cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28783709.v1
title: <b><i>Simulation study comparing length of time series</i></b>

description: This repository contains all the scripts and data used in the simulation study titled <i>“Simulation study comparing length of time series”, </i>presented in the manuscript <i>“Longer time series with missing data improve parameter estimation in State-Space mode in coral reef fish communities”</i>. There are 108 files in total.All model fits were run on the HPC cluster at James Cook University. Depending on the simulated dataset, run times ranged from several hours up to 1-2 days per fit.<b>Simulated data</b><b>multisp_sim_dat.R</b>: Simulates communities of 20 species across 41 reefs. We used this script to generate 20 simulated communities, which were saved as <b>sim_s1.RData</b> through <b>sim_s20.RData</b>.<b>Model fitting to simulated data</b><b>fit_11y.R</b>: Script to implement the <i>Short fit</i> from the manuscript. For each simulated dataset it: 1) saves posterior model parameters, 2) computes diagnostics (divergent transitions, tree depth saturation, E-BFMI), and 3) generates effective sample size (ESS) and R-hat plots. Example output: input simulated dataset <b>sim_s1.RData </b>and the output <b>fit_11y_s1.RData. </b>We include all fit output files up to <b>fit_11y_s20.RData</b>. We did not include the diagnostics figures in this repository, but users can get them by running the code.<b>fit_18y.R</b>: Script to implement the <i>Intermediate fit</i> from the main text. It follows the same process as above. Output files range from <b>fit_18y_s1.RData </b>up to<b> fit_18y_s20.RData</b><b>fit_25yNA.R</b>: Script to implement the <i>Missing-data fit</i> from the main text. It follows the same process as above. Output files range from <b>fit_25yNA_s1.RData </b>up to<b> fit_25yNA_s20.RData</b><b>fit_25yc.R</b>: Script to implement the <i>Full fit</i> from the main text. It follows the same process as above. Output files range from <b>fit_25yc_s1.RData </b>up to<b> fit_25yc_s20.RData</b><b>Stan model</b><b>MARPLN_LV.stan</b>: Stan code for the multivariate autoregressive Poisson-Lognormal model with the latent variables. This model is used in the files <b>fit_11y.R</b>,<b> fit_18y.R</b> and <b>fit_25yc.R</b><b>MARPLN_LV_withNA.stan</b>: Same as the model above, but it can also handle missing data. This model is used in the file<b> fit_25yNA.R.</b><b>Figure and analysis script</b><b>Figure 2.R</b>: This script calculates the accuracy and precision estimates for all key parameters across simulations and generates Figure 2 from the manuscript.<br>
DOI: 10.6084/m9.figshare.28774304
title: <b><i>Simulation study comparing number of sampled reefs</i></b>

description: This repository contains all the scripts and data used in the simulation study titled <i>“Simulation study comparing number of sampled reefs”, </i>presented in the manuscript <i>“Longer time series with missing data improve parameter estimation in State-Space mode in coral reef fish communities”</i>. There are 66 files in total.All model fits were run on the HPC cluster at James Cook University. Depending on the simulated dataset, run times ranged from several hours up to 1-2 days per fit.<b>Simulated data</b><b>multisp_sim_dat_reefs.R</b>: Simulates communities of 20 species across 40 reefs. We used this script to generate 20 simulated communities, which were saved as <b>sim_40vs20_s1.RData</b> through <b>sim_40vs20_s20.RData</b>.<b>Model fitting to simulated data</b><b>fit_20reefs.R</b>: Script to implement the <i>20 reefs fit</i> from the manuscript. For each simulated dataset, it: 1) saves posterior model parameters, 2) computes diagnostics (divergent transitions, tree depth saturation, E-BFMI), and 3) generates effective sample size (ESS) and R-hat plots. Example output: input simulated dataset <b>sim_40vs20_s1.RData </b>and the output <b>fit_20r_s1.RData</b>. We include all fit output files up to <b>fit_20r_s20.RData</b>. We did not include the diagnostic figures in this repository, but users can get them by running the code.<b>fit_40reefs.R</b>: Script to implement the <i>40 reefs fit</i> from the manuscript. It follows the same process as above. Output files range from <b>fit_40r_s1.RData </b>up to<b> fit_40r_s20.RData</b><b>Stan model</b><b>MARPLN_LV.stan</b>: Stan code for the multivariate autoregressive Poisson-Lognormal model with the latent variables. This model is used in the file <b>fit_20reefs.R</b><b>MARPLN_LV_withNA.stan</b>: Same as the model above, but it can also handle missing data. This model is used in the file<b> fit_40reefs.R.</b><b>Figure and analysis script</b><b>Figure 3.R</b>: This script calculates the accuracy and precision estimates for all key parameters across simulations and generates Figure 3 from the manuscript.<br>
DOI: 10.6084/m9.figshare.28774304.v1
title: <b><i>Simulation study comparing number of sampled reefs</i></b>

description: This repository contains all the scripts and data used in the simulation study titled <i>“Simulation study comparing number of sampled reefs”, </i>presented in the manuscript <i>“Longer time series with missing data improve parameter estimation in State-Space mode in coral reef fish communities”</i>. There are 66 files in total.All model fits were run on the HPC cluster at James Cook University. Depending on the simulated dataset, run times ranged from several hours up to 1-2 days per fit.<b>Simulated data</b><b>multisp_sim_dat_reefs.R</b>: Simulates communities of 20 species across 40 reefs. We used this script to generate 20 simulated communities, which were saved as <b>sim_40vs20_s1.RData</b> through <b>sim_40vs20_s20.RData</b>.<b>Model fitting to simulated data</b><b>fit_20reefs.R</b>: Script to implement the <i>20 reefs fit</i> from the manuscript. For each simulated dataset, it: 1) saves posterior model parameters, 2) computes diagnostics (divergent transitions, tree depth saturation, E-BFMI), and 3) generates effective sample size (ESS) and R-hat plots. Example output: input simulated dataset <b>sim_40vs20_s1.RData </b>and the output <b>fit_20r_s1.RData</b>. We include all fit output files up to <b>fit_20r_s20.RData</b>. We did not include the diagnostic figures in this repository, but users can get them by running the code.<b>fit_40reefs.R</b>: Script to implement the <i>40 reefs fit</i> from the manuscript. It follows the same process as above. Output files range from <b>fit_40r_s1.RData </b>up to<b> fit_40r_s20.RData</b><b>Stan model</b><b>MARPLN_LV.stan</b>: Stan code for the multivariate autoregressive Poisson-Lognormal model with the latent variables. This model is used in the file <b>fit_20reefs.R</b><b>MARPLN_LV_withNA.stan</b>: Same as the model above, but it can also handle missing data. This model is used in the file<b> fit_40reefs.R.</b><b>Figure and analysis script</b><b>Figure 3.R</b>: This script calculates the accuracy and precision estimates for all key parameters across simulations and generates Figure 3 from the manuscript.<br>
DOI: 10.15468/dl.vwppku
title: Occurrence Download

description: A dataset containing 1499 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Colombia, Peru, Ecuador, Panama)",
 "OccurrenceStatus is Present",
 "TaxonKey is Bactris gasipaes"
 ]
}

 The dataset includes 1499 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020064-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30494351
title: misteli_optoloop_Fig4E

description: Data of Figure 4E from Stortz et al, OptoLoop manuscript (Misteli Lab)<br>
DOI: 10.6084/m9.figshare.30494351.v2
title: misteli_optoloop_Fig4E

description: Data of Figure 4E from Stortz et al, OptoLoop manuscript (Misteli Lab)<br>
DOI: 10.6084/m9.figshare.30494351.v1
title: misteli_optoloop_Fig4D

description: Data of Figure 4D from Stortz et al, OptoLoop manuscript (Misteli Lab)<br>
DOI: 10.15468/dl.a6qcph
title: Occurrence Download

description: A dataset containing 65545 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Bradypus variegatus, Cabassous centralis, Cabassous unicinctus, Choloepus didactylus, Cyclopes dorsalis, Dasypus novemcinctus, Myrmecophaga tridactyla, Priodontes maximus, Tamandua mexicana, Tamandua tetradactyla)"
 ]
}

 The dataset includes 65545 records from 758 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020014-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8mun62
title: Occurrence Download

description: A dataset containing 4361727 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acanella arbuscula, Antipathella subpinnata, Antipathes dichotoma, Callogorgia verticillata, Corallium johnsoni, Corallium rubrum, Dendrophyllia cornigera, Dendrophyllia ramea, Desmophyllum dianthus, Desmophyllum pertusum, Enallopsammia rostrata, Isidella elongata, Keratoisis, Leiopathes glaberrima, Madrepora oculata, Paragorgia arborea, Paramuricea placomus, Primnoa resedaeformis, Solenosmilia variabilis, Stichopathes, Viminella flagellum)",
 "HasCoordinate is true",
 "Geometry POLYGON((-40 36, 15 36, 15 72, -40 72, -40 36))"
 ]
}

 The dataset includes 4361727 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020036-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14286/ukhbjp
title: Consequences of land-use change and human activity on anadromous salmonids and the ecosystem services that they provide

description: This is the OBIS extraction of the Ocean Tracking Network and Norwegian University of Science and Technology (NTNU) Consequences of land-use change and human activity on anadromous salmonids and the ecosystem services that they provide, consisting of the release tagging metadata, i.e. the location and date when the tagged animal was released, and summarized detection events of tagged individuals.
 If readers are interested in the source dataset they may also inquire with the project PIs as listed here or on the OTN web site (https://members.oceantrack.org/project?ccode=V2LCHASES).Abstract:Brown trout may live the entire life in freshwater (resident trout) or occasionally migrate to sea (sea trout). In theory, individuals should migrate to sea if such behavior increases reproductive success. It has been shown, that migratory differences not only rely to resident or migratory individuals. Within a seaward migrating group of trout, large differences in distance migrated away from the river can often be found. Some stay close, while other migrates far away. In this project, we will aim to map physiologically differences between juvenile trout that become residents or migrate to sea and between short and long distance migratory sea trout. Seaward migration is a behavior that can be expected when the gain for the individual fish is higher than the cost. Consequently, one can expect that this behavior will be changed or disappear if sea conditions are so negative for sea trout that it loses reproductive potential by migrating to sea.
DOI: 10.15468/dl.gaq55r
title: Occurrence Download

description: A dataset containing 5926556 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)) eeacellcode,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) familycount,
 COUNT(*) occurrences,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'BE'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (CAST(occurrence.taxonkey AS INTEGER) = 212 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 212 OR CAST(occurrence.kingdomkey AS INTEGER) = 212 OR CAST(occurrence.phylumkey AS INTEGER) = 212 OR CAST(occurrence.classkey AS INTEGER) = 212 OR CAST(occurrence.orderkey AS INTEGER) = 212 OR CAST(occurrence.familykey AS INTEGER) = 212 OR CAST(occurrence.genuskey AS INTEGER) = 212 OR CAST(occurrence.specieskey AS INTEGER) = 212)
 AND (occurrence."year" &gt;= 2010 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year",
 GBIF_EEARGCODE(1000, occurrence.decimallatitude, occurrence.decimallongitude, COALESCE(occurrence.coordinateuncertaintyinmeters, 1000))
ORDER BY
 occurrences

 The dataset's 5926556 records were derived from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020032-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2g485x
title: Occurrence Download

description: A dataset containing 12142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "Country is Canada",
 "Geometry POLYGON((-73.90105 45.41201,-73.93937 45.4495,-73.97398 45.43076,-73.97487 45.42666,-73.9693 45.42421,-73.9686 45.4203,-73.9628 45.41753,-73.96512 45.4146,-73.95676 45.40824,-73.95471 45.40379,-73.94287 45.40199,-73.93185 45.40472,-73.9265 45.40423,-73.92209 45.40489,-73.91954 45.40766,-73.90105 45.41201))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dryobates pubescens"
 ]
}

 The dataset includes 12142 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020065-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/g2z1f-nex65
title: Particle-image-velocimetry data of cylinder wakes
DOI: 10.25549/whittington-ouc11399fc8y
title: Dick Whittington Photography Collection, 1924-1987

description: The "Dick" Whittington Studio was the largest and finest photography studio in the Los Angeles area from 1924 to 1987. Specializing in commercial photography, the Whittington Studio took photographs for nearly every major business and organization in Los Angeles; in so doing, they documented the growth and commercial development of Los Angeles. Clients included Max Factor, the Broadway, Bullock's, and May Co. department stores, the California Fruit Growers Association, Signal Oil, Shell Oil, Union Oil, Van de Kamp's bakeries, Forest Lawn, Sparkletts Water, CBS, Don Lee Television, Goodyear Tire and Rubber, real estate developers, construction companies, automobile, aircraft, and railroad companies, and drive-in theaters. Another notable client was the University of Southern California, which contracted with the Whittington Studios for coverage of athletic and other events. The collection consists primarily of roughly 500,000 negatives; the rest are photoprints. Supporters The collection is only partially digitized, but thanks to the generous help of the National Endowment for the Humanities (NEH) and the National Historical Publications and Records Commission (NHPRC), the USC Libraries has digitized 76,645 at-risk negatives in obsolete formats from the 1920s to 1940s.
DOI: 10.25549/whittington-ouc11399e8h2
title: Dick Whittington Photography Collection, 1924-1987

description: The "Dick" Whittington Studio was the largest and finest photography studio in the Los Angeles area from 1924 to 1987. Specializing in commercial photography, the Whittington Studio took photographs for nearly every major business and organization in Los Angeles; in so doing, they documented the growth and commercial development of Los Angeles. Clients included Max Factor, the Broadway, Bullock's, and May Co. department stores, the California Fruit Growers Association, Signal Oil, Shell Oil, Union Oil, Van de Kamp's bakeries, Forest Lawn, Sparkletts Water, CBS, Don Lee Television, Goodyear Tire and Rubber, real estate developers, construction companies, automobile, aircraft, and railroad companies, and drive-in theaters. Another notable client was the University of Southern California, which contracted with the Whittington Studios for coverage of athletic and other events. The collection consists primarily of roughly 500,000 negatives; the rest are photoprints. Supporters The collection is only partially digitized, but thanks to the generous help of the National Endowment for the Humanities (NEH) and the National Historical Publications and Records Commission (NHPRC), the USC Libraries has digitized 76,645 at-risk negatives in obsolete formats from the 1920s to 1940s.
DOI: 10.25549/whittington-ouc11399f1ig
title: Dick Whittington Photography Collection, 1924-1987

description: The "Dick" Whittington Studio was the largest and finest photography studio in the Los Angeles area from 1924 to 1987. Specializing in commercial photography, the Whittington Studio took photographs for nearly every major business and organization in Los Angeles; in so doing, they documented the growth and commercial development of Los Angeles. Clients included Max Factor, the Broadway, Bullock's, and May Co. department stores, the California Fruit Growers Association, Signal Oil, Shell Oil, Union Oil, Van de Kamp's bakeries, Forest Lawn, Sparkletts Water, CBS, Don Lee Television, Goodyear Tire and Rubber, real estate developers, construction companies, automobile, aircraft, and railroad companies, and drive-in theaters. Another notable client was the University of Southern California, which contracted with the Whittington Studios for coverage of athletic and other events. The collection consists primarily of roughly 500,000 negatives; the rest are photoprints. Supporters The collection is only partially digitized, but thanks to the generous help of the National Endowment for the Humanities (NEH) and the National Historical Publications and Records Commission (NHPRC), the USC Libraries has digitized 76,645 at-risk negatives in obsolete formats from the 1920s to 1940s.
DOI: 10.25549/whittington-ouc11399erfl
title: Dick Whittington Photography Collection, 1924-1987

description: The "Dick" Whittington Studio was the largest and finest photography studio in the Los Angeles area from 1924 to 1987. Specializing in commercial photography, the Whittington Studio took photographs for nearly every major business and organization in Los Angeles; in so doing, they documented the growth and commercial development of Los Angeles. Clients included Max Factor, the Broadway, Bullock's, and May Co. department stores, the California Fruit Growers Association, Signal Oil, Shell Oil, Union Oil, Van de Kamp's bakeries, Forest Lawn, Sparkletts Water, CBS, Don Lee Television, Goodyear Tire and Rubber, real estate developers, construction companies, automobile, aircraft, and railroad companies, and drive-in theaters. Another notable client was the University of Southern California, which contracted with the Whittington Studios for coverage of athletic and other events. The collection consists primarily of roughly 500,000 negatives; the rest are photoprints. Supporters The collection is only partially digitized, but thanks to the generous help of the National Endowment for the Humanities (NEH) and the National Historical Publications and Records Commission (NHPRC), the USC Libraries has digitized 76,645 at-risk negatives in obsolete formats from the 1920s to 1940s.
DOI: 10.5517/ccdc.csd.cc2kncf1
title: CSD 2373063: Experimental Crystal Structure Determination

description: Related Article: Y. Avila, M.C. Vázquez, O. Piedra, J. Rodríguez-Hernández, L. Reguera, M. Ávila, E. Reguera|2025|J.Phys.Chem.Solids|209||doi:10.1016/j.jpcs.2025.113260
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kncg2
title: CSD 2373064: Experimental Crystal Structure Determination

description: Related Article: Y. Avila, M.C. Vázquez, O. Piedra, J. Rodríguez-Hernández, L. Reguera, M. Ávila, E. Reguera|2025|J.Phys.Chem.Solids|209||doi:10.1016/j.jpcs.2025.113260
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25549/whittington-ouc11399erfj
title: Dick Whittington Photography Collection, 1924-1987

description: The "Dick" Whittington Studio was the largest and finest photography studio in the Los Angeles area from 1924 to 1987. Specializing in commercial photography, the Whittington Studio took photographs for nearly every major business and organization in Los Angeles; in so doing, they documented the growth and commercial development of Los Angeles. Clients included Max Factor, the Broadway, Bullock's, and May Co. department stores, the California Fruit Growers Association, Signal Oil, Shell Oil, Union Oil, Van de Kamp's bakeries, Forest Lawn, Sparkletts Water, CBS, Don Lee Television, Goodyear Tire and Rubber, real estate developers, construction companies, automobile, aircraft, and railroad companies, and drive-in theaters. Another notable client was the University of Southern California, which contracted with the Whittington Studios for coverage of athletic and other events. The collection consists primarily of roughly 500,000 negatives; the rest are photoprints. Supporters The collection is only partially digitized, but thanks to the generous help of the National Endowment for the Humanities (NEH) and the National Historical Publications and Records Commission (NHPRC), the USC Libraries has digitized 76,645 at-risk negatives in obsolete formats from the 1920s to 1940s.
DOI: 10.5517/ccdc.csd.cc2knch3
title: CSD 2373065: Experimental Crystal Structure Determination

description: Related Article: Y. Avila, M.C. Vázquez, O. Piedra, J. Rodríguez-Hernández, L. Reguera, M. Ávila, E. Reguera|2025|J.Phys.Chem.Solids|209||doi:10.1016/j.jpcs.2025.113260
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.