From: paradis Date: Tue, 13 Jan 2009 09:02:52 +0000 (+0000) Subject: correcting errors in Rd files X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=762d28a9a2b50774a29b3d58a1e84fde4b6f898f;p=ape.git correcting errors in Rd files git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@59 6e262413-ae40-0410-9e79-b911bd7a66b7 --- diff --git a/man/compar.gee.Rd b/man/compar.gee.Rd index b0468a4..e44b433 100644 --- a/man/compar.gee.Rd +++ b/man/compar.gee.Rd @@ -52,7 +52,7 @@ compar.gee(formula, data = NULL, family = "gaussian", phy, \code{compar.gee} returns an object of class \code{"compar.gee"} with the following components: \item{call}{the function call, including the formula.} - \code{effect.assign}{a vector of integers assigning the coefficients + \item{effect.assign}{a vector of integers assigning the coefficients to the effects (used by \code{drop1}).} \item{nobs}{the number of observations.} \item{coefficients}{the estimated coefficients (or regression parameters).} diff --git a/man/corClasses.Rd b/man/corClasses.Rd index cd1e0c4..fc5d7ff 100644 --- a/man/corClasses.Rd +++ b/man/corClasses.Rd @@ -6,12 +6,14 @@ Classes of phylogenetic correlation structures (\code{"corPhyl"}) available in \pkg{ape}. - \item{corBrownian}{Brownian motion model (Felsenstein 1985)} - \item{corMartins}{The covariance matrix defined in Martins and Hansen - (1997)} - \item{corGrafen}{The covariance matrix defined in Grafen (1989)} - \item{corPagel}{The covariance matrix defined in Freckelton et al. (2002)} - \item{corBlomberg}{The covariance matrix defined in Blomberg et al. (2003)} + \itemize{ + \item{corBrownian}{Brownian motion model (Felsenstein 1985)} + \item{corMartins}{The covariance matrix defined in Martins and Hansen + (1997)} + \item{corGrafen}{The covariance matrix defined in Grafen (1989)} + \item{corPagel}{The covariance matrix defined in Freckelton et al. (2002)} + \item{corBlomberg}{The covariance matrix defined in Blomberg et al. (2003)} + } See the help page of each class for references and detailed description. diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd index 2cee8e2..49571b1 100644 --- a/man/dist.dna.Rd +++ b/man/dist.dna.Rd @@ -40,6 +40,7 @@ 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 @@ -110,7 +111,7 @@ dist.dna(x, model = "K80", variance = FALSE, \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 diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd index b525dcc..b9622ef 100644 --- a/man/plot.phylo.Rd +++ b/man/plot.phylo.Rd @@ -140,23 +140,23 @@ \code{plot.phylo} returns invisibly a list with the following components which values are those used for the current plot: - \item{type} - \item{use.edge.length} - \item{node.pos} - \item{show.tip.label} - \item{show.node.label} - \item{font} - \item{cex} - \item{adj} - \item{srt} - \item{no.margin} - \item{label.offset} - \item{x.lim} - \item{y.lim} - \item{direction} - \item{tip.color} - \item{Ntip} - \item{Nnode} + \item{type}{} + \item{use.edge.length}{} + \item{node.pos}{} + \item{show.tip.label}{} + \item{show.node.label}{} + \item{font}{} + \item{cex}{} + \item{adj}{} + \item{srt}{} + \item{no.margin}{} + \item{label.offset}{} + \item{x.lim}{} + \item{y.lim}{} + \item{direction}{} + \item{tip.color}{} + \item{Ntip}{} + \item{Nnode}{} } \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} \seealso{ diff --git a/man/read.dna.Rd b/man/read.dna.Rd index af26aa7..f2f2cff 100644 --- a/man/read.dna.Rd +++ b/man/read.dna.Rd @@ -46,7 +46,8 @@ read.dna(file, format = "interleaved", skip = 0, sequential formats, see below). The names of the sequences are read in the file unless the `seq.names' option is used. Particularities for each format are detailed below. - + +\itemize{ \item{Interleaved:}{the function starts to read the sequences when it finds 10 contiguous characters belonging to the ambiguity code of the IUPAC (namely A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, and @@ -73,7 +74,7 @@ read.dna(file, format = "interleaved", skip = 0, leading spaces before this character). These lines are taken as taxa names after removing the ``>'' and the possible leading and trailing spaces. All the data in the file before the first sequence is ignored.} -} +}} \value{ a matrix or a list (if \code{format = "fasta"}) of DNA sequences stored in binary format, or of mode character (if \code{as.character = diff --git a/man/subtrees.Rd b/man/subtrees.Rd index edca731..bc171a8 100644 --- a/man/subtrees.Rd +++ b/man/subtrees.Rd @@ -20,10 +20,10 @@ subtrees(tree, wait=FALSE) returns invisibly for each subtree a list with the following components: - \item{tip.label} - \item{node.label} - \item{Ntip} - \item{Nnode} + \item{tip.label}{} + \item{node.label}{} + \item{Ntip}{} + \item{Nnode}{} } \examples{ ### Random tree with 12 leaves diff --git a/man/write.dna.Rd b/man/write.dna.Rd index 8a692f1..318a341 100644 --- 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 diff --git a/man/yule.cov.Rd b/man/yule.cov.Rd index ac6a749..dbdc044 100644 --- a/man/yule.cov.Rd +++ b/man/yule.cov.Rd @@ -39,6 +39,7 @@ yule.cov(phy, formula, data = NULL) The function needs three things: +\itemize{ \item a phylogenetic tree which may contain multichotomies; \item a formula which specifies the predictors of the model described @@ -56,8 +57,9 @@ yule.cov(phy, formula, data = NULL) order than for the labels, then the values for the nodes sequentially from the root to the most terminal nodes (i.e. in the order given by \code{phy$edge}). +} - The user must obtain the values for the nodes separately. +The user must obtain the values for the nodes separately. Note that the method in its present implementation assumes that the change in a species trait is more or less continuous between two nodes