[Vegan-commits] r2822 - in pkg/vegan: data inst man

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

Author: jarioksa
Date: 2014-01-06 15:02:57 +0100 (Mon, 06 Jan 2014)
New Revision: 2822

Modified:
   pkg/vegan/data/BCI.rda
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/BCI.Rd
Log:
update botanical names in BCI

Modified: pkg/vegan/data/BCI.rda
===================================================================
(Binary files differ)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2014-01-06 13:43:20 UTC (rev 2821)
+++ pkg/vegan/inst/ChangeLog	2014-01-06 14:02:57 UTC (rev 2822)
@@ -7,6 +7,24 @@
 	* new version opened with the CRAN release of vegan_2.0-10 on
 	December 12, 2013.
 
+	* BCI: names checked after http://www.theplantlist.org, but kept
+	the old (alphabetic) order of species. The changes are: Abarema
+	macradenium -> A. macradenia, Apeiba aspera -> A. glabra,
+	Aspidosperma cruenta -> A. desmanthum, Chlorophora tinctoria ->
+	Maclura t., Coccoloba manzanillensis -> C. manzinellensis, Cupania
+	sylvatica -> C. seemannii, Dipteryx panamensis -> D. oleifera,
+	Eugenia coloradensis -> E. florida, Eugenia oerstedeana ->
+	E. oerstediana, Lonchocarpus latifolius -> L. heptaphyllus (this
+	is ambiguous, since Hebestichma cubense is another alternative),
+	Phoebe cinnamomifolia -> Cinnamomum triplinerve, Tabebuia guayacan
+	-> Handroanthus g. Guarea is ambiguous: data have three taxa
+	(fuzzy, grandifolia and guidonia), but theplanlist.org says
+	grandifolia is an ill. synonym of guidonia. This change allows
+	matching 206 of 225 BCI species with
+	http://datadryad.org/resource/doi:10.5061/dryad.63q27. In
+	addition, there are two vars of Swartzia simplex in BCI which
+	could be matched at species level.
+	
 	* dune data sets: use 4+4 letter CEP names for species instead of
 	old 3+3 names. Botanical nomenclature was updated: Leontodon
 	autumnalis -> Scorzoneroides (Leoaut -> Scorautu), Potentilla

Modified: pkg/vegan/man/BCI.Rd
===================================================================
--- pkg/vegan/man/BCI.Rd	2014-01-06 13:43:20 UTC (rev 2821)
+++ pkg/vegan/man/BCI.Rd	2014-01-06 14:02:57 UTC (rev 2822)
@@ -8,9 +8,15 @@
 }
 \usage{data(BCI)}
 \format{
-  A data frame with 50 plots (rows) of 1 hectare with counts of trees on each
-  plot with total of 225 species (columns). Full Latin names are used
-  for tree species.
+  
+  A data frame with 50 plots (rows) of 1 hectare with counts of trees
+  on each plot with total of 225 species (columns). Full Latin names
+  are used for tree species. The names were updated against
+  \url{http://www.theplantlist.org} in Jan 2014 (see ChangeLog 2.1-41
+  for details) which allows matching 206 of species against
+  \url{http://datadryad.org/resource/doi:10.5061/dryad.63q27} (Zanne
+  et al., 2014).
+
  }
 \details{
   Data give the numbers of trees at least 10 cm in
@@ -28,11 +34,24 @@
 \source{
   \url{http://www.sciencemag.org/cgi/content/full/295/5555/666/DC1}
 }
+
 \references{
+  
   Condit, R, Pitman, N, Leigh, E.G., Chave, J., Terborgh, J., Foster,
-  R.B., \enc{Nuñez}{Nunez}, P., Aguilar, S., Valencia, R., Villa, G., Muller-Landau,
-  H.C., Losos, E. & Hubbell, S.P. (2002). Beta-diversity in tropical
-  forest trees. \emph{Science} 295, 666--669.
+  R.B., \enc{Nuñez}{Nunez}, P., Aguilar, S., Valencia, R., Villa, G.,
+  Muller-Landau, H.C., Losos, E. & Hubbell, S.P. (2002).
+  Beta-diversity in tropical forest trees. \emph{Science} 295,
+  666--669.
+
+  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).
+
 }
 \seealso{\code{\link[BiodiversityR]{BCI.env}} in \pkg{BiodiversityR}
   package for environmental data  (coordinates are given below in the