various bug fixes

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

diff --git a/man/write.dna.Rd b/man/write.dna.Rd
index 8a692f1491993badbe70231d20f47f2e87c1a716..fb87ae71e8f5b2be5f63dbff78cf1fba013e1a1d 100644 (file)
--- a/man/write.dna.Rd
+++ b/man/write.dna.Rd
@@ -45,16 +45,16 @@ write.dna(x, file, format = "interleaved", append = FALSE,
   With the interleaved and sequential formats, the sequences must be all
   of the same length. The names of the sequences are not truncated.
 
-  The argument `indent' specifies how the rows of nucleotides are
+  The argument \code{indent} specifies how the rows of nucleotides are
   indented. In the interleaved and sequential formats, the rows with
   the taxon names are never indented; the subsequent rows are indented
-  with 10 spaces by default (i.e. if `indent = NULL)'. In the FASTA
+  with 10 spaces by default (i.e., if \code{indent = NULL}). In the FASTA
   format, the rows are not indented by default. This default behaviour
-  can be modified by specifying a value to `indent': the rows are then
-  indented with `indent' (if it is a character) or `indent' spaces (if
-  it is a numeric). For example, specifying `indent = "   "' or `indent
-  = 3' will have exactly the same effect (use `indent = "\t"' for a
-  tabulation).
+  can be modified by specifying a value to \code{indent}: the rows are then
+  indented with ``indent'' (if it is a character) or `indent' spaces (if
+  it is a numeric). For example, specifying \code{indent = "   "} or
+  \code{indent = 3} will have the same effect (use \code{indent = "\\t"}
+  for a tabulation).
 
   The different options are intended to give flexibility in formatting
   the sequences. For instance, if the sequences are very long it may be
@@ -76,7 +76,7 @@ write.dna(x, file, format = "interleaved", append = FALSE,
 \value{
   None (invisible `NULL').
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \references{
   Anonymous. FASTA format description.
   \url{http://www.ncbi.nlm.nih.gov/BLAST/fasta.html}