In EricArcher/PAMsbuoy: Manipulation and filtering for PAM (Passive Acoustic Monitoring) data collected from sonobuoys

# Make Plots with proper titles

r paste0(reportText$cruiseName, ' (', reportText$cruiseAbbr, ')') Sonobuoy Report

r format(Sys.time(), format='%a %b %d %Y')

Navy surplus sonobuoys (type-r reportText$sonobuoyType) were deployed from the survey vessel during r reportText$cruiseAbbr; this report includes deployments conducted between r format(min(detSummary$UTC), format='%b %d %Y') and r format(max(detSummary$UTC), format='%b %d %Y') on the vessel(s) r formatListGrammar(reportText$myVessels). Sonobuoys were programmed to allow for best performance (Table 1). Sonobuoy signals were received via shipboard antenna cabled to a Winradio sonobuoy receiver (model WR-G39WSBE). Recordings were digitized at a r reportText$sampleRate kHz sampling rate with a r reportText$recordingSystem and recorded to hard drive using Pamguard software (Pamguard version xxxx, Gillespie et al. 2008).

Detection and localization of calls used the Pamguard DIFAR module (Miller et al. 2014); sonobuoys were calibrated following methods developed by Miller et al. (2014). Calibrations consisted of [x] number of samples, with each sample consisting of [x] s clips with a minimum interval of [x] s between clips. Classification settings were customized for calibration on vessel noise and for analysis of specific call types (Table 2).

A total of r reportText$nSonobuoys sonobuoys were deployed at r nrow(distinct(detSummary, station)) locations throughout the study area (Fig. 1)r reportText$vesselText (Table 1). Deployments included r reportText$nStations sonobuoy stations and r reportText$nOpportunistic sonobuoys deployed opportunistically in the presence of sighted cetaceans (Table 1). r if(reportText$nOpportunistic > 0) opportunisticPlot$text Acoustic detections included species name r formatListGrammar(unique(detSummary$Species)) (Table 2, Figure 2).

Literature

# Gillespie, D., Gordon, J., McHugh, R., McLaren, D., Mellinger, D. K., Redmond, P., Thode, A., Trinder, P., and Deng, X.Y. 2008. PAMGUARD: Semiautomated, open source software for realtime acoustic detection and localisation of cetaceans, Proc. Inst. Acoustics.

# Miller, Brian S., D. Gillespie, G. Weatherup, S. Calderan, and M. C. Double. 2014. Software for the localization of baleen whale calls using DIFAR sonobuoys: PAMGuard DIFAR. Report to the International Whaling Commission SC/65b/SH06. 7pp.

knitr::include_graphics(paste0(outDir, '/Figures/stationPlot.jpeg'))

if(reportText$nOpportunistic > 0) {
  knitr::include_graphics(paste0(outDir, '/Figures/opportunisticPlot.jpeg'))
}

knitr::include_graphics(paste0(outDir, '/Figures/detectionPlot.jpeg'))

detSumTables <- list.files(paste0(outDir, '/Tables'), pattern='detectionSummaryTable_[0-9]*', full.names=TRUE)
detSumHeader <- list.files(paste0(outDir, '/Tables'), pattern='detectionSummaryTableHeader', full.names=TRUE)
for(tbl in seq_along(detSumTables)) {
  cat('  \n#####  \n')
  if(tbl == 1) {
    cat('Table 2: description and title here  \n')
  } else {
    cat('Table 2 (cont.)  \n')
  }
  cat("![](", detSumHeader,")")
  cat("![](",detSumTables[tbl],")\n")
}

EricArcher/PAMsbuoy documentation built on March 3, 2021, 5:56 a.m.