Package: monitoR 1.0.7

Sasha D. Hafner

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.

Authors:Sasha D. Hafner <[email protected]> and Jon Katz <[email protected]>, with code for the Fourier transform from the seewave package, and code for the readMP3 function from the tuneR package. Therese Donovan provided creative direction and database design support.

monitoR_1.0.7.tar.gz
monitoR_1.0.7.tar.gz(r-4.5-noble)monitoR_1.0.7.tar.gz(r-4.4-noble)
monitoR_1.0.7.tgz(r-4.4-emscripten)monitoR_1.0.7.tgz(r-4.3-emscripten)
monitoR.pdf |monitoR.html
monitoR/json (API)
NEWS

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

Peer review:

Datasets:
  • btnw - Black-Throated Green Warbler (_Setophaga virens_) Song
  • oven - Ovenbird (_Seiurus aurocapilla_) Song
  • survey - Sample Acoustic Survey
  • survey_anno - Annotations for 'survey'

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

51 exports 2 stars 1.85 score 3 dependencies 5 dependents 2 mentions 96 scripts 455 downloads

Last updated 7 years agofrom:e07ae7423d. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-linuxNOTEAug 21 2024

Exports:batchBinMatchbatchCorMatchbindEventsbinMatchchangeSampRatecollapseClipscombineBinTemplatescombineCorTemplatescompareTemplatescorMatchcutWavedbDownloadCardRecorderIDdbDownloadResultdbDownloadSurveydbDownloadTemplatedbSchemadbUploadAnnodbUploadResultdbUploadSurveydbUploadTemplateeventEvalfileCopyRenamefindPeaksgetDetectionsgetPeaksgetTemplatesgray.1gray.2gray.3makeBinTemplatemakeCorTemplatemp3Subsamprainbow.1readBinTemplatesreadCorTemplatesreadMP3showshowPeakstemplateCommenttemplateComment<-templateCutofftemplateCutoff<-templateNamestemplateNames<-templatePathtemplatePath<-timeAligntopo.1viewSpecwriteBinTemplateswriteCorTemplates

Dependencies:MASSsignaltuneR

monitoR Quick Start

Rendered frommonitoR_QuickStart.Rnwusingknitr::knitron Aug 21 2024.

Last update: 2018-02-14
Started: 2014-05-22

Readme and manuals

Help Manual

Help pageTopics
Batch Template DetectionbatchBinMatch batchCorMatch
Summarize/Archive Manually Derived Sound EventsbindEvents
Black-Throated Green Warbler (_Setophaga virens_) Songbtnw
Resample Wave objectschangeSampRate
Summarize/Archive Song EventscollapseClips
Combine Acoustic Template ListscombineBinTemplates combineCorTemplates
Compare Performance of TemplatescompareTemplates
Extract Shorter Wave Objects from other Wave ObjectscutWave
Retrieve Card-Recorder ID Values or Survey Names from a DatabasedbDownloadCardRecorderID dbDownloadSurvey
Create 'detectionList' Objects from Data Stored in a DatabasedbDownloadResult
Retrieve templates from an acoustics databasedbDownloadTemplate
Upload a MySQL Database Schema to Create Tables in an Acoustics DatabasedbSchema
Upload Spectrogram Annotations to an Acoustics DatabasedbUploadAnno
Upload Detection Results to an Acoustics DatabasedbUploadResult
Upload Survey Metadata to an Acoustics DatabasedbUploadSurvey
Upload Acoustic Templates to a DatabasedbUploadTemplate
Class '"detectionList"'detectionList-class
Evaluate Detected Events with Known Event Sources and TimeseventEval
Indexing (Extraction) Methods for 'monitoR' Package[,detectionList-method [,TemplateList-method [,templateScores-method [-methods
Copy and Rename Sound Files from Portable MediafileCopyRename
Find Score Peaks and Detections in a 'templateScores' ObjectfindPeaks
Extract Detections or Peaks from a 'detectionList' ObjectgetDetections getPeaks
Extract a Template ListgetTemplates
Make an Acoustic TemplatemakeBinTemplate makeCorTemplate
Automated Acoustic Monitoring-overview and examplesmonitoR-package monitoR
Extract Short Surveys from Longer mp3 Recordingsmp3Subsamp
Ovenbird (_Seiurus aurocapilla_) Songoven
Methods for the 'plot' Functionplot,detectionList,ANY-method plot,TemplateList,ANY-method plot-methods
Read MP3 Files into a Wave ObjectreadMP3
Read Acoustic Templates from a Local DiskreadBinTemplates readCorTemplates
Methods for the 'show' and 'summary' Functionsshow,binTemplateList-method show,corTemplateList-method show,detectionList-method show,templateScores-method show-methods summary,binTemplateList-method summary,corTemplateList-method summary,detectionList-method summary,TemplateList-method summary,templateScores-method summary-methods
View or Verify Detections or PeaksshowPeaks
Color Vectors for Spectrogramsgray.1 gray.2 gray.3 rainbow.1 specCols topo.1
Sample Acoustic Survey (Short)survey
Annotations for 'survey'survey_anno
Class '"Template"'binTemplate-class corTemplate-class Template-class
Query or Set Template CutoffstemplateComment templateComment<-
Query or Set Template CutoffstemplateCutoff templateCutoff<-
Class '"TemplateList"'binTemplateList-class corTemplateList-class TemplateList-class
Calculate Spectrogram Template Matching ScoresbinMatch corMatch
Names of TemplatestemplateNames templateNames<-
Song clip path of TemplatestemplatePath templatePath<-
Class '"templateScores"'templateScores-class
Condense Detections or Peaks from Multiple TemplatestimeAlign
Interactively View and Annotate SpectrogramsviewSpec
Write Acoustic Templates to Text FileswriteBinTemplates writeCorTemplates