Overview

This repo is associated with the following article:

Smeele, Simeon Q. "Using relative brain size as predictor variable: Serious pitfalls and solutions." Ecology and Evolution 12.9 (2022): e9273.

Previous title was: On the use of relative brain size.

All results can be reproduced by running manuscript.Rmd. This rmarkdown contains all R code to generate and analyse the data.

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Requirements

To run the Bayesian models Stan needs to be installed. This is not an R package, but Stan can be run from R. For installation see: https://mc-stan.org/users/interfaces/.

The R code requires three libraries: cmdstanr to run the Stan engine, scales for transparent colours and knitr for the compilation of the pdf. All three can be installed from CRAN. To finish installing cmdstanr see: https://mc-stan.org/cmdstanr/.

All models can be run within seconds on a normal PC. The compilation of the Bayesian models might take up to a minute the first time code is run, unless the compiled models are also downloaded. Models run on 4 threads. If your computer has less computing power, models can also be run on a single thread. For this change the parallel_chains setting for all fitting calls in the markdown.

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Meta data

• figures/DAG.key: Keynote version of Figure 1

• figures/DAG.pdf: pdf version of Figure 1

• figures/predictor.pdf: pdf version of Figure 3

• figures/response.pdf: pdf version of Figure 2

• models/run SEM with ulam as front-end.R: code to run structural equation model with ulam as front-end

• models/predictor: compiled Stan model

• models/predictor.stan: Stan code for Bayesian linear model of Case II

• models/response: compiled Stan model

• models/response.stan: Stan code for the Bayesian linear model of Case I

• models/sem: compiled Stan model

• models/sem.stan: Stan code for the structural equation model of Case II

• supplemental figures/predictor 1000.pdf: pdf of the results for relative brain size as predictor variable with a sample size of 1000

• supplemental figures/predictor 20.pdf: pdf of the results for relative brain size as predictor variable with a sample size of 20

• supplemental figures/predictor informative.pdf: pdf of the results for relative brain size as predictor variable with informative priors

• supplemental figures/predictor strong brain.pdf: pdf of the results with a strong brain size effect supplemental figures/predictor strong body.pdf: pdf of the results with a strong body size effect

• supplemental figures/predictor vague.pdf: pdf of the results for relative brain size as predictor variable with vague priors

• supplemental figures/response 1000.pdf: pdf of the results for relative brain size as response variable with a sample size of 1000

• supplemental figures/response case iii.pdf: pdf of the results for relative brain size as response variable with an additional path from body to z

• supplemental figures/response 20.pdf: pdf of the results for relative brain size as response variable with a sample size of 20

• supplemental figures/response informative.pdf: pdf of the results for relative brain size as response variable with informative priors

• supplemental figures/response vague.pdf: pdf of the results for relative brain size as response variable with vague priors

• supplemental models/predictor_informative: compiled Stan model

• supplemental models/predictor_informative.stan: Stan code for Bayesian model of Case II with informative priors

• supplemental models/predictor_vague: compiled Stan model

• supplemental models/predictor_vague.stan: Stan code for Bayesian model of Case II with vague priors

• supplemental models/response_informative: compiled Stan model

• supplemental models/response_informative.stan: Stan code for Bayesian model of Case I with informative priors

• supplemental models/response_vague: compiled Stan model

• supplemental models/response_vague.stan: Stan code for Bayesian model of Case I with vague priors

• supplemental models/sem_informative: compiled Stan model

• supplemental models/sem_informative.stan: Stan code for the structural equation model of Case II with informative priors

• supplemental models/sem_vague: compiled Stan model

• supplemental models/sem_vague.stan: Stan code for the structural equation model of Case II with vague priors

• .gitignore: file that tells Git which files should not be tracked

• Using_relative_brain_size_as_predictor_variable-_serious_pitfalls_and_solutions.Rproj: R project file, if code is opened from this project the working directory is set automatically

• README.md: markdown file with all information for this repository

• bibliography.bib: BibTex file with all references

• manuscript.Rmd: Rmarkdown file to compile the manuscript, including generating data and results, includes the Appendix with supplemental methods and results

• manuscript.pdf: pdf version of the main text

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Session info

R version 4.1.0 (2021-05-18)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Catalina 10.15.7

Packages: scales_1.1.1, cmdstanr_0.4.0

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Maintainers and contact

Please contact Simeon Q. Smeele, ssmeele@ab.mpg.de, if you have any questions or suggestions.