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. Repo contents and structure are described below.
These data are in the process of being published to the SCAR Antarctic Biodiversity Portal at biodiversity.aq.
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).
The data directory contains SSAFS pup census input data files, the full, standardized data set, and the Darwin Core Archive files.
SSAFS Pup Census Darwin Core Archive files. These data are published at
ssafs-pup-counts-full.csv is the full SSAFS Pup Census dataset, presented as a long data CSV file. This file contains four columns:
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).
location: the location of the census. SSI means South Shetland Islands, STI means San Telmo Islets, and CS means Cape Shirreff.
count, sd: The census count and standard deviation values, respectively. Standard deviation values only exist when all individual observer census counts are available.
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 Islets counts, respectively.
Input files used by create-ssafs-pup_census.R to create the full SSAFS Pup Census data set. Specifically:
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.
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.
All code for this project can be found in the R directory.
This project uses renv to manage the project environment. Users can clone this repo and run renv::restore() as described in the renv docs.
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