[Picante-commits] r61 - pkg/man

[noreply at r-forge.r-project.org]

Author: skembel
Date: 2008-04-26 01:57:35 +0200 (Sat, 26 Apr 2008)
New Revision: 61

Added:
   pkg/man/pruning.Rd
Removed:
   pkg/man/pruneMissing.Rd
   pkg/man/sample.prune.Rd
   pkg/man/shared.history.Rd
Log:
Combine pruning functions into a single file

Deleted: pkg/man/pruneMissing.Rd
===================================================================
--- pkg/man/pruneMissing.Rd	2008-04-25 23:47:58 UTC (rev 60)
+++ pkg/man/pruneMissing.Rd	2008-04-25 23:57:35 UTC (rev 61)
@@ -1,20 +0,0 @@
-\name{pruneMissing}
-\alias{pruneMissing}
-\title{ Prune tips with missing data from a tree }
-\description{
-  Prune tips with missing data from a tree
-}
-\usage{
-pruneMissing(x,tree)
-}
-\arguments{
-  \item{x}{ Vector of trait data with names corresponding to tip.labels }
-  \item{tree}{ phylo object }
-}
-\value{
-  Returns a list
-  \item{tree}{ Pruned phylo object }
-  \item{data}{ Corresponding trait data sorted in tip.label order }  
-}
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\keyword{manip}

Added: pkg/man/pruning.Rd
===================================================================
--- pkg/man/pruning.Rd	                        (rev 0)
+++ pkg/man/pruning.Rd	2008-04-25 23:57:35 UTC (rev 61)
@@ -0,0 +1,23 @@
+\name{prune.sample}
+\alias{prune.sample}
+\alias{prune.missing}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Prune tree to match community data or trait data }
+\description{
+  Prune a phylogenetic tree to include only species present in a community data set or with trait data}
+\usage{
+prune.sample(samp, phylo)
+prune.missing(x, phylo)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{phylo}{ phylo object }
+  \item{samp}{ Community data matrix }
+  \item{x}{ trait data }
+}
+
+\value{
+  Returns a pruned phylo object
+}
+\author{ Steve Kembel <skembel at berkeley.edu> }
+\keyword{manip}

Deleted: pkg/man/sample.prune.Rd
===================================================================
--- pkg/man/sample.prune.Rd	2008-04-25 23:47:58 UTC (rev 60)
+++ pkg/man/sample.prune.Rd	2008-04-25 23:57:35 UTC (rev 61)
@@ -1,21 +0,0 @@
-\name{sample.prune}
-\alias{sample.prune}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ Prune tree to include species in community }
-\description{
-  Prune tree to include species in community
-}
-\usage{
-sample.prune(samp, phylo)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{samp}{ Community data matrix }
-  \item{phylo}{ phylo object }
-}
-
-\value{
-  Returns a phylo object pruned to include only the species present in samp.
-}
-\author{ Steve Kembel <skembel at berkeley.edu> }
-\keyword{manip}

Deleted: pkg/man/shared.history.Rd
===================================================================
--- pkg/man/shared.history.Rd	2008-04-25 23:47:58 UTC (rev 60)
+++ pkg/man/shared.history.Rd	2008-04-25 23:57:35 UTC (rev 61)
@@ -1,21 +0,0 @@
-\name{shared.history}
-\alias{shared.history}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ Shared history of a tree }
-\description{
-  Shared history of a tree
-}
-\usage{
-shared.history(t)
-}
-
-\arguments{
-  \item{t}{ phylo object }
-}
-
-\value{
-  Numeric shared history estimate
-}
-
-\author{ David Ackerly <dackerly at berkeley.edu> }
-\keyword{univar}