Package: SqueakR 1.3.0

Simon Ogundare

SqueakR: An Experiment Interface for 'DeepSqueak' Bioacoustics Research

Data processing and visualizations for rodent vocalizations exported from 'DeepSqueak'. These functions are compatible with the 'SqueakR' Shiny Dashboard, which can be used to visualize experimental results and analyses.

Authors:Simon Ogundare [aut, cre]

SqueakR_1.3.0.tar.gz
SqueakR_1.3.0.zip(r-4.5)SqueakR_1.3.0.zip(r-4.4)SqueakR_1.3.0.zip(r-4.3)
SqueakR_1.3.0.tgz(r-4.5-any)SqueakR_1.3.0.tgz(r-4.4-any)SqueakR_1.3.0.tgz(r-4.3-any)
SqueakR_1.3.0.tar.gz(r-4.5-noble)SqueakR_1.3.0.tar.gz(r-4.4-noble)
SqueakR_1.3.0.tgz(r-4.4-emscripten)SqueakR_1.3.0.tgz(r-4.3-emscripten)
SqueakR.pdf |SqueakR.html✨
SqueakR/json (API)
NEWS

# Install 'SqueakR' in R:
install.packages('SqueakR', repos = c('https://osimon81.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/osimon81/squeakr/issues

Pkgdown site:https://osimon81.github.io

Datasets:

On CRAN:

Conda:

bioacousticsdeepsqueak

4.65 score 9 stars 5 scripts 136 downloads 34 exports 137 dependencies

Last updated 3 years agofrom:c6e94ddc06. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 26 2025
R-4.5-winOKMar 26 2025
R-4.5-macOKMar 26 2025
R-4.5-linuxOKMar 26 2025
R-4.4-winOKMar 26 2025
R-4.4-macOKMar 26 2025
R-4.4-linuxOKMar 26 2025
R-4.3-winOKMar 26 2025
R-4.3-macOKMar 26 2025

Exports:add_timepoint_dataadd_to_experimentanalyze_factorautosqueakRpipelinecreate_experimentdescribe_experimentplotClustersplotContoursplotCorrelationsplotDeltaHistogramplotDensitySplitByCustomplotDensitySplitByDurationplotDensitySplitByFrequencyplotDensityStackedByCustomplotDensityStackedByDurationplotDensityStackedByFrequencyplotEthnogramplotEthnogramSplitByTonalityplotPrincipalBoxplotplotSummaryPDFplotSunburstAnimalsplotSunburstExperimentersplotSurfaceremove_experiment_datasave_experimentscore_timepoint_datasemisqueakRpipelinesqueakrANOVAsqueakRDashboardsqueakrSummaryunblind_all_idsunblind_data_idunblind_data_nameupdate_experiment

Dependencies:abindaskpassbackportsbase64encbayestestRbootbroombslibcachemcarcarDatacellrangerclicolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tabledatawizardDerivdigestdoBydplyreffectsizeevaluatefansifarverfastmapfontawesomeFormulafsgarglegenericsggcorrplotggeasygghighlightggplot2ggpubrggrepelggsciggsignifgluegoogledrivegooglesheets4gridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttridsinsightisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslparameterspbkrtestperformancepillarpkgconfigplotlyplyrpolynomprettyunitsprogresspromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadxlreformulasrematchrematch2reportreshape2rlangrlistrmarkdownrstatixsassscalesshinyshinydashboardsourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8uuidvctrsviridisLitewithrxfunXMLxtableyaml

SqueakR

Rendered fromSqueakR.Rmdusingknitr::rmarkdownon Mar 26 2025.

Last update: 2022-06-25
Started: 2022-06-14

Readme and manuals

Help Manual

Help pageTopics
Add Timepoint Dataadd_timepoint_data
Add Scored Data to Experiment Objectadd_to_experiment
Analyze Factoranalyze_factor
Fully-Automatic Experiment CreationautosqueakRpipeline
Create New Experimentcreate_experiment
DeepSqueak Example Datadeepsqueak_data
Describe Experimentdescribe_experiment
3D Call Clusters (Custom Label) PlotplotClusters
2D Call ContoursplotContours
Plot Correlation MatrixplotCorrelations
Plot Delta Frequency HistogramplotDeltaHistogram
Plot Density Graph, Splitting Groups by Custom LabelplotDensitySplitByCustom
Plot Density Graph, Splitting Groups by DurationplotDensitySplitByDuration
Plot Density Graph, Splitting Groups by FrequencyplotDensitySplitByFrequency
Plot Density Graph Stacked by Custom LabelsplotDensityStackedByCustom
Plot Density Graph Stacked by DurationplotDensityStackedByDuration
Plot Density Graph Stacked by FrequencyplotDensityStackedByFrequency
Plot EthnogramplotEthnogram
Plot Tonality-colored EthnogramplotEthnogramSplitByTonality
Plot Principal Frequency Box-PlotplotPrincipalBoxplot
Export PDFplotSummaryPDF
Sunburst Plot for Animal DistributionplotSunburstAnimals
Sunburst Plot for Experimenter DistributionplotSunburstExperimenters
3D Surface Plot for Call DatasetsplotSurface
Remove Data from Experiment Fileremove_experiment_data
Save Experiment Locallysave_experiment
Score Timepoint Datascore_timepoint_data
Semi-Automatic Experiment CreationsemisqueakRpipeline
Generate ANOVA tables for Detected CallssqueakrANOVA
Launch SqueakR DashboardsqueakRDashboard
Summary Statistics for ExperimentsqueakrSummary
Decode Experiment IDsunblind_all_ids
Find Matching Experiment IDunblind_data_id
Find Matching Experiment Nameunblind_data_name
Updates Experiment Object Metadataupdate_experiment