ATN WC tag QC workflow — atn_wc

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

atn_wc_qc(
  wd = NULL,
  datadir = NULL,
  meta.file = NULL,
  outdir = NULL,
  collab.id = NULL,
  wc.akey = NULL,
  wc.skey = NULL,
  dropIDs = NULL,
  model = "rw",
  vmax = 3,
  time.step = 6,
  proj = NULL,
  reroute = FALSE,
  dist = 1000,
  buffer = 0.5,
  centroids = TRUE,
  cut = FALSE,
  min.gap = 72,
  QCmode = "nrt",
  p.int = 6,
  output = FALSE,
  ...
)

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.
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).
collab.id: the Wildlife Computers ID for a collaborator sharing data
wc.akey: a user's Access Key issued by Wildlife Computers for their API
wc.skey: a user's Secret Key issued by Wildlife Computers for their API
dropIDs: the ATN DeploymentID's that are to be ignored during the QC process
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
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.
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.
p.int: prediction interval to use for sub-sampling predicted locations (default = 6 h)
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.
...: additional arguments to be passed to SSM model fitting, see aniMotum::fit_ssm & aniMotum::route_path for details.