Abstract
| Original language | English (US) |
|---|---|
| Pages (from-to) | 217-223 |
| Number of pages | 7 |
| Journal | Methods in Ecology and Evolution |
| Volume | 3 |
| Issue number | 2 |
| DOIs | |
| State | Published - 2012 |
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In: Methods in Ecology and Evolution, Vol. 3, No. 2, 2012, p. 217-223.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - phytools: An R package for phylogenetic comparative biology (and other things)
AU - Revell, L.J.
N1 - Cited By :1267 Export Date: 17 April 2018 Correspondence Address: Revell, L.J.; Department of Biology, University of Massachusetts Boston, Boston, MA 02125, United States; email: liam.revell@umb.edu References: Baum, B.R., Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees (1992) Taxon, 41, pp. 3-10; Bininda-Emonds, O.R.P., The evolution of supertrees (2004) Trends in Ecology and Evolution, 19, pp. 315-322; Blomberg, S.P., Garland Jr, T., Ives, A.R., Testing for phylogenetic signal in comparative data: behavioral traits are more labile (2003) Evolution, 57, pp. 717-745; Bollback, J.P., SIMMAP: stochastic character mapping of discrete traits on phylogenies (2006) BMC Bioinformatics, 7, p. 88; Bradley, J.-C., Lang, A.S.I.D., Koch, S., Neylon, C., Collaboration using open notebook science in academia (2011) Collaborative Computational Technologies for Biomedical Research, pp. 425-452. , (eds S. Ekins, M.A.Z. Hupcey & A.J. Williams) John Wiley & Sons, Hoboken, NJ; Butler, D., Elecronic notebooks: a new leaf (2005) Nature, 436, pp. 20-21; Cavalli-Sforza, L.L., Edwards, A.W.F., Phylogenetic analysis: models and estimation procedures (1967) American Journal of Human Genetics, 19, pp. 233-257; Csardi, G., Nepusz, T., The igraph software package for complex network research (2006) InterJournal, Complex Systems, p. 1695; Felsenstein, J., Phylogenies and the comparative method (1985) American Naturalist, 125, pp. 1-15; Felsenstein, J., (2004) Inferring Phylogenies, , Sinauer, Sunderland, MA; Freckleton, R.P., Harvey, P.H., Pagel, M., Phylogenetic analysis and comparative data: a test and review of evidence (2002) American Naturalist, 160, pp. 712-726; Garland Jr, T., Dickerman, A.W., Janis, C.M., Jones, J.A., Phylogenetic analysis of covariance by computer simulation (1993) Systematic Biology, 42, pp. 265-292; Genz, A., Azzalini, A., (2011), http://cran.r-project.org/package=mnormt, mnormt: The Multivariate Normal and t Distributions. R Package Version 1.4-0; Gilbert, P., (2011), http://cran.r-project.org/package=numDeriv, numDeriv: Accurate Numerical Derivatives. R package Version 2010.11-1; Graffelman, J., (2010), http://cran.r-project.org/package=calibrate, calibrate: Calibration of Scatterplot and Biplot Axes. R Package Version 1.7; Harmon, L.J., Weir, J.T., Brock, C.D., Glor, R.E., Challenger, W., GEIGER: investigating evolutionary radiations (2008) Bioinformatics, 24, pp. 129-131; Harvey, P.H., Pagel, M.D., (1991) The Comparative Method in Evolutionary Biology, , Oxford University Press, Oxford UK; Huelsenbeck, J.P., Nielsen, R., Bollback, J.P., Stochastic mapping of morphological characters (2003) Systematic Biology, 52, pp. 131-158; Ives, A.R., Midford, P.E., Garland Jr, T., Within-species variation and measurement error in phylogenetic comparative methods (2007) Systematic Biology, 56, pp. 252-270; Jackson, C.H., Multi-state models for panel data: the msm package for R (2011) Journal of Statistical Software, 38, pp. 1-29; Lindenfors, P., Revell, L.J., Nunn, C.L., Sexual dimorphism in primate aerobic capacity: a phylogenetic test (2010) Journal of Evolutionary Biology, 23, pp. 1183-1194; Losos, J.B., (2009) Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles, , University of California Press, Berkeley, CA; Losos, J.B., Seeing the forest for the trees: the limitations of phylogenies in comparative biology (2011) American Naturalist, 177, pp. 709-727; Mahler, D.L., Revell, L.J., Glor, R.E., Losos, J.B., Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles (2010) Evolution, 64, pp. 2731-2745; Nielsen, R., Mapping mutations on phylogenies (2002) Systematic Biology, 51, pp. 729-739; O'Meara, B.C., Ané, C., Sanderson, M.J., Wainwright, P.C., Testing for different rates of continuous trait evolution using likelihood (2006) Evolution, 60, pp. 922-933; Pagel, M., Inferring the historical patterns of biological evolution (1999) Nature, 401, pp. 877-884; Paradis, E., (2006) Analysis of Phylogenetics and Evolution with R, , Springer, New York, NY; Paradis, E., Claude, J., Strimmer, K., APE: analyses of phylogenetics and evolution in R language (2004) Bioinformatics, 20, pp. 289-290; Plummer, M., Best, N., Cowles, K., Vines, K., CODA: convergence diagnosis and output analysis for MCMC (2006) R News, 6, pp. 7-11; Pybus, O.G., Harvey, P.H., Testing macro-evolutionary models using incomplete molecular phylogenies (2000) Proceedings of the Royal Society, B, 267, pp. 2267-2272; (2011) R: A Language and Environment for Statistical Computing, , R Development Core Team R Foundation for Statistical Computing, Vienna, Austria; (2011), http://cran.r-project.org/package=phylobase, R Hackathon (alphabetically: Bolker, B., Butler, M., Cowan, P., de Vienne, D., Eddelbuettel, D., Holder, M., Jombart, T., Kembel, S., Michonneau, F., Orme, D., O'Meara, B., Paradis, E., Regetz, J., Zwickl, D.) phylobase: Base Package for Phylogenetic Structures and Comparative Data. R Package Version 0.6.3; Ragan, M.A., Phylogenetic inference based on matrix representation of trees (1992) Molecular Phylogenetics and Evolution, 1, pp. 53-58; Revell, L.J., On the analysis of evolutionary change along single branches in a phylogeny (2008) American Naturalist, 172, pp. 140-147; Revell, L.J., Size-correction and principal components for interspecific comparative studies (2009) Evolution, 63, pp. 3258-3268; Revell, L.J., Phylogenetic signal and linear regression on species data (2010) Methods in Ecology and Evolution, 1, pp. 319-329; Revell, L.J., Collar, D.C., Phylogenetic analysis of the evolutionary correlation using likelihood (2009) Evolution, 63, pp. 1090-1100; Revell, L.J., Harmon, L.J., Collar, D.C., Phylogenetic signal, evolutionary process, and rate (2008) Systematic Biology, 57, pp. 591-601; Revell, L.J., Harrison, A.S., PCCA: a program for phylogenetic canonical correlation analysis (2008) Bioinformatics, 24, pp. 1018-1020; Revell, L.J., Mahler, D.L., Peres-Neto, P.R., Redelings, B.D., A new method for identifying exceptional phenotypic diversification Evolution, , (in press) doi: 10.1111/j.1558-5646.2011.01435.x; Schliep, K.P., phangorn: phylogenetic analysis in R (2011) Bioinformatics, 27, pp. 592-593; Sidlauskas, B., Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach (2008) Evolution, 62, pp. 3135-3156; Turlach, B.A., Weingessel, A., (2010), http://cran.r-project.org/package=quadprog, quadprog: Functions to Solve Quadratic Programming Problems. R Package Version 1.5-3; Xie, Y., (2011), http://cran.r-project.org/package=animation, animation: A Gallery of Animations in Statistics and Utilities to Create Animations. R Package Version 2.0-4UR - https://www.scopus.com/inward/record.uri?eid=2-s2.0-84867364321&doi=10.1111%2fj.2041-210X.2011.00169.x&partnerID=40&md5=fbfed636a6aa87cfc30895bf25faa9b3
PY - 2012
Y1 - 2012
N2 - 1.Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2.The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3.I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4.Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment. © 2011 The Author. Methods in Ecology and Evolution © 2011 British Ecological Society.
AB - 1.Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2.The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3.I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4.Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment. © 2011 The Author. Methods in Ecology and Evolution © 2011 British Ecological Society.
U2 - 10.1111/j.2041-210X.2011.00169.x
DO - 10.1111/j.2041-210X.2011.00169.x
M3 - Article
SN - 2041-210X
VL - 3
SP - 217
EP - 223
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
IS - 2
ER -