WC_workflow

Source: vignettes/WC_workflow.Rmd

Wildlife Computers (WC) tag QC workflow

The first step to initiate any ArgosQC workflow is to construct a JSON config file (see WC_config_file).

The diag files show the SSM fit (red) overlaid on the tag-measured Argos &/or GPS locations (blue). The dark grey vertical bars denote the time period tags were actively recording locations but the seal(s) had not yet gone to sea (no recorded diving activity). By default, the QC model does not fit to data in these time periods. These plots help judge whether the SSM fits have artefacts that need addressing - typically only addressed during a delayed-mode QC workflow.

The map file shows the SSM-predicted tracks (blue) and current last estimated location (red) for each deployed tag. The map files are annotated by the QC date so they are not overwritten by successive QC runs.

Output .CSV files

The QC’s main outputs are the Wildlife Computers tag data files appended with the same QC’d location variables as the SMRU tag QC output files: ssm_lat, ssm_lon, ssm_x, ssm_y, ssm_x_se, ssm_y_se. The output .CSV files necessarily depend on the specific type of Wildlife Computers tag(s) that is/are being QC’d. Currently, the ArgosQC workflow accommodates SPOT, SPLASH and SCOUT tag data. Combined across these tag types, the following output .CSV files (per Wildlife Computers) are provided:

  • DSA
  • ECDHistos
  • FastGPS
  • Histos
  • Locations
  • MinMaxDepth
  • MixLayer
  • PDTs
  • SST

Where one of these files can have a data structure that differs between specific tag types, the file names are appended with the tag type. For example, the ECDHistos file structure differs between SCOUT DSA and SCOUT TEMP 361A tags, so these file names appear as either ECDHistos_SCOUT_DSA or ECDHistos_SCOUT_TEMP_361A. Similar scenarios for other tag types/versions will be incorporated as required in future versions of ArgosQC.

In the generic metadata case, ie. for all programs other than ATN, each of the WC QC output file names are appended with the species’ common name and the QCmode suffix - _nrt or _dm. For ATN data and metadata, each file is appended with the AnimalAphiaID, the ATN ADRProjectID and the QCmode suffix - _nrt or _dm.

Metadata .CSV file

If an input deployment metadata file is provided then the output metadata file contains all the original metadata records plus the following variables describing the QC workflow applied to the data:

  • qc_start_date - the track datetime (UTC) at which the QC workflow was started.
  • qc_end_date - the track datetime (UTC) at which the QC workflow was ended.
  • qc_proj4string - the projection used for QC’ing the locations, as a proj4string.
  • qc_method - denotes the ArgosQC R package was used.
  • qc_version - denotes the version number of the ArgosQC R package used.
  • qc_run_date - the datetime (UTC) when the QC was applied to the data.

ssmoutputs .CSV file

The ssmoutputs file contains the SSM-predicted locations at the pred.int specified prediction interval. The time of the first location is set to the time of the first tag-measured location passed to the model. This may or may not be the first tag-measured location in the tag locations data file, depending on whether the animal-borne tag was immediately at sea. The location coordinates are provided as: lon, lat, x, y, and location uncertainty as x_se, y_se. The planar coordinates and uncertainty estimates always have units in km. Their coordinate projection is provided in the metadata .CSV file (qc_proj4string).