Package: monitoR 1.2

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 [aut, cre], Jon Katz [aut], Jerome Sueur [aut], Thierry Aubin [aut], Caroline Simonis [aut], Uwe Ligges [aut]), Therese Donovan [ctb]

monitoR_1.2.tar.gz
monitoR_1.2.zip(r-4.7)monitoR_1.2.zip(r-4.6)monitoR_1.2.zip(r-4.5)
monitoR_1.2.tgz(r-4.6-any)monitoR_1.2.tgz(r-4.5-any)
monitoR_1.2.tar.gz(r-4.7-any)monitoR_1.2.tar.gz(r-4.6-any)
monitoR_1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
monitoR/json (API)

# Install 'monitoR' in R:

install.packages('monitoR', repos = c('https://jonkatz2.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jonkatz2/monitor/issues

Datasets:

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

On CRAN:

7.20 score 10 stars 5 packages 105 scripts 659 downloads 2 mentions 51 exports 3 dependencies

Last updated from:4613676412. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	142
source / vignettes	OK	171
linux-release-x86_64	WARNING	115
macos-release-arm64	WARNING	133
macos-oldrel-arm64	WARNING	255
windows-devel	WARNING	111
windows-release	WARNING	99
windows-oldrel	WARNING	124
wasm-release	OK	91

Exports:batchBinMatch batchCorMatch bindEvents binMatch changeSampRate collapseClips combineBinTemplates combineCorTemplates compareTemplates corMatch cutWave dbDownloadCardRecorderID dbDownloadResult dbDownloadSurvey dbDownloadTemplate dbSchema dbUploadAnno dbUploadResult dbUploadSurvey dbUploadTemplate eventEval fileCopyRename findPeaks getDetections getPeaks getTemplates gray.1 gray.2 gray.3 makeBinTemplate makeCorTemplate mp3Subsamp rainbow.1 readBinTemplates readCorTemplates readMP3 show showPeaks templateComment templateComment<-templateCutoff templateCutoff<-templateNames templateNames<-templatePath templatePath<-timeAlign topo.1 viewSpec writeBinTemplates writeCorTemplates

Dependencies:MASS signal tuneR

monitoR Quick Start

Getting started | Spectrogram cross correlation | Binary point matching | Other functions

Rendered frommonitoR_QuickStart.Rnwusingknitr::knitr

Last update: 2018-02-13
Started: 2018-01-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Batch Template Detection	batchBinMatch batchCorMatch
Summarize/Archive Manually Derived Sound Events	bindEvents
Black-Throated Green Warbler (_Setophaga virens_) Song	btnw
Resample Wave objects	changeSampRate
Summarize/Archive Song Events	collapseClips
Combine Acoustic Template Lists	combineBinTemplates combineCorTemplates
Compare Performance of Templates	compareTemplates
Extract Shorter Wave Objects from other Wave Objects	cutWave
Retrieve Card-Recorder ID Values or Survey Names from a Database	dbDownloadCardRecorderID dbDownloadSurvey
Create 'detectionList' Objects from Data Stored in a Database	dbDownloadResult
Retrieve templates from an acoustics database	dbDownloadTemplate
Upload a MySQL Database Schema to Create Tables in an Acoustics Database	dbSchema
Upload Spectrogram Annotations to an Acoustics Database	dbUploadAnno
Upload Detection Results to an Acoustics Database	dbUploadResult
Upload Survey Metadata to an Acoustics Database	dbUploadSurvey
Upload Acoustic Templates to a Database	dbUploadTemplate
Class '"detectionList"'	detectionList-class
Evaluate Detected Events with Known Event Sources and Times	eventEval
Indexing (Extraction) Methods for 'monitoR' Package	[,detectionList-method [,TemplateList-method [,templateScores-method [-methods
Copy and Rename Sound Files from Portable Media	fileCopyRename
Find Score Peaks and Detections in a 'templateScores' Object	findPeaks
Extract Detections or Peaks from a 'detectionList' Object	getDetections getPeaks
Extract a Template List	getTemplates
Make an Acoustic Template	makeBinTemplate makeCorTemplate
Automated Acoustic Monitoring-overview and examples	monitoR-package monitoR
Extract Short Surveys from Longer mp3 Recordings	mp3Subsamp
Ovenbird (_Seiurus aurocapilla_) Song	oven
Methods for the 'plot' Function	plot,detectionList,ANY-method plot,TemplateList,ANY-method plot-methods
Read MP3 Files into a Wave Object	readMP3
Read Acoustic Templates from a Local Disk	readBinTemplates readCorTemplates
Methods for the 'show' and 'summary' Functions	show,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 Peaks	showPeaks
Color Vectors for Spectrograms	gray.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 Cutoffs	templateComment templateComment<-
Query or Set Template Cutoffs	templateCutoff templateCutoff<-
Class '"TemplateList"'	binTemplateList-class corTemplateList-class TemplateList-class
Calculate Spectrogram Template Matching Scores	binMatch corMatch
Names of Templates	templateNames templateNames<-
Song clip path of Templates	templatePath templatePath<-
Class '"templateScores"'	templateScores-class
Condense Detections or Peaks from Multiple Templates	timeAlign
Interactively View and Annotate Spectrograms	viewSpec
Write Acoustic Templates to Text Files	writeBinTemplates writeCorTemplates