Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 9,277

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

phytools: an R package for phylogenetic comparative biology (and other things)

Open access
Revell, Liam J.·2012·Methods in Ecology and Evolution
DOI 10.1111/j.2041-210x.2011.00169.x
Open this paper in CoChat — free account

Abstract

Summary: 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.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1111/j.2041-210x.2011.00169.x

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 38

  1. 10.2307/1222480 · DOI
  2. 10.1016/j.tree.2004.03.015 · DOI
  3. 10.1111/j.0014-3820.2003.tb00285.x · DOI · Paper page
  4. 10.1186/1471-2105-7-88 · DOI · Paper page
  5. Bradley J.‐C., 2011, Collaborative Computational Technologies for Biomedical Research, 425
  6. 10.1038/436020a · DOI
  7. 10.1007/s00122-008-0801-8 · DOI · Paper page
  8. Csardi G., 2006, The igraph software package for complex network research, InterJournal, Complex Systems, 1695
  9. Felsenstein J., 2004, Inferring Phylogenies
  10. 10.1086/343873 · DOI · Paper page
  11. 10.1093/sysbio/42.3.265 · DOI · Paper page
  12. 10.1093/bioinformatics/btm538 · DOI
  13. Harvey P.H., 1991, The Comparative Method in Evolutionary Biology, 10.1093/oso/9780198546412.001.0001 · DOI · Paper page
  14. 10.1080/10635150390192780 · DOI
  15. 10.1080/10635150701313830 · DOI · Paper page
  16. 10.18637/jss.v038.i08 · DOI · Paper page
  17. 10.1111/j.1420-9101.2010.01983.x · DOI
  18. 10.1525/9780520943735 · DOI
  19. 10.1086/660020 · DOI · Paper page
  20. 10.1111/j.1558-5646.2010.01026.x · DOI · Paper page
  21. 10.1080/10635150290102393 · DOI
  22. 10.1111/j.0014-3820.2006.tb01171.x · DOI
  23. 10.1038/44766 · DOI · Paper page
  24. 10.1007/978-0-387-35100-1 · DOI
  25. 10.1093/bioinformatics/btg412 · DOI · Paper page
  26. Plummer M., 2006, CODA: convergence diagnosis and output analysis for MCMC, R News, 6, 7
  27. 10.1098/rspb.2000.1278 · DOI
  28. R Development Core Team, 2011, R: A Language and Environment for Statistical Computing
  29. 10.1016/1055-7903(92)90035-F · DOI
  30. 10.1086/588078 · DOI
  31. 10.1111/j.1558-5646.2009.00804.x · DOI
  32. 10.1111/j.2041-210X.2010.00044.x · DOI · Paper page
  33. 10.1111/j.1558-5646.2009.00616.x · DOI
  34. 10.1080/10635150802302427 · DOI · Paper page
  35. 10.1093/bioinformatics/btn065 · DOI
  36. Revell L.J., A new method for identifying exceptional phenotypic diversification, Evolution
  37. 10.1093/bioinformatics/btq706 · DOI
  38. 10.1111/j.1558-5646.2008.00519.x · DOI · Paper page

Cited by

See all 9,277

Metadata

Authors
Revell, L. J.
Venue
Methods in Ecology and Evolution
Publisher
Wiley
Published
2011-12-15
Volume
3
Issue
2
Pages
217-223
ISSN
2041-210X (ISSN-L)
DOI
10.1111/j.2041-210x.2011.00169.x
OpenAlex
W1605984840
Cited by
9,277
References
1
FWCI
33.97
Type
journal article
Language
en
Open access
bronze
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.