R/time.R

In TobieSurette/gulf.data: Southern Gulf of St Lawrence Data Access

#' Trawl Event Times
#' 
#' @description These are functions for extracting the times at which various events occur during trawling. 
#'              For example, there are the start and stop times determined by on-board observers or trawl touchdown and 
#'              liftoff times.
#' 
#' @param x Data object.
#' 
#' @examples 
#' x <- read.scsset(2020)
#' time(x, "start")
#' 
#' x <- read.esonar(2020, tow.id = "GP354F")
#' time(x, "start")
#' time(x, "stop")

# @describeIn time Extract event times for \code{scsset} data.
#' @export
time.scsset <- function(x, event = "start", location, position, probe, ...){
   # Parse 'event' argument:
   event <- match.arg(tolower(event), c("start", "end", "stop", "haul", "touchdown", "liftoff"))
   if (event == "end") if (length(intersect(grep("end", names(x)), grep("time", names(x)))) == 0) event <- "stop" 
   
   # Treat 'stop' and 'end' as synonyms:
   names(x) <- gsub("end", "stop", names(x))
   event <- gsub("end", "stop", event)
   
   # Attach touchdown times:
   if ((event == "touchdown") & (length(grep("touchdown", names(x))) == 0)){
      file <- locate(package = "gulf.data", keywords = c(unique(year(x)), "event", "times"))
      t <- read.csv(file)
      t <- t[t$location == "footrope" & (t$position == "center") & t$event == "touchdown", ]
      ix <- match(x[c("date", "tow.id")], t[c("date", "tow.id")])
      t <- t$time[ix]
      t[is.na(t)] <- ""
      x$touchdown.time <- t
   }
      
   # Attach liftoff times:
   if ((event == "liftoff") & (length(grep("liftoff", names(x))) == 0)){
      file <- locate(package = "gulf.data", keywords = c(unique(year(x)), "event", "times"))
      t <- read.csv(file)
      t <- t[t$location == "footrope" & (t$position == "center") & t$event == "liftoff", ]
      ix <- match(x[c("date", "tow.id")], t[c("date", "tow.id")])
      t <- t$time[ix]
      t[is.na(t)] <- ""
      x$liftoff.time <- t
   }   
   
   # Result variable:
   v <- rep("", nrow(x))
   
   # Regular naming:
   var <- paste0(event, ".time")
   if (var %in% names(x)){
      ix <- which((gulf.utils::deblank(x[,var]) != "")  &  !is.na(x[,var]))
      v[ix] <- x[ix,var]
   }
   
   # Look in logbook variables:
   var <- paste0(event, ".time.logbook")
   if (var %in% names(x)){
      ix <- which((v == "") & (deblank(x[,var]) != "")  &  !is.na(x[,var]))
      v[ix] <- x[ix,var]
   }
   
   # Convert to time class:
   ix <- gsub(" ", "", v) != ""
   r <- as.POSIXct(rep(NA, length(v)))
   r[ix] <- as.POSIXct(paste(as.character(gulf.utils::date(x[ix, ])), v[ix]))
   
   return(r)
}

# @describeIn time Extract time stamps or event times for \code{probe} data.
#' @export
time.probe <- function(x, event, ...){
   if (!is.null(gulf.metadata::project(x))){
      if ((gulf.metadata::project(x) == "scs") & !missing(event)){
         year <- unique(gulf.utils::year(x))
         y <- data.frame(date = as.character(unique(gulf.utils::date(x))), tow.id = tow.id(x), stringsAsFactors = FALSE)
         z <- read.scsset(year)
         r <- gulf.utils::time(z[gulf.utils::match(y[gulf.metadata::key(z)], z[gulf.metadata::key(z)]), ], event = event, ...)
         return(r)
      }
   }
 
   r <- gulf.utils::time(as.data.frame(x), ...)
   
   return(r)  
}