  nonstationary nucleotide frequencies. \emph{Molecular Biology and
+    Evolution}, \bold{13}, 1375--1383.
+
   Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein
   molecules. in \emph{Mammalian Protein Metabolism}, ed. Munro, H. N.,
   pp. 21--132, New York: Academic Press.
@@ -173,7 +185,7 @@ dist.dna(x, model = "K80", variance = FALSE,
   substitutions in the control region of mitochondrial DNA in humans and
   chimpanzees. \emph{Molecular Biology and Evolution}, \bold{10}, 512--526.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{read.GenBank}}, \code{\link{read.dna}},
   \code{\link{write.dna}},  \code{\link{DNAbin}},