monitoR: Acoustic Template Detection in R

Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.

Author
Sasha D. Hafner <sdh11@cornell.edu> and Jon Katz <jonkatz4@gmail.com>, with code for the Fourier transform from the seewave package (by Jerome Sueur, Thierry Aubin, and Caroline Simonis), and code for the readMP3 function from the tuneR package (by Uwe Ligges). Therese Donovan provided creative direction and database design support.
Date of publication
2015-09-18 13:36:02
Maintainer
Sasha D. Hafner <sdh11@cornell.edu>
License
GPL-2
Version
1.0.4
URLs

View on CRAN

Man pages

batchDetection
Batch Template Detection
bindEvents
Summarize/Archive Manually Derived Sound Events
btnw
Black-Throated Green Warbler (_Setophaga virens_) Song
changeSampRate
Resample Wave objects
collapseClips
Summarize/Archive Song Events
combineTemplates
Combine Acoustic Template Lists
compareTemplates
Compare Performance of Templates
cutw
Deprecated Function to Extract Shorter Wave Objects from...
cutWave
Extract Shorter Wave Objects from other Wave Objects
dbDownload
Retrieve Card-Recorder ID Values or Survey Names from a...
dbDownloadResult
Create 'detectionList' Objects from Data Stored in a Database
dbDownloadTemplate
Retrieve templates from an acoustics database
dbSchema
Upload a MySQL Database Schema to Create Tables in an...
dbUploadAnno
Upload Spectrogram Annotations to an Acoustics Database
dbUploadResult
Upload Detection Results to an Acoustics Database
dbUploadSurvey
Upload Survey Metadata to an Acoustics Database
dbUploadTemplate
Upload Acoustic Templates to a Database
detectionList-class
Class '"detectionList"'
eventEval
Evaluate Detected Events with Known Event Sources and Times
fileCopyRename
Copy and Rename Sound Files from Portable Media
findPeaks
Find Score Peaks and Detections in a 'templateScores' Object
getDetections
Extract Detections or Peaks from a 'detectionList' Object
getTemplates
Extract a Template List
index-methods
Indexing (Extraction) Methods for 'monitoR' Package
internals
'monitoR' Internal Functions
makeTemplate
Make an Acoustic Template
monitoR-package
Automated Acoustic Monitoring-overview and examples
mp3Subsamp
Extract Short Surveys from Longer mp3 Recordings
oven
Ovenbird (_Seiurus aurocapilla_) Song
plot-methods
Methods for the 'plot' Function
readMP3
Read MP3 Files into a Wave Object
readTemplates
Read Acoustic Templates from a Local Disk
show-methods
Methods for the 'show' and 'summary' Functions
showPeaks
View or Verify Detections or Peaks
specCols
Color Vectors for Spectrograms
survey
Sample Acoustic Survey (Short)
survey_anno
Annotations for 'survey'
Template-class
Class '"Template"'
templateComment
Query or Set Template Cutoffs
templateCutoff
Query or Set Template Cutoffs
TemplateList-class
Class '"TemplateList"'
templateMatching
Calculate Spectrogram Template Matching Scores
templateNames
Names of Templates
templatePath
Song clip path of Templates
templateScores-class
Class '"templateScores"'
timeAlign
Condense Detections or Peaks from Multiple Templates
viewSpec
Interactively View and Annotate Spectrograms
writeTemplates
Write Acoustic Templates to Text Files

Files in this package

monitoR
monitoR/inst
monitoR/inst/CITATION
monitoR/inst/doc
monitoR/inst/doc/monitoR_QuickStart.R
monitoR/inst/doc/monitoR_QuickStart.Rnw
monitoR/inst/doc/monitoR_QuickStart.pdf
monitoR/NAMESPACE
monitoR/NEWS
monitoR/data
monitoR/data/oven.rda
monitoR/data/survey.rda
monitoR/data/survey_anno.rda
monitoR/data/btnw.rda
monitoR/data/datalist
monitoR/R
monitoR/R/specCols.R
monitoR/R/dBweight.R
monitoR/R/dbDownloadResult.R
monitoR/R/Methods-summary.R
monitoR/R/batchCorMatch.R
monitoR/R/writeOneBinTemplate.R
monitoR/R/templateComment.R
monitoR/R/combineBinTemplates.R
monitoR/R/dbDownloadCardRecorderID.R
monitoR/R/dbUploadAnno.R
monitoR/R/ftwindow.R
monitoR/R/getTemplates.R
monitoR/R/bindEvents.R
monitoR/R/batchBinMatch.R
monitoR/R/Methods-plot.R
monitoR/R/templateNames.R
monitoR/R/collapseClips.R
monitoR/R/binMatch.R
monitoR/R/windows.R
monitoR/R/Methods-show.R
monitoR/R/spectro.R
monitoR/R/compareTemplates.R
monitoR/R/writeOneCorTemplate.R
monitoR/R/makeCorTemplate.R
monitoR/R/getDetections.R
monitoR/R/cutWave.R
monitoR/R/Methods-index.R
monitoR/R/writeCorTemplates.R
monitoR/R/readBinTemplates.R
monitoR/R/rbindf.R
monitoR/R/fileCopyRename.R
monitoR/R/templatePath.R
monitoR/R/cutw.R
monitoR/R/readMP3.R
monitoR/R/dbDownloadTemplate.R
monitoR/R/stft.R
monitoR/R/writeBinTemplates.R
monitoR/R/findDetections.R
monitoR/R/corMatch.R
monitoR/R/templateCutoff.R
monitoR/R/dbUploadTemplate.R
monitoR/R/makeBinTemplate.R
monitoR/R/dbSchema.R
monitoR/R/readOneCorTemplate.R
monitoR/R/eventEval.R
monitoR/R/dbDownloadSurvey.R
monitoR/R/timeAlign.R
monitoR/R/dbUploadResult.R
monitoR/R/getClip.R
monitoR/R/viewSpec.R
monitoR/R/getPeaks.R
monitoR/R/changeSampRate.R
monitoR/R/readCorTemplates.R
monitoR/R/dbUploadSurvey.R
monitoR/R/combineCorTemplates.R
monitoR/R/showPeaks.R
monitoR/R/findPeaks.R
monitoR/R/Classes.R
monitoR/R/readOneBinTemplate.R
monitoR/R/mp3Subsamp.R
monitoR/vignettes
monitoR/vignettes/monitoR_QuickStart.Rnw
monitoR/MD5
monitoR/README
monitoR/build
monitoR/build/vignette.rds
monitoR/DESCRIPTION
monitoR/ChangeLog
monitoR/man
monitoR/man/dbDownload.Rd
monitoR/man/TemplateList-class.Rd
monitoR/man/Template-class.Rd
monitoR/man/combineTemplates.Rd
monitoR/man/eventEval.Rd
monitoR/man/showPeaks.Rd
monitoR/man/viewSpec.Rd
monitoR/man/plot-methods.Rd
monitoR/man/changeSampRate.Rd
monitoR/man/compareTemplates.Rd
monitoR/man/findPeaks.Rd
monitoR/man/templateNames.Rd
monitoR/man/fileCopyRename.Rd
monitoR/man/index-methods.Rd
monitoR/man/cutWave.Rd
monitoR/man/survey_anno.Rd
monitoR/man/btnw.Rd
monitoR/man/cutw.Rd
monitoR/man/specCols.Rd
monitoR/man/dbUploadAnno.Rd
monitoR/man/writeTemplates.Rd
monitoR/man/templateMatching.Rd
monitoR/man/oven.Rd
monitoR/man/detectionList-class.Rd
monitoR/man/dbDownloadTemplate.Rd
monitoR/man/survey.Rd
monitoR/man/getDetections.Rd
monitoR/man/bindEvents.Rd
monitoR/man/timeAlign.Rd
monitoR/man/batchDetection.Rd
monitoR/man/dbUploadResult.Rd
monitoR/man/internals.Rd
monitoR/man/dbUploadTemplate.Rd
monitoR/man/mp3Subsamp.Rd
monitoR/man/templateScores-class.Rd
monitoR/man/templatePath.Rd
monitoR/man/dbDownloadResult.Rd
monitoR/man/templateCutoff.Rd
monitoR/man/dbUploadSurvey.Rd
monitoR/man/templateComment.Rd
monitoR/man/makeTemplate.Rd
monitoR/man/readTemplates.Rd
monitoR/man/collapseClips.Rd
monitoR/man/readMP3.Rd
monitoR/man/monitoR-package.Rd
monitoR/man/dbSchema.Rd
monitoR/man/show-methods.Rd
monitoR/man/getTemplates.Rd