cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0159287.10fu
title: SH0159287.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159288.10fu
title: SH0159288.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159289.10fu
title: SH0159289.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159290.10fu
title: SH0159290.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159291.10fu
title: SH0159291.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159292.10fu
title: SH0159292.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159293.10fu
title: SH0159293.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159294.10fu
title: SH0159294.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159295.10fu
title: SH0159295.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0159296.10fu
title: SH0159296.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.cfdyvd
title: Occurrence Download

description: A dataset containing 1241200 records in GBIF matching the query:

 SELECT gbifid, datasetkey, specieskey, kingdom, phylum, class, "order", family, genus, species, scientificname, decimallatitude, decimallongitude, eventdate, institutioncode, "year" AS obs_year, basisofrecord, coordinateuncertaintyinmeters, issue
 FROM occurrence
 WHERE
 decimallatitude IS NOT NULL
 AND decimallongitude IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND coordinateuncertaintyinmeters IS NOT NULL
 AND coordinateuncertaintyinmeters &gt; 0
 AND coordinateuncertaintyinmeters &lt;= 200.0
 AND decimallatitude &gt;= -37.42857426825602
 AND decimallatitude &lt;= -33.06103686093294
 AND decimallongitude &gt;= 16.698349630102356
 AND decimallongitude &lt;= 23.025648717621866
 AND GBIF_Within('POLYGON ((23.025649 -37.428574, 23.025649 -33.061037, 16.698350 -33.061037, 16.698350 -37.428574, 23.025649 -37.428574))', decimallatitude, decimallongitude) = TRUE
 

 The dataset's 1241200 records were derived from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016553-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18506854
title: Test anonymous upload

description: This is a test
DOI: 10.5281/zenodo.18506855
title: Test anonymous upload

description: This is a test
DOI: 10.15468/dl.ttvzr4
title: Occurrence Download

description: A dataset containing 2388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Cenostigma pluviosum"
 ]
}

 The dataset includes 2388 records from 169 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016563-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/ink4kt
title: Replication Data for The Underreported Death Toll of Wars: A Probabilistic Reassessment From a Survey With UCDP Coders

description: # Replication Package for The Underreported Death Toll of Wars: A Probabilistic Reassessment From a Survey With UCDP Coders

This replication package reproduces all main results reported in the paper, including every figure and table in both the main text and the appendix.

## Overview

The full replication can be executed via the shell script: `run_all_replication.sh`

This script runs all required R scripts in the correct order. Alternatively, each part of the analysis can be run independently using the individual R files contained in the repository. The scripts automatically install any required R packages that are not already present on the user's system. All necessary files are located in the .zip-file.

In addition to the scripts and data used to replicate the analysis, we also provide a set of 100 random draws for all events in the UCDP GED dataset (v23.1). These draws were generated using `uncertainUCDP` package, and are stored in the file: `UCDP_GED_v23.1_100draws.csv`. The script used to generate these draws is included in the replication package as: `generate_UCDP_draws.R`. Users interested in generating their own set of draws can run this script independently.

## Runtime and Computational Requirements

Running the full replication takes approximately 12 hours on a Mac M2 Pro (12 cores, 32 GB RAM). The runtime is almost entirely driven by the script: `optimize_and_test_distributions.R`, which performs the optimization and testing of the various probabilistic distributions. This script is parallelized to take advantage of multiple CPU cores. The more cores available, the faster this part of the replication will run. By default, the script will use all available cores minus one. To change this, modify line 21 in `optimize_and_test_distributions.R` that registers the parallel backend. Note: the script is set up to work on Unix-like operating systems (Linux, MacOS). Running on Windows may require additional modifications of the parallelization setup.

Important: `optimize_and_test_distributions.R` only needs to be run once. It saves intermediate result objects to disk, which are then reused by all subsequent scripts. If these objects are already present, the remaining scripts run comparatively quickly.

## Outputs

The replication package produces:
 - 2 data objects
 - 3 result objects
 - 10 figures
 - 10 tables

All outputs correspond exactly to those reported in the main text and appendix of the paper.

## Notes

Users who wish to inspect, modify, or rerun specific components of the analysis can do so by executing the relevant R scripts individually, provided that the required intermediate objects have already been generated.
DOI: 10.15468/dl.e2saaf
title: Occurrence Download

description: A dataset containing 1409 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.52084 -17.60163,-42.92057 -17.60163,-42.92057 5.99578,-75.52084 5.99578,-75.52084 -17.60163))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Boa constrictor"
 ]
}

 The dataset includes 1409 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016564-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/g2ez-zhkr
title: POPs (persistent organic pollutants) at Birkenes II

description: Measurement of POPs (persistent organic pollutants) at Birkenes II
DOI: 10.48597/6p7u-eu2g
title: POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/mrgk-du9u
title: Chlordane at Trollhaugen

description: Measurement of Chlordane at Trollhaugen
DOI: 10.48597/9ptn-2ghn
title: POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/jr94-d7xu
title: POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/kawg-kzcc
title: POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/rq87-22yd
title: POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/zyax-vuxx
title: Chlordane at Trollhaugen

description: Measurement of Chlordane at Trollhaugen
DOI: 10.48597/9cde-rybj
title: Measurement of POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/f2d6-bphw
title: Measurement of POPs (persistent organic pollutants) at Birkenes II

description: Measurement of POPs (persistent organic pollutants) at Birkenes II
DOI: 10.48597/hdjq-gjru
title: Measurement of POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.5285/5a715fd9-aefa-40cc-bbb6-56984b6db554
title: UK Environmental Change Network (ECN) stream water chemistry data: 1992-2012

description: Stream water chemistry data from the UK Environmental Change Network (ECN) terrestrial sites. Variables measured include pH, conductivity, alkalinity, aluminium, calcium, chloride, ammonium, nitrate nitrogen, phosphate phosphorous, potassium, sulphate sulphur, sodium, total nitrogen and total dissolved phosphorous. The data are collected by dip samples at ECN's terrestrial sites (where there is a stream present) using a standard protocol. They represent continuous weekly records from 1992 to 2012. 

The sites at which these data are collected are: Cairngorms, Glensaugh, Moor House-Upper Teesdale, North Wyke, Rothamsted, Sourhope, Wytham and Y Wyddfa (Snowdon).

ECN is the UK's long-term environmental monitoring programme. It is a multi-agency programme sponsored by a consortium of fourteen government departments and agencies. These organisations contribute to the programme through funding either site monitoring and/or network co-ordination activities. These organisations are: Agri-Food and Biosciences Institute, Biotechnology and Biological Sciences Research Council, Cyfoeth Naturiol Cymru - Natural Resources Wales, Defence Science & Technology Laboratory, Department for Environment, Food and Rural Affairs, Environment Agency, Forestry Commission, Llywodraeth Cymru - Welsh Government, Natural England, Natural Environment Research Council, Northern Ireland Environment Agency, Scottish Environment Protection Agency, Scottish Government and Scottish Natural Heritage. 
description: Water chemistry data from the UK Environmental Change Network (ECN) terrestrial sites. These data are collected by dip samples at all of ECN's terrestrial sites (where there is a stream present) using a standard protocol. They represent continuous weekly records from 1992 to 2012. Temporal extent of the dataset represents the earliest date on which data was collected relating to this dataset, and does not necessarily represent the date that all sites included in this dataset initiated data collection. All data collected are managed by the ECN Data Centre at CEH Lancaster according to defined protocols (http://www.ecn.ac.uk/measurements/terrestrial/wc).
DOI: 10.48597/jqgs-y3w6
title: Measurement of POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.48597/qwah-2zda
title: Measurement of POPs (persistent organic pollutants) at Trollhaugen

description: Measurement of POPs (persistent organic pollutants) at Trollhaugen
DOI: 10.5285/4c9613ce-de52-41b1-9fde-7c41f9199686
title: UK Environmental Change Network (ECN) carabid beetle data: 1992-2012

description: Carabid beetle data from the UK Environmental Change Network (ECN) terrestrial sites. The count of individual species is recorded. These data are collected by pitfall traps at all of ECN's terrestrial sites using a standard protocol. They represent continuous fortnightly records from 1992 to 2012. ECN is the UK's long-term environmental monitoring programme. It is a multi-agency programme sponsored by a consortium of fourteen government departments and agencies. These organisations contribute to the programme through funding either site monitoring and/or network co-ordination activities. These organisations are: Agri-Food and Biosciences Institute, Biotechnology and Biological Sciences Research Council, Cyfoeth Naturiol Cymru - Natural Resources Wales, Defence Science & Technology Laboratory, Department for Environment, Food and Rural Affairs, Environment Agency, Forestry Commission, Llywodraeth Cymru - Welsh Government, Natural England, Natural Environment Research Council, Northern Ireland Environment Agency, Scottish Environment Protection Agency, Scottish Government and Scottish Natural Heritage.
description: Data are collected by pitfall traps at all of ECN's terrestrial sites using a standard protocol. Prior to deposit of the data in the EIDC, data are managed by the ECN Data Centre at CEH Lancaster according to defined protocols. 

Verification steps include numeric range checks (i.e. checking if a value falls within a specified range), categorical checks (e.g. checking that a species code appears on the standard code list), formatting (i.e. that the dataset conforms to the specified data format) and logical integrity checks (i.e. checking the data make sense, e.g. that the dates in one dataset match those in a related dataset).

Appropriate range settings for ECN variables have been selected following discussion with specialists in each field. Where data fall outside these ranges, a cautious approach has been adopted towards discarding data on the principle that apparent errors may be valid outliers. Such values are discarded only if there is a clear explanation (e.g. an instrumentation error) and corrections are made where possible. If the reason is unclear, the values are stored, but are qualified using pre-defined quality codes or free-text descriptions. Data providers also use these codes or free text to describe factors affecting sampling outside their control, instrument damage or site management effects.