R/batchCorMatch.R

In jonkatz2/monitoR: Acoustic Template Detection in R

# For running multiple surveys and templates from specified directories
# Modified: 2015 JULY 21

batchCorMatch <-
function(
  dir.template,         # Directory with template files
  dir.survey = '.',       # Directory with surveys 
  ext.template = 'ct',    # 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  (corMatch)
  cor.method = 'pearson', # Method used by cor function (see ?cor) (corMatch)
  warn = TRUE,            # Set to FALSE to surpress warnings (corMatch)
  time.source = 'filename', # 'filename' or 'fileinfo' as the mtime source (corMatch)
  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 <- readCorTemplates(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 corMatch for', survey.files[i], '. . .\n')
    scores <- corMatch(survey = survey.files.full[i], templates = templates, parallel = parallel, show.prog = show.prog, cor.method = cor.method, 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)
}