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# For running multiple surveys and templates from specified directories
# Modified: 2013 JUNE 14
batchBinMatch <-
function(
dir.template, # Directory with template files
dir.survey='.', # Directory with surveys
ext.template='bt', # Extension for template files
ext.survey='wav', # Extension for survey files
templates, # Or provides template list directly
parallel=FALSE, # If TRUE, mclapply is used for correlation calculations, for parallel processing (Linux or Mac OS X only). If FALSE lapply is used. (corMatch & findPeaks)
show.prog=FALSE, # If TRUE, progress is displayed during correlation calculations (binMatch)
warn=TRUE, # Set to FALSE to surpress warnings (binMatch)
time.source='filename', # 'filename' or 'fileinfo' as the mtime source (binMatch)
fd.rat=1, # Factor to multiply template duration by for determining frame width (findPeaks)
... # Additional arguments to the spectro function
) {
# Read in templates
if(missing(templates)) {
if(missing(dir.template)) stop('Both arguments dir.template and templates are missing--one is needed')
cat('Reading in templates. .')
templates <- readBinTemplates(dir=dir.template, ext=ext.template, parallel=parallel)
cat(' . done.\n')
}
# Create a vector of survey file names
survey.files <- list.files(path=dir.survey, pattern=paste0('*\\.', ext.survey, '$'))
survey.files.full <- list.files(path=dir.survey, pattern=paste0('*\\.', ext.survey, '$'), full.names=TRUE)
detects <- NULL
for(i in 1:length(survey.files)) {
cat('\nCalling binMatch for', survey.files[i], '. . .\n')
scores <- binMatch(survey=survey.files.full[i], templates=templates, parallel=parallel, show.prog=show.prog, warn=warn, time.source=time.source)
cat('\nCalling findPeaks for output from', survey.files[i], '. . .\n')
pks <- findPeaks(score.obj=scores, parallel=parallel)
detects <- rbind(detects, getDetections(pks, id=survey.files[i]))
}
return(detects)
}
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