cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26117323
title: supporting_data_pesob5_240617.xlsx

description: The dataset contains data on saproxylic beetles collected across various sites in Western Palaearctic oak forests. The data is organized in different sheets, with data3 being one of the primary sheets. This sheet includes information on trophic groups, species presence and absence, site details, trapping methods, geographic coordinates, sampling personnel, and beetle body lengths.
DOI: 10.6084/m9.figshare.26117323.v1
title: supporting_data_pesob5_240617.xlsx

description: The dataset contains data on saproxylic beetles collected across various sites in Western Palaearctic oak forests. The data is organized in different sheets, with data3 being one of the primary sheets. This sheet includes information on trophic groups, species presence and absence, site details, trapping methods, geographic coordinates, sampling personnel, and beetle body lengths.
DOI: 10.25574/01336
title: Chandra X-ray Observatory ObsId 01336
DOI: 10.25574/01354
title: Chandra X-ray Observatory ObsId 01354
DOI: 10.15468/dl.hbhntp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepomis gibbosus",
 "Country is Venezuela (Bolivarian Republic of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022115-250711103210423/datasets/export for details.
DOI: 10.15468/dl.qxy69b
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Setaria adhaerens vertillata, Setaria ambigua, Setaria ambigua major, Setaria ambigua ramiflora, Setaria ambigua schulteissii, Setaria ambigua schulteissii, Setaria ambigua major, Setaria ambigua ramiflora, Setaria ambigua latifolia, Setaria ambigua major)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022117-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q6rpjw
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hordeum murinum",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 208 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022118-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14415142
title: Analysis Code and benchmark data processing code for the publication Demography, Dynamics and Data: Growing Confidence for Simulating Changes in the World's Forests

description: Code related to the publication Eckes-Shephard et al 2025

The code contains analysis code for the publication and processing code for the benchmark data used in the publication. The processed benchmark observations are also deposited as .csv in folder /observations/2_processed.

/model_outputs:



contains all model outputs used in this publication, usually as .nc file, mostly in "D-BEN" format*. The subfolder structure can vary, but is kept to conform with the functions in DBEN-helper_functions_clean.R


/observations: 

      /1_raw/README: 



contains the referenes to the dataset origins that were used by Process_observations.R, to create benchmarking files into /2_processed


     /1_raw/temperature_data:



contains scripts and data used for mean - temperature analysis (in supplementary materials)


    /2_processed: 



benchmarking observations created by Process_observations.R


/scripts (download from github):



Eckes-Shephard_et_al2025.Rmd: Analysis script that creates the Figures and Supplementary figures for the publication Eckes-Shephard. et al2025.

DBEN_helper_functions.R: set of demographic-benchmarking-analysis specific functions that is used by Eckes-Shephard_et_al2025.R.

Process_observations.R: Script that creates the benchmark files (in 2_processed) used in Eckes-Shephard_et_al2025.R

Format_DBEN_Eckes-Shephard_et_al2025.R:  a Format, quantity, and layer definition of D-BEN outputs to be compatible for managing outputs and data in DGVM-Tools format.  For mort information, see https://github.com/MagicForrest/DGVMTools. Note that this Format is not the same as the D-BEN data-format described below.


*D-BEN format:

From the informal demographic benchmarking initiative, where the format has been discussed with members of the demographic vegetation modelling community. the format is not settled yet, but the table S3.1 in the simulation protocol reflects (Supplementary notes S1) the version that modellers tried to adhere to for this analysis.

 

Get started:



checkout the github repository https://github.com/teatree1212/DBEN_Eckes_Shephard_et_al; https://zenodo.org/records/15870478

into the git repository, download and unzip model_outputs.zip and observations.zip from this zenodo repository.

inside folder "scripts", render the file Eckes-Shephard_et_al2025.Rmd by doing Rscript -e "rmarkdown::render('Eckes-Shephard_et_al2025.Rmd')"
DOI: 10.5281/zenodo.14415143
title: Analysis Code and benchmark data processing code for the publication Demography, Dynamics and Data: Growing Confidence for Simulating Changes in the World's Forests

description: Code related to the publication Eckes-Shephard et al 2025

The code contains analysis code for the publication and processing code for the benchmark data used in the publication. The processed benchmark observations are also deposited as .csv in folder /observations/2_processed.

/model_outputs:



contains all model outputs used in this publication, usually as .nc file, mostly in "D-BEN" format*. The subfolder structure can vary, but is kept to conform with the functions in DBEN-helper_functions_clean.R


/observations: 

      /1_raw/README: 



contains the referenes to the dataset origins that were used by Process_observations.R, to create benchmarking files into /2_processed


     /1_raw/temperature_data:



contains scripts and data used for mean - temperature analysis (in supplementary materials)


    /2_processed: 



benchmarking observations created by Process_observations.R


/scripts (download from github):



Eckes-Shephard_et_al2025.Rmd: Analysis script that creates the Figures and Supplementary figures for the publication Eckes-Shephard. et al2025.

DBEN_helper_functions.R: set of demographic-benchmarking-analysis specific functions that is used by Eckes-Shephard_et_al2025.R.

Process_observations.R: Script that creates the benchmark files (in 2_processed) used in Eckes-Shephard_et_al2025.R

Format_DBEN_Eckes-Shephard_et_al2025.R:  a Format, quantity, and layer definition of D-BEN outputs to be compatible for managing outputs and data in DGVM-Tools format.  For mort information, see https://github.com/MagicForrest/DGVMTools. Note that this Format is not the same as the D-BEN data-format described below.


*D-BEN format:

From the informal demographic benchmarking initiative, where the format has been discussed with members of the demographic vegetation modelling community. the format is not settled yet, but the table S3.1 in the simulation protocol reflects (Supplementary notes S1) the version that modellers tried to adhere to for this analysis.

 

Get started:



checkout the github repository https://github.com/teatree1212/DBEN_Eckes_Shephard_et_al; https://zenodo.org/records/15870478

into the git repository, download and unzip model_outputs.zip and observations.zip from this zenodo repository.

inside folder "scripts", render the file Eckes-Shephard_et_al2025.Rmd by doing Rscript -e "rmarkdown::render('Eckes-Shephard_et_al2025.Rmd')"
DOI: 10.15468/dl.vfp8sq
title: Occurrence Download

description: A dataset containing 8504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Jatropha curcas, Jatropha curcas, Jatropha curcas)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8504 records from 321 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022119-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5xcbsw
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AEU5285"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022120-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqevkx
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phalera torpida"
 ]
}

 The dataset includes 24 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022121-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bgrajh
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Setaria aspera, Setaria aspera, Setaria carnei, Setaria conglomerata, Setaria conglomerata, Setaria decipiens, Setaria decipiens, Setaria decipiens, Setaria decipiens, Setaria decipiens)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 35 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022122-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.um4dag
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hordeum murinum",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 431 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022124-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7kfkps
title: Occurrence Download

description: A dataset containing 394 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tropaeolum polyphyllum"
 ]
}

 The dataset includes 394 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022123-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jke3pm
title: Occurrence Download

description: A dataset containing 104983 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coronella austriaca, Rana dalmatina, Podarcis muralis, Rana arvalis, Bufo calamita, Pelobates fuscus, Rana dalmatina, Epidalea calamita, Bombina variegata, Triturus cristatus, Coronella austriaca, Hyla arborea, Lacerta agilis, Bufotes viridis, Pelophylax lessonae)",
 "Year is one of (2020, 2021, 2022, 2023, 2024)",
 "DecimalLatitude is greater than or equal to 47.53364139636112",
 "DecimalLatitude is less than or equal to 54.8769089978912",
 "DecimalLongitude is greater than or equal to 6.033629",
 "DecimalLongitude is less than or equal to 15.037743",
 "Year is not null",
 "HasCoordinate is TRUE",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 104983 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022105-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zsydzp
title: Occurrence Download

description: A dataset containing 779944 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coronella austriaca, Rana dalmatina, Podarcis muralis, Rana arvalis, Bufo calamita, Pelobates fuscus, Rana dalmatina, Epidalea calamita, Bombina variegata, Triturus cristatus, Coronella austriaca, Hyla arborea, Lacerta agilis, Bufotes viridis, Pelophylax lessonae)",
 "Year is one of (2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024)",
 "DecimalLatitude is greater than or equal to 44.95782311925129",
 "DecimalLatitude is less than or equal to 58.30331634439415",
 "DecimalLongitude is greater than or equal to -10.001896207643075",
 "DecimalLongitude is less than or equal to 30.31691447027875",
 "Year is not null",
 "HasCoordinate is TRUE",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 779944 records from 3206 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022104-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmktdl
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011008-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jstexw
title: Occurrence Download

description: A dataset containing 20459864 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 20459864 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079679-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5hawj
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015451-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wuzp3i
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010997-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hq2c7j
title: Occurrence Download

description: A dataset containing 1465563854 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aves"
 ]
}

 The dataset includes 1465563854 records from 10463 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098411-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/sey-vbb-a4z
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9qv-hyw-azv
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jh6-7gb-20y
title: Hamites

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6h7-thx-ml0
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ejf-laz-49h
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c14-qhr-ej1
title: Sorites orbiculus (Forsskål in Niebuhr, 1775)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/py2-t2g-7sg
title: Haplophragmoides canariensis (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4rz-21z-tm3
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kjs-n3e-r0n
title: Olcostephanus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jw2-ppz-4cz
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y61-dhb-dk8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xbr-4la-fkz
title: Asterorotalia pulchella (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/28z-2wx-saf
title: Quinqueloculina bicostata d'Orbigny, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ftf-qtg-6dq
title: Hibolithes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/azv-6q7-gw5
title: †Lenticulina subalata (Reuss, 1854)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2b3-gn8-map
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6qv-cx8-ltc
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cg9-v4a-a3l
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wxs-cjd-zaz
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r86-2be-e2e
title: †Uvigerina acuminata Hosius, 1895

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vwk-0ba-v39
title: †Glandulina surinamensis Hofker, 1983

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4h7-kl0-qdj
title: Hibolithes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2b1-3es-zq9
title: Ammoglobigerina globigeriniformis (Parker & Jones, 1865)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k3t-q4z-0ey
title: Siphonaperta arenata (Said, 1949)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1pt-ggy-jnq
title: Triloculina oblonga (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/trn-0ch-ydp
title: Calcarina hispida Brady, 1876

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kza-0jm-g11
title: Pseudonodosinella elongata (Grzybowski, 1898)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yv9-jxl-8pz
title: Lenticulina antillea (Cushman, 1923)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/96m-ggd-3nv
title: Fursenkoina schreibersiana (Cžjžek, 1848)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t24-439-b6z
title: Pseudobelus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/21f-g62-z2q
title: Ammotium inflatum (Shchedrina, 1946)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/al1-9ye-53c
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7pn-4kv-dxk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hs8-rjs-zss
title: Bolivina lanceolata Parker, 1954

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ts2-3aa-h8t
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.29839472
title: Rhytidhysteron alignment files

description: Additions of new host records of <i>Rhytidhysteron</i> associated with <i>Tetradium ruticarpum</i> in southeastern China and taxonomic revisions
DOI: 10.6084/m9.figshare.29839472.v1
title: Rhytidhysteron alignment files

description: Additions of new host records of <i>Rhytidhysteron</i> associated with <i>Tetradium ruticarpum</i> in southeastern China and taxonomic revisions
DOI: 10.15468/dl.3vn79e
title: Occurrence Download

description: A dataset containing 404658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Agrilus planipennis, Anoplophora glabripennis, Enaphalodes rufulus, Saperda candida, Tetropium gracilicorne, Xylotrechus namanganensis, Rhyzobius lophanthae, Hylobitelus xiaoi, Megaplatypus mutatus, Platypus quercivorus, Polygraphus proximus, Xylosandrus crassiusculus, Xylosandrus germanus, Xylosandrus mutilatus, Hermetia illucens, Ceratitis capitata, Toumeyella parvicornis, Icerya purchasi, Corythucha arcuata, Bombus impatiens, Dryocosmus kuriphilus, Brachyponera chinensis, Linepithema humile, Pheidole megacephala, Solenopsis invicta, Solenopsis richteri, Tapinoma melanocephalum, Wasmannia auropunctata, Megachile sculpturalis, Trissolcus japonicus, Sirex ermak, Vespa mandarinia, Argyresthia cupressella, Hyphantria cunea, Lymantria mathura, Dendrolimus sibiricus, Dendrolimus superans, Sagittaria platyphylla, Spirodela punctata, Paederia foetida, Ludwigia kentiana, Humulus scandens, Ampelopsis glandulosa, Salvinia minima, Salvinia molesta)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year is not null",
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 404658 records from 546 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013008-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.