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/working/auteur/man/rjmcmc.data.Rd

http://github.com/eastman/auteur
Unknown | 47 lines | 31 code | 16 blank | 0 comment | 0 complexity | 954922df7bbc9edbf5ae2848ff9d9588 MD5 | raw file
 1\name{rjmcmc.data}
 2\alias{primates}
 3\alias{chelonia}
 4\alias{urodela}
 5\title{example datasets for auteur}
 6\description{Provides example body-size data and a corresponding phylogeny}
 7\usage{data(primates); data(chelonia); data(urodela)}
 8\details{Each object is a list of two items, a \code{phy} object and a \code{dat} object.  The \code{phy} object is a phylogenetic tree of class 'phylo' (see \code{\link[ape]{read.tree}}).  The \code{dat} object 
 9is a named vector of body sizes for each group.}
10
11\references{ Data are from the following sources:
12
13\code{PRIMATES}
14
15\itemize{
16		\item{REDDING DW, C DEWOLFF, and AO MOOERS. 2010. Evolutionary distinctiveness, threat status and ecological oddity in primates. Conservation Biology 24:1052-1058.}
17		
18		\item{VOS RA and AO MOOERS. 2006. A new dated supertree of the Primates. Chapter 5. In: VOS RA (Ed.) Inferring large phylogenies: the big tree problem. [Ph.D. thesis]. Burnaby BC, Canada: Simon Fraser University.}
19}
20	
21\code{TURTLES}
22
23\itemize{
24		\item{JAFFE, G SLATER, and M ALFARO. in review, Evolution. Ecological habitat and body size evolution in turtles. }
25}	
26
27\code{SALAMANDERS}
28
29\itemize{
30
31		\item{ADAMS DC, CM BERNS, KH KOZAK, and JJ WIENS. 2009. Are rates of species diversification correlated with rates of morphological evolution? Proceedings of the Royal Society of London B 276:2729-2738. }
32		
33		\item{BONETT RM, PT CHIPPINDALE, PE MOLER, RW VAN DEVENDER, and DB WAKE. 2009. Evolution of gigantism in amphiumid salamanders. PLoSONE 4(5):e5615.}
34		
35		\item{EASTMAN JM and A STORFER. in review, Science. Hybridism swallows salamander diversity.}
36		
37		\item{KOZAK KH, RW MENDYK, and JJ WIENS. 2009. Can Parallel Diversification Occur in Sympatry? Repeated Patterns of Body-Size Evolution in Coexisting Clades of North American Salamanders. Evolution 63:1769-1784.}
38		
39		\item{WEISROCK DW, TJ PAPENFUSS, JR MACEY, SN LITVINCHUK, R POLYMENI, IH UGURTAS, E ZHAO, H JOWKAR, and A LARSON. 2006. A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata). Molecular Phylogenetics and Evolution 41:368-383.}
40		
41		\item{WIENS JJ and JT HOVERMAN. 2008. Digit reduction, body size, and paedomorphosis in salamanders. Evolution and Development 10:449-463.}
42		
43		\item{ZHANG P, Y-Q CHEN, H ZHOU, X-L WANG, TJ PAPENFUSS, DB WAKE and L-H QU. 2006. Phylogeny, evolution, and biogeography of Asiatic salamanders (Hynobiidae). Proceedings of the National Academy of Sciences USA 103:7360-7365.}
44		
45		\item{ZHANG P and DB WAKE. 2009. Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution. 53:492-508. }
46}
47}