R/massLoss.R

In sashahafner/biogas: Process Biogas Data and Predict Biogas Production

# General function for bottle mass loss and biogas leakage

massLoss <- function(
  # Main arguments 
  dat,                  # Data frame
  time.name,            # Name of time column (for sorting only)
  m.pre.name = NULL,    # Name of column holding the mass before venting 
  m.post.name,          # Name of column holding the mass after venting 
  id.name               # Name of id to group by 
  ) {
  
  # Check arguments
  # NTS: add checks later

  # Main calculations~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  # Sort data frame
  dat <- dat[order(dat[, id.name], dat[, time.name]), ]
  # make if loops for if the substrate changes 

  # Loop through bottles
  for(i in unique(dat[, id.name])) {
    which.id <- which(dat[, id.name]==i)
    n.id <- length(which.id)

    dat[which.id, 'mass.tot']  <- c(0, -diff(dat[which.id, m.post.name]))

    # Calculation of cummulative mass loss due to leakage and by venting
    dat[which.id, 'cmass.tot'] <- cumsum(dat[which.id, 'mass.tot'])

    if (!is.null(m.pre.name)) {
      dat[which.id, 'mass.vent'] <- dat[which.id, m.pre.name] - dat[which.id, m.post.name]
      dat[which.id, 'mass.leak'] <- c(0, dat[which.id, 
                                      m.post.name][-n.id] - dat[which.id, m.pre.name][-1])
      dat[which.id, 'cmass.vent'] <- cumsum(dat[which.id, 'mass.vent'])
      dat[which.id, 'cmass.leak'] <- cumsum(dat[which.id, 'mass.leak'])
    }
  }

  return(dat)
}