README.md

In gobbios/EloSteepness.data: Data Sets for Package EloSteepness

This package contains the data, code and results to replicate the analyses for Extending Bayesian Elo-rating to quantify dominance hierarchy steepness.

To install EloSteepness.data you require the devtools package (which you can get via install.packages("devtools")). You also require EloRating (install.packages("EloRating"))

At this point you need to decide whether you want to install the vignettes (which include the relevant code to replicate the analyses). You could proceed without installing the vignettes and download the documents that contain the relevant code here and here instead (which will save time during installation of the package).

Either strategy installs the package and allows access to the data.

without vignettes

Use:

devtools::install_github("gobbios/EloSteepness.data", build_vignettes = FALSE)

That should do the trick, give access to the data files. But note that in order to actually run the code in the vignettes, you need to install the packages listed below anyway.

with vignettes

For this to work, it's probably a good idea to install cmdstanr first (more info here).

install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
cmdstanr::check_cmdstan_toolchain(fix = TRUE)
cmdstanr::install_cmdstan(cores = 2)

Also EloSteepness itself should probably be installed next (see here for instructions if the following does not work).

install.packages("EloSteepness")

And finally, the following packages are required for some of the analyses as well:

install.packages("brms")
install.packages("ape")

With this done, use:

devtools::install_github("gobbios/EloSteepness.data", build_vignettes = TRUE, dependencies = TRUE)

Note that this will likely take at least several minutes.

Replication of analyses

In the vignette method_evaluation (if you installed the package this document should be available directly from R: vignette("method_evaluation", package = "EloSteepness.data")) you can find the code to replicate the method evaluation (or download the file here).

In the vignette vignette("phylogenetic_examples", package = "EloSteepness.data") you can find the code to replicate the two examples using steepness in a comparative analysis (or download the file here).

Both vignettes use small subsets of the data for illustrative purposes, but also allow replication of the full analyses.

Replication of additional figures

In the vignette vignette("additional_figures", package = "EloSteepness.data") you can find the code to reproduce the figures in the manuscript that are not primary results (or download the file here).

References

References for the empirical data sets used are in the document empirical_references (vignette("empirical_references", package = "EloSteepness.data"), or download the file here).

gobbios/EloSteepness.data documentation built on Oct. 18, 2022, 11:19 p.m.