R/bindEvents.R

In jonkatz2/monitoR: Acoustic Template Detection in R

# Modified: 2015 JULY 21

bindEvents <-
function(
   rec, 
   file, 
   by.species = TRUE, 
   parallel = FALSE, 
   return.times = FALSE
) {

   # Read in the event file
   if(!inherits(file, 'data.frame')) events <- read.csv(file = file)
   else events <- file
   events['duration'] <- events[, 'end.time']-events[, 'start.time']
   if(by.species) {
      spp <- events$name
      events <- split(events, events$name)
      events <- lapply(events, function(x) data.frame(x, start.time.collapsed = cumsum(x$duration)-x$duration, end.time.collapsed = cumsum(x$duration)))
   } else {
      events$start.time.collapsed = cumsum(events$duration)-events$duration
      events$end.time.collapsed = cumsum(events$duration)
   }

   # Collapse recording
   # CAN SIMPLIFY THIS A BIT BY USING A SINGLE LAPPLYFUN AS IN SCCCOR ETC
   if(parallel && by.species) {
      collapsed <- parallel::mclapply(X = events, FUN = function(x) collapseClips(rec = rec, start.times = x$start.time, end.times = x$end.time), max(1, parallel::detectCores()-1))
      #events <- unsplit(events, spp)
   } else if(by.species) {
      collapsed <- lapply(X = events, FUN = function(x) collapseClips(rec = rec, start.times = x$start.time, end.times = x$end.time))
      #events <- unsplit(events, spp)
   } else {
      collapsed <- list(collapseClips(rec = rec, start.times = events$start.time, end.times = events$end.time))
   }

   if(return.times) return(list(times = events, wave = collapsed)) else return(collapsed)
}