MGPMMammals

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")

License

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

Please, read the following:

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.
#>   Dryad Digital Repository https://doi.org/10.5061/dryad.5kh0b362
#> 
#> 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.