Livestock Informatics Toolkit (LIT)

Catie McVey 2022-05-04

Summary

The goal of this project is to develop a toolkit of algorithms that combine the flexibility of classic information theory approaches with the power of modern Unsupervised Machine Learning (UML) to better facilitate the analysis large complex data sets produced from a range of PLF sensor platforms. These algorithms will emphasize knowledge discovery over prediction in an effort to extract more complete and robust information about behavioral patterns.

List of Vignetts:

Visualizing Heterogenous Behavioral Patterns in Repeated Measures Data Using Data Mechanics Plots

Visualizing Temporally Complex Behavioral Patterns Using Tubeplots

Publications:

McVey, C.; Hsieh, F.; Manriquez, D.; Pinedo, P.; Horback, K. Livestock Informatics Toolkit: A Case Study in Visually Characterizing Complex Behavioral Patterns across Multiple Sensor Platforms, Using Novel Unsupervised Machine Learning and Information Theoretic Approaches. Sensors 2022, 22, 1. doi: https://doi.org/10.3390/s22010001

McVey C, Hsieh F, Manriquez D, Pinedo P and Horback K (2020) Mind the Queue: A Case Study in Visualizing Heterogeneous Behavioral Patterns in Livestock Sensor Data Using Unsupervised Machine Learning Techniques. Front. Vet. Sci. 7:523. doi: 10.3389/fvets.2020.00523

Chou E, McVey C, Hsieh YC, Enriquez S, Hsieh F. (2020) Extreme-K categorical samples problem. arXiv. arXiv:2007.15039

List of Functions:

compareEncodings

pghist

dmplot

dmplotGrid

groupTubeplot

tubeplot

calcEntropy

relativeEntropy

KLDdist

ensembleDist

MITest

bivarTreeTest

normTreeDist

cutreeEnsemble

simTimeBudgets

permuteNetworkTensor

permuteEdgeWeights

permuteNodeID

How to Install LIT:

Step 1: Click on the “View Project on GITHUB button above

Step 2: Download the tarball file with the “.tat.gz” file extension

Step 3: In RStudio click on the “Install” button under the packages tab to open the install wizard

Step 4: In the “install from” dropdown box select the “Package Archive File” option

Step 5: Click the “Browse” button. Navigate to and select the tarball file dowloaded in Step 2

Step 6: Click the “Install” button to install the LIT package to your R package library.

Congrats! You can now load up and work with the LIT package just like any other package you download from CRAN. Be sure to check the GITBUT repro regularly for package updates and improvements

If you need to report any bugs, patch requests can be submitted through the GITHUB repro, or you can contact me (Catie) through my LinkedIn