Rethomics Tutorial
Introduction
First Steps
Getting R
Installing rethomics packages
List of
rethomics
packages
The
rethomics
workflow
Working with metadata files
What are metadata?
Make them exhaustive
Put replicates together
Linking metadata
Take home message
behavr tables
Variables and metavariables
Operating on
behavr
tables
Playing with toy data
Generalities
Data
Metadata
Data & Metadata
Summerise data
Stitching
DAM2 data, in practice
Aims
Prerequisites
Background
Getting the data
Experiment design to standard metadata
Our toy experiment
Metadata
Linking
Loading
Note on datetime
ZT0
Start and stop time
Quality control
Detecting anomalies
How to exclude animals?
Apply functions when loading
Next steps
Sleep analysis with ethoscope
Visualisation with ggetho
Aims
Prerequisites
Lessons from ggplot
Some behavioural data
The
ggetho()
function
Tile plots
Per individual
Sorted individual
Group averages
Population plots
One population
Several populations
Wrapping data
LD annotations
Basics
Changing LD colours
LD in the background
Phase and period
Regime change
Coordinate and scales
Plot limits
Time scale units
Coordinate systems
Periodograms
Miscelaneous
Next steps
Published with bookdown
Rethomics, a framework for high-throughput behaviour analysis in R
Sleep analysis with ethoscope