This repository is an R project that contains the data, code, figures, and documentation relevant to the Cape Shirreff PHOcid Census (CS-PHOC) dataset and data paper. Repo contents and structure are described below.
This project uses renv to manage the project environment. Users can clone this repo and run renv::restore() as described in the renv docs.
The paper describing the CS-PHOC dataset can be obtained here, and is cited as (preferred):
Woodman, S.M., Borras-Chavez, R., Goebel, M.E., Torres, D., Aguayo, A., Krause, D.J. CS-PHOC: weekly census counts of Southern Ocean phocids at Cape Shirreff, Livingston Island. Sci Data 11, 895 (2024). https://doi.org/10.1038/s41597-024-03744-9
Code to generate figures from the manuscript can be found in R/manuscript_figures.R.
If using the data, please cite the dataset (https://doi.org/10.48361/gklk1u) and the manuscript (https://doi.org/10.1038/s41597-024-03744-9) as appropriate. The Zenodo link is the version of this repo that was part of the manuscript peer review. Interested parties can access the CS-PHOC dataset in two ways:
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Access Darwin Core Archive event and occurrence tables published through the SCAR Antarctic Biodiversity Portal at https://ipt-obis.gbif.us/resource?r=usamlr_cs-phoc (recommended)
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Download the events and counts CSV files included in this repo: cs-phoc-events.csv and cs-phoc-counts.csv. If using these files, be sure to read the CSV file readme.
Examples of loading and using CS-PHOC data can be found in the R/cs-phoc_examples. R, as well as the code used to generate the figures for the manuscript. For any questions, please contact sam.woodman@noaa.gov.
Darwin Core Archive (DwCA) tables have specific data and metadata standards and requirements. Thus, there are several formatting differences for the CS-PHOC dataset presented as DwCA tables through the SCAR Antarctic Biodiversity Portal, relative to this dataset presented as CSV files in this repo:
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When using Darwin Core terms, all location information is captured at the Event level. This is in contrast to the CS-PHOC CSV files, where the location information is part of the counts CSV file. To meet DwCA requirements, we created different events for surveys of the Core census locations (CCLs) and Punta San Telmo (PST). Specifically, for the DwCA event table, events for counts for the CCLs have a "-1" suffix, while events for counts for the PST location have a "-2". For instance, for event_id 1 where both locations were surveyed, in the DwCA event table there are two events with unique eventIDs: 1-1 and 1-2. For survey windows where only the CCLs were surveyed, such as event_id 1, there is only one event (as with eventID 186-1).
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For the the Darwin Core standard, count data are referred to and recorded as occurrence records. To be Darwin Core-compliant, occurrence data needs to both be long (i.e., one count per record) and have unique occurrenceID values. The counts CSV file is wide, meaning there are different columns (rather than rows) for counts of different sexes/age classes, and thus needed to be made long. This was done using pivot_longer. To generate unique occurrenceID values after making the count data long, we appended two "-#" codes to the count_id values: one for age class and one for sex. For the age class code: adult=1, juvenile=2, pup=3, and unknown=4. For the pup code, female=1, male=2, and unknown=3. For example, for the DwCA record for the juvenile female count of 1 from the record with count_id=102-1-195932, the occurrenceID is "102-1-195932-2-1" (i.e., count_id-{age class coide}-{sex code}).
Other notes for the DwCA tables:
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As of writing, the sex value "Unknown" (or "Indeterminate", see here) is not picked up when the data is published. Thus, in the DwCA data counts the sex for animals recorded as "Unknown" are listed as "NA".
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As of writing, the age class (i.e., lifeStage) value "Pup" is not yet recognized by GBIF. See this issue for more details, and to track when this information may be included in the DwCA tables. Until this issue is resolved, the value for lifeStage will be "NA"" in the DwCA CS-PHOC tables for records where the lifeStage (i.e., age class) was either "pup" or "Unknown". Users interested in this level of detail will need to refer to the data presented in the CSV files.
├── R
├── data_to_dwca.R : generating DwCA tables for publication at biodiversity.aq
├── import_*.R : importing files from 'data/pre' into the AMLR Pinnipeds database
├── cs-phoc_examples.R: example code for using the CS-PHOC dataset
├── manuscript_*.R : generating CS-PHOC dataset, and manuscript figures
├── smw_qc.R : early and ad-hoc CS-PHOC census data qc and explorations
├── data
├── dwca : Darwin Core Archive tables; presented in the manuscript
├── manuscript: standardized CSV files; referenced in the manuscript
├── pre : historical data files; now imported into the database
├── figures : figures and table; included in the manuscript
├── other : exploratory plots
├── renv : renv files, for managing renv environment
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