DomArchive: a century of a published dominance data

DomArchive is a data package compiling dominance interaction data published over a century of research. The goal of the package is to facilitate comparative research on the structure and function of dominance hierarchies. The archive contains 434 agonistic interaction datasets, totaling over 241,000 interactions.

Installing the package

To install the package with the vignette, run (requires devtools package):

devtools::install_github("DomArchive/DomArchive", build_vignettes = TRUE)

To view an introductory vignette about how to use the package, run:

vignette('introduction', package = "DomArchive")

What's in the package?

The package contains three primary elements:

1. dom.data - a list containing both data and metadata. Each element of the list is a unique data entry, named after the first author and year of publication. Each element of the list contains two named elements -- matrix containing the interaction sociomatrix and metadata containing the metadata associated with the data. In cases where data are in an edgelist rather than a matrix, the first named element is edgelist instead of matrix.

2. dom.metadata - a dataframe containing the metadata for the complete dataset. The information in the dom.metadata dataframe is exactly identical to what you would get if you extracted and combined every metadata element in dom.data.

3. subset_archive() - a function for selecting subsets of the data based upon the metadata. Users can either provide a vector of fileids specifying the datasets to return, or the users can provide paired columns and values lists specifying metadata columns and the associated values to retain for each column.

Metadata

Here is a summary of the metadata associated with each datafile:

Metadata Column	Meaning	Potential values
fileid	Unique identifier for data
order	Order (taxonomic rank)
species	Species name
common_name	Common name
study_site	Nation where study was conducted
captivity	Captive or free-ranging animals?	"Captive", "Natural"
sex	Males, females, or both?	"M", "F", "MF"
age	What age classes?	"Adult", "Non-Adult", "Mixed"
measure	What behavior was measured?
data_location	Where is data in reference (e.g., Tb1)?
countbinary	Are data raw counts or binary? (edgelists are counts)	"Count", "Binary"
repeat_group	Are there multiple datasets for this group?	"Yes", "No"
groupid	Unique identifier for social group
matrix_edgelist	Are data in matrix or edgelist format?	"Matrix", "Edgelist"
edgelist_time_meaning	For edgelist data, what is the meaning (units) of the "time" column
note	Miscellaneous notes
full_citation	Source for the data

Additionally, metadata includes some quantities calculated from the interaction data. Calculations were made using functions in the compete package (https://github.com/jalapic/compete).

Quantity	Details
number_individuals	Number of individuals in the dataset
number_interactions	Number of interactions in the dataset
interactions_per_individual	Number of interactions per individual
proportion_unknown	Proportion of relationships for which there are no observations (matrix data only)
dci	Directional consistency index (Van Hooff & Wensing 1987) (count matrix data only)
ttri	Triangle transitivity index (Shizuka & McDonald 2012) (matrix data only)
ds_steepness	Hierarchy steepness calculated from David's Scores (de Vries et al 2006) (count matrix data only)
modified_landaus_h	Modified Landau's h` measure of linearity (de Vries 1995) (matrix data only)

Get involved

If you would like to contribute data to the package, or if you find issues that would like to see addressed, please create an Issue. We appreciate your input!