The Retrospective Analysis of Antarctic Tracking (Standardised) Data from the Scientific Committee on Antarctic Research

Study Extent

Sampling

Method steps

1. Data Collection Starting from 2010, the core group of RAATD compiled a catalogue of existing (both published and unpublished) tracking data by contacting international experts and asking them to contribute data. The data collection phase ended in 2016. Besides directly contacting researchers, the team also harvested data from existing repositories, including the Australian Antarctic Data Center (https://data.aad.gov.au/), the Integrated Marine Observing System (http://imos.org.au/), PANGAEA (https://www.pangaea.de/), BirdLife International (http://www.seabirdtracking.org/), the Antarctic Biodiversity Portal (http://www.biodiversity.aq/), Ocean Biogeographic Information System (http://www.iobis.org/), and the Global Biodiversity Information Facility (http://www.gbif.org/).
2. Associated metadata Where available, information on the deployment site and relevant characteristics of the animal at the time of deployment was standardized by the data editors. Where age class and sex were known, these were included in the metadata
3. Data standardization Location dates and times were converted to UTC (Coordinated Universal Time). Records with missing latitude or longitude values were removed, and all longitudes were transformed to lie between 180° W and 180° E. Data files were row-ordered by individual, with rows within an individual in their correct temporal sequence. Near-duplicate positions were removed, those positions defined as having occurred 3 seconds or less after an existing position fix from the same animal, and which had identical longitude and latitude values (for GPS devices) or longitude and latitude values that differed by less than 1e-05 and which had the same location quality value (for PTT devices). Entries in the age class, breeding stage, device type, location quality, scientific, common, and abbreviated name, sex, and deployment site columns were validated against controlled vocabularies. Mandatory entries (e.g. deployment date, device type, individual animal identifier) were checked for missing values. Deployment locations were recorded by the original field team either at the individual animal level (using e.g. a hand-held GPS device) or at the deployment-site level (i.e. one deployment location per group of animals). The latter was common for deployments at colonies, whereas the former was most common for non-colony deployments (e.g. on seals and whales). Where deployment locations were not recorded by the field team, the first location estimate(s) in the tracking data were used. Deployment site names were standardized to colony granularity wherever possible (e.g. to the beach-on-island level). Periods at the start or end of deployments were identified and discarded if there was evidence that location data during these periods did not represent the animals’ at-sea movement. For example, tags may have been turned on early (thereby recording locations prior to their deployment on animals) or animals may have remained at the deployment site, e.g. the breeding colony, for an extended period at the start or end of the tag deployment. Some tracks also showed a marked deterioration in the frequency and quality (for PTTs) of location estimates near the end of a track. Such locations were visually identified based on maps of each track in conjunction with plots of location distance from deployment site against time. This information is captured in the location_to_keep column appended to each species’ raw data file (1 = keep, 0 = discard).
4. Data filtering The trimmed data were subjected to a number of automated quality control checks to remove individual deployments that: 1) were flagged for removal by the Data Editor Group (using the keepornot column in the metadata file); 2) had fewer than 20 location records; and 3) had deployments lasting less than 1 day. Additionally, individual deployments were checked to ensure that: 1) duplicate records in PTTs (locations occurring within 2 min of each other) were removed; 2) PTT Argos Z-class locations were reclassified as B-class locations (the least precise Argos location quality class that has an associated error variance; Jonsen et al. 2005); and 3) locations implying unrealistic travel rates (> 10 m s-1 for penguins and marine mammals and > 30 m s-1 for flying seabirds) were removed. Note that the definition of “duplicate locations” in this filtering context is more aggressive than that used during data standardization: for standardization purposes, the intention was to keep the data as close to original as possible, whereas for filtering the presence of multiple positions in a short period of time (< 2 min) has a negative effect on the filter performance. A state-space model (SSM) was used to estimate locations at regular time intervals (1 h for GPS data; 2 h for Argos data; 12 h for GLS data) and account for measurement error in the original observations (Jonsen et al. 2005, Block et al. 2011). The data were SSM-filtered and subject to a final quality control where tracks that failed to converge, as judged by nlminb convergence criteria (Nash 2014), were re-fit using different initial values. If re-fit tracks continually failed to converge they were removed from the final filtered dataset. For converged tracks, longitude and latitude residuals were examined for systematic trends indicative of lack of fit. Tracks that failed this inspection were removed from the final filtered dataset.
5. Data publication The core working team of RAATD established a data sharing and publication agreement with all data providers in 2017. The standardized (trimmed) data are held here. The filtered data are published in international repositories (see details below, in the ‘Filtered Data’ section).

1. Pygoscelis adeliae
   common name: Adelie penguin rank: species
2. Aptenodytes forsteri
   common name: Emperor penguin rank: species
3. Thalassarche melanophris
   common name: Black browed albatross rank: species
4. Eudyptes chrysolophus
   common name: Macaroni penguin rank: species
5. Aptenodytes patagonicus
   common name: King penguin rank: species
6. Thalassarche chrysostoma
   common name: Grey headed albatross rank: species
7. Diomedea exulans
   common name: Wandering albatross rank: species
8. Phoebetria palpebrata
   common name: Light mantled albatross rank: species
9. Phoebetria fusca
   common name: Dark mantled sooty albatross rank: species
10. Thalassoica antarctica
    common name: Antarctic petrel rank: species
11. Procellaria aequinoctialis
    common name: White-chinned petrel rank: species
12. Mirounga leonina
    common name: Southern elephant seals rank: species
13. Leptonychotes weddellii
    common name: Weddell seals rank: species
14. Lobodon carcinophagus
    common name: Crabeater seals rank: species
15. Arctocephalus gazella
    common name: Antarctic fur seals rank: species
16. Megaptera novaeangliae
    common name: Humpback whales rank: species