various updates

man/getAnnotationsGenBank.Rd

@@ -27,7 +27,7 @@ getAnnotationsGenBank(access.nb, quiet = TRUE)
   A warning is given if some accession numbers are not found on GenBank.
 }
 \value{
-  On of the followings: (i) a data frame if \code{access.nb} contains a
+  One of the followings: (i) a data frame if \code{access.nb} contains a
   single accession number; (ii) a list of data frames if
   \code{access.nb} contains several accession numbers, the names are set
   with \code{access.nb} (if some accession numbers are not found on

man/image.DNAbin.Rd

@@ -38,7 +38,7 @@
     symbols (ignored if the previous is \code{FALSE}).}
   \item{scheme}{a predefined color scheme. For amino acid options are "Ape_AA",
     "Zappo_AA", "Clustal", "Polarity" and "Transmembrane_tendency", for
-    nucleotides "Ape_NT" and"RY_NT".}
+    nucleotides "Ape_NT" and "RY_NT".}
   \item{\dots}{further arguments passed to
     \code{\link[graphics]{image.default}} (e.g., \code{xlab},
     \code{cex.axis}).}

man/kronoviz.Rd

@@ -6,8 +6,8 @@
   same scale.
 }
 \usage{
-kronoviz(x, layout = length(x), horiz = TRUE, ..., 
-         direction = ifelse(horiz, "rightwards", "upwards"), side=2) 
+kronoviz(x, layout = length(x), horiz = TRUE, ...,
+         direction = ifelse(horiz, "rightwards", "upwards"), side = 2)
 }
 \arguments{
   \item{x}{a list of (rooted) trees of class \code{"phylo"}.}
@@ -16,10 +16,10 @@ kronoviz(x, layout = length(x), horiz = TRUE, ...,
   \item{horiz}{a logical specifying whether the trees should be plotted
     rightwards (the default) or upwards.}
   \item{\dots}{further arguments passed to \code{plot.phylo}.}
-  \item{direction}{a character string specifying the direction of the tree. Four
-  values are possible: "rightwards" (the default), "leftwards", "upwards", and 
-  "downwards".}
-  \item{side}{Where to put the axis, see example.} 
+  \item{direction}{a character string specifying the direction of the
+    tree. Four values are possible: "rightwards" (the default),
+    "leftwards", "upwards", and "downwards".}
+  \item{side}{Where to put the axis, see example.}
 }
 \details{
   The size of the individual plots is proportional to the size of the
@@ -33,8 +33,8 @@ kronoviz(x, layout = length(x), horiz = TRUE, ...,
 \examples{
 TR <- replicate(10, rcoal(sample(11:20, size = 1)), simplify = FALSE)
 kronoviz(TR)
-kronoviz(TR, side=1)
+kronoviz(TR, side = 1)
 kronoviz(TR, horiz = FALSE, type = "c", show.tip.label = FALSE)
-kronoviz(TR, direction="d", side=c(1,2))
+kronoviz(TR, direction = "d", side = c(1,2))
 }
 \keyword{hplot}

man/write.nexus.Rd

@@ -2,7 +2,7 @@
 \alias{write.nexus}
 \title{Write Tree File in Nexus Format}
 \usage{
-write.nexus(..., file = "", translate = TRUE, digits=10)
+write.nexus(..., file = "", translate = TRUE, digits = 10)
 }
 \arguments{
   \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a

man/write.tree.Rd

@@ -13,8 +13,9 @@ write.tree(phy, file = "", append = FALSE,
   \item{append}{a logical, if \code{TRUE} the tree is appended to the file
     without erasing the data possibly existing in the file, otherwise
     the file (if it exists) is overwritten (\code{FALSE} the default).}
-  \item{digits}{a numeric giving the number of digits used for printing
-    branch lengths. For negative numbers no branch lengths are printed.}
+  \item{digits}{a numeric giving the number of (significant) digits used
+    for printing branch lengths (see details). For negative numbers no
+    branch lengths are printed.}
   \item{tree.names}{either a logical or a vector of mode character. If
     \code{TRUE} then any tree names will be written prior to the tree on
     each line. If character, specifies the name of \code{"phylo"}
@@ -43,6 +44,10 @@ write.tree(phy, file = "", append = FALSE,
   and trailing right parentheses are deleted; the other spaces are
   replaced by underscores; the commas, colons, semicolons, and the other
   parentheses are replaced with dashes.
+
+  The argument \code{digits} gives the number of \emph{significant}
+  digits (not rounding). For instance, if \code{digits = 2} the branch
+  length 1.234e-7 is printed as 1.23e-7 (not 0).
 }
 \references{
   Felsenstein, J. The Newick tree format.