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swaRmverse

Description

An R package for the comparative analysis of collective motion data in the swarm space. Based on the packages trackdf and swaRm, swaRmverse aims to standardize how data of collective motion are analyzed and support the comparison of properties within and across species and contexts.

swaRmverse is a work in progress, functions are likely to change as the package gets developed.

Publication

Further information on the functionality of the package, along with some use cases, will be soon available in our accompanying publication:

Papadopoulou M, Garnier S, King AJ. swaRmverse: an R package for the comparative analysis of collective motion. Under review.

The swarm space and the included metrics are first described here:

Papadopoulou M., Furtbauer I., O'Bryan L.R., Garnier S., Georgopoulou D.G., Bracken A.M., Christensen C. and King A.J. (2023) Dynamics of collective motion across time and species. Philosophical Transactions of the Royal Society B 378.1874 doi:10.1098/rstb.2022.0068.

Acknowledgements

The development of this package was supported by the 2G-SWARM ONR grant awarded to Dr. Andrew J. King at Swansea University (UK).

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Version

Install

install.packages('swaRmverse')

Monthly Downloads

201

Version

0.1.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/marinapapa/swaRmverse

Homepage

https://marinapapa.github.io/swaRmverse/

Maintainer

Marina Papadopoulou

Last Published

October 10th, 2024

Functions in swaRmverse (0.1.1)

event_ids_per_set

Event Indexes per Set

Add Velocity Timeseries

Define Events of Collective Motion

do_add_set_vels

Call Add Velocity Timeseries

Add Velocity Timeseries Across Sets

calc_dur_per_event

Duration of Each Event

Adding Individual Velocity Information in Parallel - Verbose

Number of Events

calc_nn_metrics

Relative Position of Nearest Neighbor Function to Parallelize

Adding Velocity Information for Individuals in Parallel without Progress Updates

Group Metrics of Collective Motion

par_calc_global_metrics

Calculation of Group Metrics in Parallel

pairwise_metrics

Pairwise Metrics of Collective Motion in a Dataset

Metrics of Collective Motion

Adding Motion Properties in Parallel without Progress Updates

set_data_format

Data Formatting

Pick a Threshold for the Events' Definition

Adding Motion Properties in Parallel - Verbose

col_motion_metrics

Collective Motion Metrics

col_motion_metrics_from_raw

Collective Motion Metrics from Raw Data

expand_pca_swarm_space

Expand Existing Swarm Space (PCA)

Bearing Angle to Nearest Neighbor

Speed and Heading Calculation based on swaRm Package.

Group Shape Based on a OOBB

group_metrics_per_set

Group Metrics of Collective Motion in a Dataset

swaRmverse: Swarm Space Creation

Create a Swarm Space

Total Duration of All Events

multi_species_metrics

Multi-Species Collective Motion Metrics

new_species_metrics

The Collective Motion Metrics of a New Species

Nearest Neighbour Metrics

multi_species_pca

Multi-Species PCA

multi_species_pca_data

Multi-Species PCA Data

calc_global_metrics

Calculation of Group Metrics

calc_events_averages

Events Averages

Number of Events (Internal)

add_rel_pos_coords

Relative Position Coordinates

calc_pairwise_metrics

Pairwise Metrics

Minimum Bounding Box