cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14990254
title: Data and script for the analysis of "The conventional-to-organic yiled gap diminishes with increasing crop pollinator dependence"

description: Goal of the study: To conduct a meta-analysis to test whether the yield gap between conventional and organic agriculture decreases with increasing crop pollinator dependence

Metadata content: Data and R script to reproduce the analyses and the figures shown in the paper

Data

1. dataponisio.csv

This file is the dataset assembled and used in the meta-analysis by Ponisio et al. (2015).  Among several variables, this file provides information on the title of the study (column 6),crop name (column 18), and mean, SDs, and sample sizes (columns 63-68) for estimating effects sizes of yield under conventional and organic agriculture.


2. datagong.csv

This file is the dataset assembled and used in the meta-analysis by Gong et al. (2022). Among several variables, this file provides information on the title of the study (column 3),crop name (column 21), and mean, SDs, and sample sizes (columns 31-36) for estimating effects sizes of yield under conventional and organic agriculture.

3. crops.csv

This file provides information on the common crop name (column 1), crop species name (column 2), pollinator dependence (column 3), harvested organ (column 4), growth form (column 5),  woodiness (column 6),and climatic zone of crop origin (column 7).

4.phylo_crop.tre

File containing the phylogenetic tre


Scripts

1. gap_yield_dep_script

This R script curates and merges the two datasets mentioned above into a single dataset, and runs all the analyzses and constructs all the figures included in the paper.




References

Ponisio LC, M ’gonigle LK, Mace KC, Palomino J, De Valpine P, Kremen C. 2015 Diversification practices reduce organic to conventional yield gap.
 Proc. R. Soc. B Biol. Sci. 282, 20141396. (doi:10.1098/rspb.2014.1396)

Gong S, Hodgson JA, Tscharntke T, Liu Y, van der Werf W, Batáry P, Knops JMH, Zou Y. 2022 Biodiversity and yield trade-offs for organic farming.
  Ecol. Lett. 25, 1699–1710. (doi:10.1111/ele.14017)
DOI: 10.34683/sr281
title: StoneRounds Case: SR281
title: Senior-Loken Syndrome

description: StoneRounds Case SR281 was diagnosed with Senior-Loken Syndrome likely caused by mutations in the gene: IQCB1.
DOI: 10.6084/m9.figshare.27929985
title: Dataset Seasonal variations in planktonic food web structure affect stability by shifting the distribution of energy fluxes

description: This file holds the data and scripts used in the article "Seasonal variations in planktonic food web structure affect stability by shifting the distribution of energy fluxes".The csv files contain data for temperature and biological sampling (dta.csv).<br>In dta : "date" = sampling date, "Tm" = mean body size, "Compartment" = pelagic, benthic or both, "Bodymass" = mean individual body mass, "Biomass" = population biomass.<br>"get_niche_attributes_modified" is a modified function from Vagnon et al. (2021), which uses the Param_reginvert file.<br>"create.jacob" function is a modified function from Gauzens et al. (2019).<br>The R scripts used to analyse the data are scripts with a numerical prefix.Ciliates_traits : the table with the information about the functional traits.
DOI: 10.6084/m9.figshare.27929985.v1
title: Dataset Seasonal variations in planktonic food web structure affect stability by shifting the distribution of energy fluxes

description: This file holds the data and scripts used in the article "Seasonal variations in planktonic food web structure affect stability by shifting the distribution of energy fluxes".The csv files contain data for temperature and biological sampling (dta.csv).<br>In dta : "date" = sampling date, "Tm" = mean body size, "Compartment" = pelagic, benthic or both, "Bodymass" = mean individual body mass, "Biomass" = population biomass.<br>"get_niche_attributes_modified" is a modified function from Vagnon et al. (2021), which uses the Param_reginvert file.<br>"create.jacob" function is a modified function from Gauzens et al. (2019).<br>The R scripts used to analyse the data are scripts with a numerical prefix.Ciliates_traits : the table with the information about the functional traits.
DOI: 10.5281/zenodo.15025578
title: Benchmarking of T-Cell Receptor - Epitope Predictors with ePytope-TCR --- Processed benchmark data

description: This dataset contains the processed benchmark data for our publication:

"Benchmarking of T-Cell Receptor - Epitope Predictors with ePytope-TCR" Drost et al. https://www.biorxiv.org/content/10.1101/2024.11.06.622261v1
DOI: 10.5281/zenodo.15025579
title: Benchmarking of T-Cell Receptor - Epitope Predictors with ePytope-TCR --- Processed benchmark data

description: This dataset contains the processed benchmark data for our publication:

"Benchmarking of T-Cell Receptor - Epitope Predictors with ePytope-TCR" Drost et al. https://www.biorxiv.org/content/10.1101/2024.11.06.622261v1
DOI: 10.15468/dl.n7q8x6
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neolochmaea dilatipennis (Jacoby, 1886)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 290 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008780-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds006010.v1.0.0
title: POGS_fMRI
DOI: 10.15468/dl.ttrjd6
title: Occurrence Download

description: A dataset containing 13849 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.829 43.204,-79.804 43.204,-79.804 43.222,-79.829 43.222,-79.829 43.204))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 13849 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008782-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fm5m5n
title: Occurrence Download

description: A dataset containing 4916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Parodia Speg."
 ]
}

 The dataset includes 4916 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008783-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h5s9jw
title: Occurrence Download

description: A dataset containing 32776639 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal)",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Year 2017-2025"
 ]
}

 The dataset includes 32776639 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008774-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15025571
title: GCB-B-RA-25-006.R2 - Harvest time optimization for biomass productivity and combustion quality of tall wheatgrass in a semi-arid Mediterranean environment
DOI: 10.5281/zenodo.15025572
title: GCB-B-RA-25-006.R2 - Harvest time optimization for biomass productivity and combustion quality of tall wheatgrass in a semi-arid Mediterranean environment
DOI: 10.15468/dl.c8banx
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Bolivia (Plurinational State of)",
 "TaxonKey is Porzana flaviventer (Boddaert, 1783)"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075833-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jht69q
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "ScientificName" : [
 "is Sylviparus modestus"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138758-200613084148143/datasets/export for details.
DOI: 10.15468/dl.kkaxon
title: Occurrence Download

description: A dataset containing 10357 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eschscholzia californica Cham.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 10357 records from 206 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050576-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.766d4b
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pseudodiaptomus inopinus Burckhardt, 1913)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 91 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043536-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vz82r9
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Archidendron forbesii Baker f."
 ]
}

 The dataset includes 11 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014743-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4zks9k
title: Occurrence Download

description: A dataset containing 296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Etlingera elatior (Jack) R.M.Sm.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 296 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050577-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rhh8d9
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carabus ishizukai Deuve & Ohshima, 1989"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0136078-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7rakf6
title: Occurrence Download

description: A dataset containing 946 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Archidendron grandiflorum (Benth.) I.C.Nielsen"
 ]
}

 The dataset includes 946 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014762-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xmvg97
title: Occurrence Download

description: A dataset containing 1262 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Undaria pinnatifida (Harv.) Suringar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1262 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0142116-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e0aibb
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Etlingera cevuga (Seem.) R.M.Sm.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050578-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qjwgan
title: Occurrence Download

description: A dataset containing 3864 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "Geometry POLYGON((-136.30885 49.06013,-79.34167 40.45554,-59.67787 40.01162,-47.24341 49.06013,-59.12476 63.50944,-59.13948 68.83363,-64.88299 71.18706,-136.30885 73.72734,-141.02828 71.87104,-142.24627 55.09037,-136.30885 49.06013))",
 "HasGeospatialIssue is false",
 "TaxonKey is Bdellidae"
 ]
}

 The dataset includes 3864 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075816-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7a6t2
title: Occurrence Download

description: A dataset containing 225567 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Norwegian Species Observation Service",
 "Geometry POLYGON((10.0261 68.01413,17.41284 66.69991,32.39537 70.31686,25.70549 72.08943,10.0261 68.01413))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 225567 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103572-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x77cz7
title: Occurrence Download

description: A dataset containing 228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eucalyptus pellita F.Muell.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 228 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050579-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8exwvn
title: Occurrence Download

description: A dataset containing 142 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 "Country is Portugal",
 {
 "or" : [
 "DatasetKey is Flora-On: occurrence data of the flora of mainland Portugal",
 "DatasetKey is iNaturalist Research-grade Observations",
 "DatasetKey is Biodiversity4all Research-Grade Observations",
 "DatasetKey is Pl@ntNet automatically identified occurrences",
 "DatasetKey is Observation.org, Nature data from around the World",
 "DatasetKey is CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España",
 "DatasetKey is naturgucker"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Lutra lutra (Linnaeus, 1758)"
 ]
}

 The dataset includes 142 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093886-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.la1mep
title: Occurrence Download

description: A dataset containing 539 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Columba junoniae Hartert, 1916"
 ]
}

 The dataset includes 539 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050579-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hex899
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viola ×orophila Wiesb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 36 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075840-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.338gxb
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Aureliana fasciculata (Vell.) Sendtn."
 ]
}

 The dataset includes 32 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103538-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yfpveg
title: Occurrence Download

description: A dataset containing 716 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eucalyptus alba Reinw. ex Blume",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 716 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050582-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6443e9
title: Occurrence Download

description: A dataset containing 2479712 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "Geometry POLYGON((4.7603 51.89921,5.67601 51.89921,5.67601 52.50057,4.7603 52.50057,4.7603 51.89921))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 2479712 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0112566-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g27b67
title: Occurrence Download

description: A dataset containing 8419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-1.18163 40.21867,5.84962 40.21867,5.84962 43.03117,-1.18163 43.03117,-1.18163 40.21867))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio inaequidens DC."
 ]
}

 The dataset includes 8419 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075832-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvntri
title: Occurrence Download

description: A dataset containing 377 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "TaxonKey is Rhincodontidae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 377 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050585-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wdx42e
title: Occurrence Download

description: A dataset containing 339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Michelia maudiae Dunn",
 "HasCoordinate is true"
 ]
}

 The dataset includes 339 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0142135-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1fslgy
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aeonium hierrense (R.P.Murray) Pit. & Proust",
 "BasisOfRecord is Unknown evidence"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001088-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/independent-c69-18219
title: Correspondence, 1991 Feb.-May

description: Correspondence, 1991 February - May 9. PART OF A SERIES: Materials in the series fall into one of several categories related to the Independent Commission's work product: (1) Commission meeting materials, which include meeting agendas, work plans, memoranda, and articles about police misconduct that were circulated and reviewed during the Commission's internal meetings; (2) public correspondence, which includes citizen complaints against the LAPD in the form of written testimony, articles, and an audio cassette tape, as well as letters drafted by citizens in support of the LAPD; (3) summaries of interviews held with LAPD officers regarding Departmental procedures and relations; (4) public meeting materials, which include transcripts, supplementary documents, and witness statements that were reviewed at the Commission's public meetings; (5) press releases related to the formation and work product of the Commission; and (6) miscellaneous materials reviewed by the Commission during its study, including LAPD personnel and training manuals, a memorandum of understanding, and messages from the LAPD's Mobile Digital Terminal (MDT) system.
DOI: 10.15468/dl.zr3j64
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clematis tsaii W.T.Wang"
 ]
}

 The dataset includes 35 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008454-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/independent-c69-13680
title: Holliday working papers, volume III: Excessive force, improper tactics, sexual, discrimination and discourtesy complaints, 1991-04-25

description: Thomas E. Holliday working papers, volume III: Excessive force, improper tactics, sexual, discrimination and discourtesy complaints, 1991 April 25. Includes summary of Discourtesy allegations sustained. PART OF A SERIES: The staff of Gibson, Dunn & Crutcher coordinated witness interviews and conducted an extensive review of complaints filed against LAPD officers. Included in the series are summaries of witness interviews, statistics and investigative reports related to citizen complaints, an analysis on adjudicated cases involving use-of-force complaints, reports regarding LAPD's recruitment of African American officers and community oriented policing, and an excerpt from Malcolm Sparrow's Beyond 9-1-1. Also included are materials related to the firm's work product, including attorney notes, work plans, memoranda, and drafts of chapters for the Commission report.
DOI: 10.25549/independent-c69-13427
title: Los Angeles Sheriff's Department (training experts), 1991-05-28

description: Brad Seiling (Manatt, Phelps & Phillips), memorandum, 1991 May 28, to Independent Commission witness file (cc: John Spiegel, Louise LaMothe, Tom Holliday, David Huebner), re Interview with Los Angeles Sheriff's Department training experts. PART OF A SERIES: The staff of Gibson, Dunn & Crutcher coordinated witness interviews and conducted an extensive review of complaints filed against LAPD officers. Included in the series are summaries of witness interviews, statistics and investigative reports related to citizen complaints, an analysis on adjudicated cases involving use-of-force complaints, reports regarding LAPD's recruitment of African American officers and community oriented policing, and an excerpt from Malcolm Sparrow's Beyond 9-1-1. Also included are materials related to the firm's work product, including attorney notes, work plans, memoranda, and drafts of chapters for the Commission report.