IMOS SMRU SRDL QC workflow — imos_smru

Wrapper function that executes the complete workflow from data download to SSM-appended tag data files output as CSV files.

imos_smru_qc(
  wd = NULL,
  cids = NULL,
  sp = NULL,
  smru.usr = NULL,
  smru.pwd = NULL,
  datadir = NULL,
  meta.file = NULL,
  outdir = NULL,
  dropIDs = NULL,
  proj = NULL,
  model = "rw",
  vmax = 3,
  time.step = 6,
  reroute = FALSE,
  dist = 1000,
  buffer = 0.5,
  centroids = TRUE,
  cut = FALSE,
  min.gap = 72,
  QCmode = "nrt",
  output = FALSE,
  dwnld = TRUE,
  ...
)

Arguments

wd: the path to the working directory that contains: 1) the data directory where tag data files are stored (if source = local); 2) the metadata directory where all metadata files are stored; and 3) the destination directory for QC output.
cids: SMRU campaign (AODN sattag_program) ID's
sp: the species being QC'd - currently, either "sese" or "ortu"
smru.usr: SMRU data server username as a string
smru.pwd: SMRU data server password as a string
datadir: the name of the data directory (to be added to the wd path).
meta.file: the metadata filename. Must reside within the wd
outdir: the name of the QC output directory where CSV files will be written (to be added to the wd path).
dropIDs: the SMRU ref ID's that are to be ignored during the QC process
proj: the proj4string to be used for the location data & for the SSM-estimated locations. The default (NULL) will result in one of 3 projections being used, depending on whether the centroid of the observed latitudes lie in N or S polar regions, temperate or equatorial regions, or if tracks straddle (or lie close to) -180,180 longitude.
model: the aniMotum SSM model to be used for the location QC - typically either rw or crw.
vmax: for SSM fitting; max travel rate (m/s) to identify implausible locations
time.step: the prediction interval (in hours) to be used by the SSM
reroute: whether QC'd tracks should be re-routed off of land (default is FALSE). Note, in some circumstances this can substantially increase processing time. Default land polygon data are sourced from the ropensci/rnaturalearthhires R package.
dist: the distance in km from outside the convex hull of observed locations from which to select land polygon data for re-routing. Ignored if reroute = FALSE.
buffer: the distance in km to buffer rerouted locations from the coastline. Ignored if reroute = FALSE.
centroids: whether centroids are to be included in the visibility graph mesh used by the rerouting algorithm. See ?pathroutr::prt_visgraph for details. Ignored if reroute = FALSE.
cut: logical; should predicted locations be dropped if they lie within in a large data gap (default is FALSE).
min.gap: the minimum data gap duration (h) to be used for cutting predicted locations (default is 72 h)
QCmode: one of either nrt for Near Real-Time QC or dm for Delayed Mode QC.
output: logical; should fn return a list of QC-generated objects. This results in a single large object return that can be useful for troubleshooting QC errors or undesirable results.
dwnld: logical; should the tag data be downloaded from the SMRU server (default TRUE). Useful when testing so unnecessary load is not put on the SMRU server.
...: additional arguments to be passed to SSM model fitting, see aniMotum::fit_ssm for details.