R/pf_obs_type.R

In ianjonsen/foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement

##' @title Determine observation type: LS, KF, GPS, or GLS
##'
##' @param x data from `pf_dup_dates()`
##' @keywords internal
##' @md

pf_obs_type <- function(x) {
  
  ## determine observation type: LS, KF, GPS or GLS
  x$obs.type <- NA
  x$obs.type <- with(x, 
                     ifelse(!is.na(smaj) & !is.na(smin) & !is.na(eor), 
                            "KF", obs.type))
  x$obs.type <- with(x, ifelse(lc %in% c(3,2,1,0,"A","B","Z") & 
                                 (is.na(smaj) | is.na(smin) | is.na(eor)), 
                               "LS", obs.type))
  x$obs.type <- with(x, ifelse(lc == "G" & 
                                 (is.na(smaj) | is.na(smin) |is.na(eor)), 
                               "GPS", obs.type))
  x$obs.type <- with(x, ifelse(lc == "GL" & 
                                 (is.na(smaj) | is.na(smin) | is.na(eor)) & 
                                 (!is.na(x.sd) & !is.na(y.sd)), 
                               "GL", obs.type))

  ##  if any records with smaj/smin = 0 then set to NA and obs.type to "LS"
  ##  convert error ellipse smaj & smin from m to km and eor from deg to rad
  x$smaj <- with(x, ifelse(smaj == 0 | smin == 0, NA, smaj)) / 1000
  x$smin <- with(x, ifelse(smin == 0 | is.na(smaj), NA, smin)) / 1000
  x$eor <- with(x, ifelse(is.na(smaj) & is.na(smin), NA, eor)) / 180 * pi
  
  x$obs.type <- with(x, ifelse(is.na(smaj) & is.na(smin) & is.na(eor) & 
                                 (obs.type != "GL" & obs.type != "GPS"), 
                               "LS", obs.type))
  
  if(all("lon" %in% names(x), "lat" %in% names(x), "lonerr" %in% names(x), "laterr" %in% names(x))) {
    ## if GL SD's are loneer/laterr then convert from deg to km
    x$x.sd <- with(x, x.sd * 6378.137 / 180 * pi)  
    x$y.sd <- with(x, y.sd * 6378.137 / 180 * pi)
    
  } else if(all((all("lon" %in% names(x), "lat" %in% names(x)) |
             all("x" %in% names(x), "y" %in% names(x))), "x.sd" %in% names(x), "y.sd" %in% names(x))){
    ## if GL SD's are x.sd/y.sd then convert from m to km
    x$x.sd <- with(x, x.sd / 1000)  
    x$y.sd <- with(x, y.sd / 1000)
  }
  
  return(x)
}