X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fdist.dna.Rd;h=81686032b1cf0e65206ea317ca93630c6ddfa880;hb=da67dccb93d35408baa48b141fcda921772c8b9c;hp=83211d0bf96e002b119d4c3487b3a852f633f25e;hpb=2741f6e9f61e33c7b499f27c47604606d08f4bea;p=ape.git

diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd
index 83211d0..8168603 100644
--- a/man/dist.dna.Rd
+++ b/man/dist.dna.Rd
@@ -10,24 +10,24 @@ dist.dna(x, model = "K80", variance = FALSE,
   \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
+  \item{model}{a character string specifying the evolutionary model to be
     used; must be one of \code{"raw"}, \code{"N"}, \code{"TS"},
     \code{"TV"}, \code{"JC69"}, \code{"K80"} (the default),
     \code{"F81"}, \code{"K81"}, \code{"F84"}, \code{"BH87"},
-    \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"}, or
-    \code{"paralin"}.}
+    \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"},
+    \code{"paralin"}, \code{"indel"}, or \code{"indelblock"}.}
   \item{variance}{a logical indicating whether to compute the variances
     of the distances; defaults to \code{FALSE} so the variances are not
     computed.}
-  \item{gamma}{a value for the gamma parameter which is possibly used to
-    apply a gamma correction to the distances (by default \code{gamma =
-      FALSE} so no correction is applied).}
+  \item{gamma}{a value for the gamma parameter possibly used to apply a
+    correction to the distances (by default no correction is applied).}
   \item{pairwise.deletion}{a logical indicating whether to delete the
     sites with missing data in a pairwise way. The default is to delete
-    the sites with at least one missing data for all sequences.}
+    the sites with at least one missing data for all sequences (ignored
+    if \code{model = "indel"} or \code{"indelblock"}).}
   \item{base.freq}{the base frequencies to be used in the computations
-    (if applicable, i.e. if \code{method = "F84"}). By default, the
-    base frequencies are computed from the whole sample of sequences.}
+    (if applicable). By default, the base frequencies are computed from
+    the whole set of sequences.}
   \item{as.matrix}{a logical indicating whether to return the results as
     a matrix. The default is to return an object of class
     \link[stats]{dist}.}
@@ -121,6 +121,14 @@ dist.dna(x, model = "K80", variance = FALSE,
 
   \item{\code{paralin}: }{Lake (1994) developed the paralinear distance which
     can be viewed as another variant of the Barry--Hartigan distance.}
+
+  \item{\code{indel}: }{this counts the number of sites where there is an
+    insertion/deletion gap in one sequence and not in the other.}
+
+  \item{\code{indelblock}: }{same than before but contiguous gaps are
+    counted as a single unit. Note that the distance between \code{-A-} and
+    \code{A--} is 3 because there are three different blocks of gaps, whereas
+    the ``indel'' distance will be 2.}
 }}
 \value{
   an object of class \link[stats]{dist} (by default), or a numeric