DOI: 10.7291/d18d7w
title: Northern elephant seal tracking and diving – processed data

description: Northern elephant seals (Mirounga angustirostris) have been
 integral to the development and progress of biologging technology and
 movement data analysis. Adult female elephant seals at Año Nuevo State
 Park and other colonies along the west coast of North America were tracked
 annually from 2004 to 2020 for a total of 653 instrument deployments and
 561 recoveries. These high-resolution diving and location data have been
 compiled, curated, and processed. This repository has netCDF files
 containing the raw tracking and diving data. The raw data are available in
 a second repository (https://doi.org/10.7291/D10D61).
description: These data were collected from biotelemetry devices attached to
 adult female northern elephant seals (<em>Mirounga
 angustirostris</em>) from 2004 to 2020. The instruments collected
 locations (Argos and/or GPS) and continuously recorded depth throughout
 the animals' trips. Data were processed in MATLAB and R using custom
 code, the IKNOS package for dive data processing, and the aniMotum package
 for track processing. The details of data collection and processing are
 documented in the data descriptor paper associated with this dataset. In
 addition, all code used to process the data are available on GitHub and
 Zenodo. The data presented here are freely available
 for use under the CC0 (Creative Commons Zero), with attribution highly
 encouraged given to the data descriptor (DOI:
 10.1038/s41597-024-04084-4) and this Dryad repository. We
 encourage users to reach out to the data owner for richer insight into the
 dataset. Subsets of this dataset have been made available through other
 projects and data portals and we caution users that these are not
 independent northern elephant seal datasets. This includes the AniBOS/MEOP
 data portal (https://www.meop.net/database/meop-databases/), the Animal Tracking Network (ATN) (https://portal.atn.ioos.us/), Movebank (https://www.movebank.org/cms/movebank-main), and MegaMove (https://megamove.org/data-portal/). Additional data about the instrumented animals, such as morphometrics, demographics, and other biologging data (e.g., acceleration, jaw motion, temperature), are available for many of these animals but are beyond the scope of this dataset. For more information, contact the data owner. <strong>Sampling Biases</strong> Generally, we have been careful to select healthy animals for sedation and instrumentation. For animals deployed at Año Nuevo (most of the tracks), typically individuals with known site fidelity to the colony were selected and if age was known it was usually restricted to 4- to 12-year-olds. Furthermore, the data reported here span two decades of work. During this time, different studies prompted additional non-random population sampling. Examples include focusing on one age for a year, repeat tracking the same individuals two trips in a row, and intentionally selecting previously tracked females who had used a coastal foraging strategy. Many individuals in the dataset have been tracked multiple times. We strongly encourage researchers to evaluate the metadata provided carefully and contact the data owner with inquiries. <strong>Code Availability</strong> All the code written for data processing and NetCDF data import code for MATLAB, R, and Python are available at GitHub (https://github.com/rholser/NES_TrackDive_DataProcessing) and Zenodo (https://doi.org/10.5281/zenodo.12511548). Extensive documentation of functions and scripts is also provided there. In addition, the authors have provided code in Python, R, and MATLAB for basic access to the netCDF files (GitHub link). They should serve as a model to enable users unfamiliar with the format to access the data.
description: # Northern elephant seal tracking and diving – processed data Northern
 elephant seals (*Mirounga angustirostris*) have been integral to the
 development and progress of biologging technology and movement data
 analysis, which in turn continue to improve our understanding of this and
 other species. Adult female elephant seals at Ao Nuevo Reserve and other
 colonies along the west coast of North America were tracked annually from
 2004 to 2020 for a total of 653 instrument deployments and 561 recoveries.
 Here, we describe the compilation and curation of these high-resolution
 diving and location data, which are now publicly available through two
 Dryad repositories. All the processing code and workflow are also publicly
 available through GitHub and Zenodo. This data set represents 3,942,130
 dives and 610,372 locations collected from 475 individual seals with 178
 repeat samplings over 17 years. ## Description of the data and file
 structure This repository consists of netCDF-4 files containing processed
 tracking and diving data. Each file represents a single instrument
 deployment. A detailed index of the data and metadata fields within each
 file can be found in NES_netCDF_README.pdf in the associated article.
 NetCDF files are self-descriptive, so all metadata is included within the
 file. In addition, the repository includes a csv
 (NES_TrackingDiving_MetaData.csv) with all of the high-level metadata
 (animal, deployment, and tag information) from all of the netCDF files
 (for all deployments) to facilitate easier use of the dataset. This
 metadata is identical to the contents of the global attributes of the
 netCDF files. The data processing and the structure of the netCDF files
 are described in detail in the associated data paper, Costa et al. 2023,
 and a full list of variable names and descriptions can be found in the
 paper's Supplemental Information. ### Sampling Bias Generally, we
 have been careful to select presumed healthy animals for sedation and
 instrumentation. For animals deployed at Ao Nuevo (most of the tracks),
 individuals with known site fidelity to the colony were typically
 selected, and if age was known, it was usually restricted to 4 to
 12-year-olds. Furthermore, the data reported here span two decades of
 work. During this time, different studies prompted additional non-random
 population sampling. Examples include focusing on one cohort for a year,
 repeatedly tracking the same individuals (multiple trips in a row or
 across multiple years), and intentionally selecting previously tracked
 females who had used a coastal foraging strategy. Lastly, this data set is
 exclusively adult females. Data collected from other sex and age classes
 indicate some differences in habitat use and movement between these
 demographic groups, so species-wide inferences cannot necessarily be made
 from these data alone. We strongly encourage researchers to evaluate the
 metadata provided carefully and contact the data owner with inquiries. ##
 Sharing/Access information These files contain processed data only. The
 raw data, as well as intermediate processing steps, are also publicly
 available [here](https://doi.org/10.7291/D10D61). ## Code/Software All of
 the code used to process the data is available on
 [GitHub](https://github.com/rholser/NES_TrackDive_DataProcessing) and
 [Zenodo](https://doi.org/10.5281/zenodo.12511548). Diving data were
 processed using custom functions in Matlab, and tracking data were
 processed in R using the `{aniMoum}` package. Software and package
 versions used to process the data are included in the global attributes of
 each file. A full description of data processing can be found in [Costa et
 al., 2024](https://www.nature.com/articles/s41597-024-04084-4). ####
 Required Matlab toolboxes: * `{Statistics and Machine Learning}` *
 `{Mapping}` #### Required R packages: * `{tidyverse}` * `{aniMotum}` *
 `{rgeos}` * `{ggspatial}` * `{naturalearth}` * `{naturalearthdata}` * ```
 {ncdf4} ``` ## Change Log #### 27-Dec-2024 There were no changes to
 processing methods, we corrected the data and metadata contents of a few
 files: * Around a dozen wildlife computer TDR records had been incorrectly
 cut off at the start or end of a trip during manufacturer decoding. These
 were re-decoded and re-processed. * The assignment of records to TDR1 or
 TDR2 changed in one or two cases after this correction. * Kami timestamp
 corrections were reassessed and changed as needed for all records where
 the primary TDR was fixed. * Small changes to metadata (startstop and
 tagmetadata reference files) to correct how a few records were being
 identified, processed, and included in .nc files. (In particular,
 KamiLight instruments were not being identified correctly.) In addition to
 uploading corrected *.nc files, we included an updated
 NES_TrackingDiving_MetaData.csv to reflect those changes. #####
 15-May-2025 There were no changes to processing methods, we corrected the
 data and metadata contents of a few files: * Tracks for a few animals
 required additional erroneous points to be removed and quality rank
 (metadata) changes.  In addition to uploading corrected .nc files, we
 included an updated NES_TrackingDiving_MetaData.csv to reflect those
 changes. In addition, files are now packaged in zipped folders by year for
 more convenient downloading.