This R-package contains the data and the R-code for the analysis of the mammal dataset in the research article (Mitov, Bartoszek, and Stadler 2019) (see References).

## Installation

The easiest way to install this package is to use the function install_github() from the R-package devtools. The following command will install the most recent version of the master branch from the github repository of the package.

devtools::install_github("venelin/MGPMMammals")

All R and Rmd code files in MGPMMammals are distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0).

Special terms apply to the following data-files and objects:

• MGPMMammals/data/tree.rda and ALL identical or derived tree objects describing the mammal phylogenetic tree (i.e. objects of S3 class phylo), that are included in the data-files MGPMMammals/data/fitMappings*, MGPMMammals/data/bestFitToDataWithSEs.rda, MGPMMammals/data/bestModelToDataWithoutSEs.rda, MGPMMammals/fits_bootstrap_MGPM_A_F_best_clade_RR_HD.rda. All of these tree objects are derived from the Mammal phylogenetic tree published in (Bininda-Emonds et al. 2007) These data-objects are included in MGPMMammals solely for the purpose of reproducibility; Hence, the author of MGPMMammals does not hold a copyright over any of these data-objects. If you reuse any of these tree objects in a publication, please cite this publication as explained in the output of the following R-coce print(citation("MGPMMammals"), bibtex = TRUE) (see next section).
• MGPMMammals/data-raw/brain_body_database_v2.txt, MGPMMammals/data-raw/jeb_2491_sm_tables1.xlsx, MGPMMammals/data/data.BoddyEtAl.2.rda, MGPMMammals/data/values.rda, MGPMMammals/data/SEs.rda, MGPMMammals/data/valuesPPCA.rda, MGPMMammals/data/SEsPPCA.rda as well as ALL identical or derived data-objects describing the mammal taxonomy and brain and body-mass trait, which are included in in the data-files located in MGPMMammals/data/fitMappings*, MGPMMammals/data/bestFitToDataWithSEs.rda, MGPMMammals/data/bestModelToDataWithoutSEs.rda, MGPMMammals/fits_bootstrap_MGPM_A_F_best_clade_RR_HD.rda. All of these data objects are derived from the data published in (A. M. Boddy et al. 2012) and in the accompanying data-package (Boddy et al. 2012). If you reuse any of these data objects in a publication, please cite the above article as explained in the following section.

## Citing MGPMMammals

print(citation("MGPMMammals"))
#>
#> If you use R-code or analysis results from MGPMMammals in
#> publications, please cite the first one of the three articles
#> below. If you use the mammal tree, please, also cite the second
#> article below. If you use brain- and body-mass data from mammal
#> species, please, also cite the third and the fourth articles
#> below.
#>
#>   Mitov, V., Bartoszek, K., & Stadler, T. (2019). Automatic
#>   generation of evolutionary hypotheses using mixed Gaussian
#>   phylogenetic models. Proceedings of the National Academy of
#>   Sciences of the United States of America, in-press,
#>   http://doi.org/10.1073/pnas.1813823116
#>
#>   Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee,
#>   R. D. E., Beck, R. M. D., Grenyer, R., et al. (2007). The
#>   delayed rise of present-day mammals. Nature, 446(7135), 507–512.
#>
#>   Boddy, A. M., McGowen, M. R., Sherwood, C. C., Grossman, L. I.,
#>   Goodman, M., & Wildman, D. E. (2012). Comparative analysis of
#>   encephalization in mammals reveals relaxed constraints on
#>   anthropoid primate and cetacean brain scaling. Journal of
#>   Evolutionary Biology 25(5), 981–994.
#>   http://doi.org/10.1111/j.1420-9101.2012.02491.x
#>
#>   Boddy, A. M., McGowen, M. R., Sherwood, C. C., Grossman, L. I.,
#>   Goodman, M., & Wildman, D. E. (2012). Data from: Comparative
#>   analysis of encephalization in mammals reveals relaxed
#>   constraints on anthropoid primate and cetacean brain scaling.
#>
#> To see these entries in BibTeX format, use 'print(<citation>,
#> bibtex=TRUE)', 'toBibtex(.)', or set
#> 'options(citation.bibtex.max=999)'.

## Further information

For additional information about the data objects and scripts in the package, read SI Appendix, Section H from (Mitov, Bartoszek, and Stadler 2019).

# References

Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, et al. 2007. “The Delayed Rise of Present-Day Mammals.” Nature 446 (7135): 507–12. http://www.nature.com/doifinder/10.1038/nature05634.

Boddy, A M, M R McGowen, C C Sherwood, L I Grossman, M Goodman, and D E Wildman. 2012. “Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling.” Journal of Evolutionary Biology 25 (5): 981–94.

Boddy, A. M., McGowen, M. R., Sherwood, C. C., Grossman, et al. 2012. “Data from: Comparative Analysis of Encephalization in Mammals Reveals Relaxed Constraints on Anthropoid Primate and Cetacean Brain Scaling.” Dryad Digital Repository. https://doi.org/10.5061/dryad.5kh0b362.

Mitov, Venelin, Krzysztof Bartoszek, and Tanja Stadler. 2019. “Automatic Generation of Evolutionary Hypotheses Using Mixed Gaussian Phylogenetic Models.” Proceedings of the National Academy of Sciences of the United States of America. https://www.pnas.org/lookup/doi/10.1073/pnas.1813823116.