Function reference • SqueakR

Managing your Experiment

Functions for managing the experiment object and manually adding or removing data.

add_to_experiment(): Add Scored Data to Experiment Object

create_experiment(): Create New Experiment

describe_experiment(): Describe Experiment

remove_experiment_data(): Remove Data from Experiment File

save_experiment(): Save Experiment Locally

update_experiment(): Updates Experiment Object Metadata

Experiment Pipelines

Functions for creating experiments and loading them with data semi-automatically or automatically.

semisqueakRpipeline(): Semi-Automatic Experiment Creation

autosqueakRpipeline(): Fully-Automatic Experiment Creation

Cleaning DeepSqueak Data

Functions for loading data and scoring data for entry into experiment.

add_timepoint_data(): Add Timepoint Data

score_timepoint_data(): Score Timepoint Data

Data Visualization

Functions for visualizing and analyzing experimental datasets.

analyze_factor(): Analyze Factor

squeakrANOVA(): Generate ANOVA tables for Detected Calls

squeakrSummary(): Summary Statistics for Experiment

plotClusters(): 3D Call Clusters (Custom Label) Plot

plotContours(): 2D Call Contours

plotCorrelations(): Plot Correlation Matrix

plotDeltaHistogram(): Plot Delta Frequency Histogram

plotDensitySplitByCustom(): Plot Density Graph, Splitting Groups by Custom Label

plotDensitySplitByDuration(): Plot Density Graph, Splitting Groups by Duration

plotDensitySplitByFrequency(): Plot Density Graph, Splitting Groups by Frequency

plotDensityStackedByCustom(): Plot Density Graph Stacked by Custom Labels

plotDensityStackedByDuration(): Plot Density Graph Stacked by Duration

plotDensityStackedByFrequency(): Plot Density Graph Stacked by Frequency

plotEthnogram(): Plot Ethnogram

plotEthnogramSplitByTonality(): Plot Tonality-colored Ethnogram

plotPrincipalBoxplot(): Plot Principal Frequency Box-Plot

plotSummaryPDF(): Export PDF

plotSunburstAnimals(): Sunburst Plot for Animal Distribution

plotSunburstExperimenters(): Sunburst Plot for Experimenter Distribution

plotSurface(): 3D Surface Plot for Call Datasets

Example Data

An example dataset exported from DeepSqueak.

deepsqueak_data: DeepSqueak Example Data

SqueakR Dashboard

A Shiny Dashboard for conducting analyses and exploring data.

squeakRDashboard(): Launch SqueakR Dashboard

Unblinding Experiment

Functions for unblinding anonymized datasets.

unblind_all_ids(): Decode Experiment IDs

unblind_data_id(): Find Matching Experiment ID

unblind_data_name(): Find Matching Experiment Name