/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
  9. is a named vector of body sizes for each group.}
  10. \references{ Data are from the following sources:
  11. \code{PRIMATES}
  12. \itemize{
  13. \item{REDDING DW, C DEWOLFF, and AO MOOERS. 2010. Evolutionary distinctiveness, threat status and ecological oddity in primates. Conservation Biology 24:1052-1058.}
  14. \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.}
  15. }
  16. \code{TURTLES}
  17. \itemize{
  18. \item{JAFFE, G SLATER, and M ALFARO. in review, Evolution. Ecological habitat and body size evolution in turtles. }
  19. }
  20. \code{SALAMANDERS}
  21. \itemize{
  22. \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. }
  23. \item{BONETT RM, PT CHIPPINDALE, PE MOLER, RW VAN DEVENDER, and DB WAKE. 2009. Evolution of gigantism in amphiumid salamanders. PLoSONE 4(5):e5615.}
  24. \item{EASTMAN JM and A STORFER. in review, Science. Hybridism swallows salamander diversity.}
  25. \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.}
  26. \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.}
  27. \item{WIENS JJ and JT HOVERMAN. 2008. Digit reduction, body size, and paedomorphosis in salamanders. Evolution and Development 10:449-463.}
  28. \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.}
  29. \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. }
  30. }
  31. }