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 publication2017-02-17 22:15:13
MaintainerSasha D. Hafner <sdh11@cornell.edu>
LicenseGPL-2
Version1.0.5
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

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

Functions

batchBinMatch Man page
batchCorMatch Man page
bindEvents Man page
binMatch Man page
binTemplate-class Man page
binTemplateList-class Man page
blacktop.w Man page
btnw Man page
changeSampRate Man page
collapseClips Man page
combineBinTemplates Man page
combineCorTemplates Man page
compareTemplates Man page
corMatch Man page
corTemplate-class Man page
corTemplateList-class Man page
cutWave Man page
dbDownloadCardRecorderID Man page
dbDownloadResult Man page
dbDownloadSurvey Man page
dbDownloadTemplate Man page
dbSchema Man page
dbUploadAnno Man page
dbUploadResult Man page
dbUploadSurvey Man page
dbUploadTemplate Man page
dBweight Man page
detectionList-class Man page
[,detectionList-method Man page
eventEval Man page
fileCopyRename Man page
findDetections Man page
findPeaks Man page
flattop.w Man page
ftwindow Man page
getClip Man page
getDetections Man page
getOneClip Man page
getPeaks Man page
getTemplates Man page
gray.1 Man page
gray.2 Man page
gray.3 Man page
hamming.w Man page
hanning.w Man page
makeBinTemplate Man page
makeCorTemplate Man page
[-methods Man page
monitoR Man page
monitoR-package Man page
mp3Subsamp Man page
mp3Subsamp.one Man page
oven Man page
plot,detectionList,ANY-method Man page
plot-methods Man page
plot,TemplateList,ANY-method Man page
rainbow.1 Man page
rbindf Man page
readBinTemplates Man page
readClip Man page
readCorTemplates Man page
readMP3 Man page
readOneBinTemplate Man page
readOneCorTemplate Man page
rectangle.w Man page
show,binTemplateList-method Man page
show,corTemplateList-method Man page
show,detectionList-method Man page
show-methods Man page
showPeaks Man page
show,templateScores-method Man page
spectro Man page
stft Man page
summary,binTemplateList-method Man page
summary,corTemplateList-method Man page
summary,detectionList-method Man page
summary-methods Man page
summary,TemplateList-method Man page
summary,templateScores-method Man page
survey Man page
survey_anno Man page
Template-class Man page
templateComment Man page
templateComment<- Man page
templateCutoff Man page
templateCutoff<- Man page
TemplateList-class Man page
[,TemplateList-method Man page
templateNames Man page
templateNames<- Man page
templatePath Man page
templatePath<- Man page
templateScores-class Man page
[,templateScores-method Man page
timeAlign Man page
topo.1 Man page
viewSpec Man page
writeBinTemplates Man page
writeCorTemplates Man page
writeOneBinTemplate Man page
writeOneCorTemplate Man page

Files

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/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/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

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