South Shetland Antarctic fur seal (SSAFS) total synoptic pup counts. This repository is an R project that contains the data, code, and documentation relevant to the SSAFS pup census data set. This project uses renv to manage the project environment. Users can clone this repo and run renv::restore() as described in the renv docs. Repo contents and structure are described below.
As shown in the badging, the repository is linked to Zenodo and generates a Zenodo DOI on each release. However, we ask users of these data to instead cite the OBIS/GBIF dataset. This dataset has been published to the SCAR Antarctic Biodiversity Portal at biodiversity.aq, and is reliably available via the following links: https://doi.org/10.15468/kngcq4, or https://ipt-obis.gbif.us/resource?r=usamlr-ssafs-pup-census
An earlier version of this data set was published in Krause et al. 2022. See this manuscript for additional descriptions of or references to methods, other context, etc.
Meeting notes and decisions can be found here (project authors only).
This project uses renv to manage the project environment. Users can clone this repo and run renv::restore() as described in the renv docs.
├── data
├── dwca : Darwin Core Archive tables; presented in the manuscript
├── input : standardized CSV files; referenced in the manuscript
├── ssafs-pup-counts-full.csv : described below
├── R
├── data-to-dwca.R : generating DwCA tables for publication at biodiversity.aq
├── create-ssafs-pup-census-full.R : create full SSAFS pup copunt data set
├── plot.R : standard AMLR plot of the full SSAFS pup count data set
├── references : downloaded reference files
├── renv : renv files, for managing renv environment
The data directory contains SSAFS pup census input data files, the full and standardized data set, and the Darwin Core Archive files.
SSAFS Pup Census Darwin Core Archive files. These data are published at . These files were generated using data-to-dwca.R.
ssafs-pup-counts-full.csv is the full SSAFS Pup Census data set, presented as a long data CSV file. It is created by create-ssafs-pup-census-full.R. This file contains the following columns:
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season_name: the season of the census. For instance, "2022/23" means the census happened during the 2022-2023 austral summer (late December or early January).
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location: the location of the census. SSI means South Shetland Islands, STI means San Telmo Island, and CS means Cape Shirreff.
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count, sd: The census count and standard deviation values, respectively. Standard deviation values only exist when all individual observer census counts are available.
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reference: The reference in which the census count was originally published, as applicable. All records without a reference were collected by the U.S. AMLR Program, following sampling protocols described in Krause et al. 2022 or Krause and Hinke 2021 for Cape Shirreff and San Telmo Island counts, respectively.
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season_year: The 'AMLR year' of the austral summer field season. The AMLR year is the year that begins in January. For instance, for the '2000/01' season, the AMLR year is '2001.
Input files used by create-ssafs-pup-census-full.R to create the full SSAFS Pup Census data set. Specifically:
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supptable1-counts.csv contains the counts from Krause et al. 2022 Supplementary Table 1, copied as long data into a CSV file. supptable1-references.csv is the reference key for the letter-reference pairs presented in Supplementary Table 1. The data in these CSV files can be joined using the 'ReferenceLetter' column.
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other-counts.csv contains other SSAFS pup census counts. Here, 'other counts' means counts that are not a) presented in Krause et al. 2022 Supplementary Table 1, or b) of SSAFS at Cape Shirreff recorded in the U.S. AMLR Pinnipeds database.
This section contains notes for U.S. AMLR staff using this repository to update and publish the SSAFS Pup Census tables, e.g. after a field season.
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If necessary, add any new STI or SSI counts to other-counts.csv. Any new CS counts will be pulled from the the pinniped database
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Run the create-ssafs-pup-census-full.R script. This writes a new ssafs-pup-counts-full.csv file to the 'data' folder
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Restart R (optional, but recommended). Run the data_to_dwca.R script. This writes new Darwin Core Archive tables to the 'data/dwca' folder
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Push changes to GitHub. Create a new tag + release so a new Zenodo DOI is made.
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Email the SCAR Biodiversity Portal folks to scrape and publish updated files from https://github.com/us-amlr/ssafs-pup-census/tree/main/data/dwca
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