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.

AuthorSasha 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 publication2015-09-18 13:36:02
MaintainerSasha D. Hafner <sdh11@cornell.edu>
LicenseGPL-2
Version1.0.4
http://www.uvm.edu/rsenr/vtcfwru/R/?Page=monitoR/monitoR.htm

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.