[Vegan-commits] r2820 - in pkg/vegan: data inst man

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

Author: jarioksa
Date: 2014-01-06 13:31:39 +0100 (Mon, 06 Jan 2014)
New Revision: 2820

Added:
   pkg/vegan/data/dune.phylodis.rda
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/dune.taxon.Rd
   pkg/vegan/man/treedive.Rd
Log:
add data on phylogenetic distances (coalescence ages) for dune species

Added: pkg/vegan/data/dune.phylodis.rda
===================================================================
(Binary files differ)


Property changes on: pkg/vegan/data/dune.phylodis.rda
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2014-01-06 11:25:03 UTC (rev 2819)
+++ pkg/vegan/inst/ChangeLog	2014-01-06 12:31:39 UTC (rev 2820)
@@ -13,6 +13,12 @@
 	palustris -> Comarum (Potpal -> Comapalu). Rows are now arranged
 	numerically, and species names alphabetically, vascular plants
 	first, and then the two bryophytes.
+
+	Added data 'dune.phylodis' which are ages of dune species
+	extracted from
+	http://datadryad.org/resource/doi:10.5061/dryad.63q27 (Zanne AE et
+	al. 2014, Nature doi:10.1038/nature12872, published online Dec 22,
+	2013).
 	
 Version 2.1-40 (closed December 12, 2013)	
 	

Modified: pkg/vegan/man/dune.taxon.Rd
===================================================================
--- pkg/vegan/man/dune.taxon.Rd	2014-01-06 11:25:03 UTC (rev 2819)
+++ pkg/vegan/man/dune.taxon.Rd	2014-01-06 12:31:39 UTC (rev 2820)
@@ -1,16 +1,26 @@
 \name{dune.taxon}
 \alias{dune.taxon}
+\alias{dune.phylodis}
 \docType{data}
-\title{Taxonomic Classification of Dune Meadow Species}
+\title{Taxonomic Classification and Phylogeny of Dune Meadow Species}
 \description{
   Classification table of the species in the \code{\link{dune}} data
   set.
 }
-\usage{data(dune.taxon)}
+\usage{
+  data(dune.taxon)
+  data(dune.phylodis}
+}
 \format{
-  A data frame with 30 species (rows) classified into five taxonomic
-  levels (columns).
+
+  \code{dune.taxon} is data frame with 30 species (rows) classified
+  into five taxonomic levels (columns). \code{dune.phylodis} is a
+  \code{\link{dist}} object of estimated coalescence ages extracted
+  from \url{http://datadryad.org/resource/doi:10.5061/dryad.63q27}
+  (Zanne et al. 2014) using tools in packages \pkg{ape} and
+  \pkg{phylobase}.
 }
+
 \details{
   The classification of vascular plants is adapted from AGP (2003), and
   that of mosses from Hill et al. (2006).
@@ -22,12 +32,23 @@
 
   Hill, M.O et al. (2006) An annotated checklist of the mosses of Europe
   and Macaronesia. \emph{J. Bryology} \strong{28}: 198--267.
+
+  Zanne A.E., Tank D.C., Cornwell, W.K., Eastman J.M., Smith, S.A.,
+  FitzJohn, R.G., McGlinn, D.J., O’Meara, B.C., Moles, A.T., Reich,
+  P.B., Royer, D.L., Soltis, D.E., Stevens, P.F., Westoby, M., Wright,
+  I.J., Aarssen, L., Bertin, R.I., Calaminus, A., Govaerts, R.,
+  Hemmings, F., Leishman, M.R., Oleksyn, J., Soltis, P.S., Swenson,
+  N.G., Warman, L. & Beaulieu, J.M. (2014) Three keys to the radiation
+  of angiosperms into freezing environments. \emph{Nature}
+  doi:10.1038/nature12872 (published online Dec 22, 2013).
+
 }
-\note{
-  The data set was made to demonstrate \code{\link{taxondive}}, and will
-  probably be removed after a better example is found.
+
+\seealso{Functions \code{\link{taxondive}}, \code{\link{treedive}},
+  and \code{\link{treedist}} use these data sets. }
+
+\examples{ 
+  data(dune.taxon) 
+  data(dune.phylodis)
 }
-\examples{
-data(dune.taxon)
-}
 \keyword{datasets}

Modified: pkg/vegan/man/treedive.Rd
===================================================================
--- pkg/vegan/man/treedive.Rd	2014-01-06 11:25:03 UTC (rev 2819)
+++ pkg/vegan/man/treedive.Rd	2014-01-06 12:31:39 UTC (rev 2820)
@@ -3,13 +3,14 @@
 \alias{treeheight}
 \alias{treedist}  
 
-\title{ Functional Diversity estimated from a Species Dendrogram}
-\description{
-  Functional diversity is defined as the total branch length in a trait
-  dendrogram connecting all species, but excluding the unnecessary root
-  segments of the tree (Petchey and Gaston 2006).
-}
+\title{ Functional Diversity and Community Distances from Species Trees}
 
+\description{ Functional diversity is defined as the total branch
+  length in a trait dendrogram connecting all species, but excluding
+  the unnecessary root segments of the tree (Petchey and Gaston
+  2006). Tree distance is the increase in total branch length when
+  combining two sites.  }
+
 \usage{
 treedive(comm, tree, match.force = FALSE)
 treeheight(tree)
@@ -112,19 +113,22 @@
 }
 
 \examples{
-## There is no data set on species properties yet, and therefore
-## the example uses taxonomy 
+
+## There is no data set on species properties yet, and we demonstrate
+## the methods using phylogenetic trees
 data(dune)
-data(dune.taxon)
-d <- taxa2dist(dune.taxon, varstep=TRUE)
-cl <- hclust(d, "aver")
+data(dune.phylodis)
+cl <- hclust(dune.phylodis)
 treedive(dune, cl)
 ## Significance test using Null model communities.
-## The current choice fixes only site totals.
-oecosimu(dune, treedive, "r0", tree = cl)
-## Clustering of tree distances
+## The current choice fixes numbers of species and picks species
+## proportionally to their overall frequency
+oecosimu(dune, treedive, "r1", tree = cl)
+## Phylogenetically ordered community table
 dtree <- treedist(dune, cl)
-plot(hclust(dtree, "aver"))
+tabasco(dune, hclust(dtree), cl)
+## Use tree distances  in capscale
+capscale(dtree ~ 1, comm=dune)
 }
 
 \keyword{ univar }