A GIST to show how to cite Neotoma datasets, including DOIs, when dataset IDs have been provided.

cite_neotoma_datasets.R

# Pollen records citation script:
# By: Simon J. Goring
# April 29, 2024
#
# The file "pollen_counts_europe.csv" is part of the PANGEA Package
# associated with LegacyPollen v1.0 (https://doi.org/10.1594/PANGAEA.929773)
# While it is possible to write a script that pulls each zip file down using
# the DOI, here we assume an individual file is directly available in the
# working directory.
# Note that while the files in the PANGEA repository are identified using the
# `csv` extension, it appears that they are tab separated files (thus the use
# of the `read_tsv()` function from `readr`.

library(neotoma2)
library(dplyr)
library(readr)

poll <- readr::read_tsv('pollen_counts_europe.csv') %>%
    dplyr::filter(Data_Source == 'Neotoma') %>%
    dplyr::select(Dataset_ID) %>%
    dplyr::distinct() %>%
    unlist()

# Note that by default the `neotoma2` R package returns only
# 25 records, to avoid overloading either the user's memory,
# or the Neotoma API. Using the `all_data = TRUE` flag returns
# the full query set.
datasets <- neotoma2::get_datasets(poll, all_data = TRUE)

# This command prints all DOIs and a partial data citation for each
# dataset returned in the `datasets` list.
neotoma2::doi(datasets)

LICENSE.txt

Copyright 2024, Simon James Goring

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