cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15225028
title: Survival and Habitat Quality (SHQ) analysis data and code

description: This archive contains the source code and data required for reproducing the analyses and figures from the manuscript "A lifetime of experiences: Modeling habitat quality through cumulative effects on individual survival", accepted for publication by the journal Methods in Ecology and Evolution on 2025-04-07. Code and data are included to:



Perform SHQ on simulated dataThe code to simulate data for SHQ is in R/Simulate data.R. The model code to run SHQ is in models/SHQ.txt. The MCMC results from running SHQ on simulated datasets with and without missing values are in the results folder under "SHQsim_withNAs" and "SHQsim_noNAs". These results files can be read into R using the Plotting simulations.R script, which then has code for creating Figure 2. 

Compare known fate vs. SHQCode to simulate data for known fate survival analysis is in R/Simulate data.R. The model code to run known fate survival analysis is in models/Known_fate.txt. The MCMC results from running SHQ and known fate survival analysis on the same simulated dataset are saved as .RDS files in the folder "KFvsSHQ" in the results folder. These results files can be read into R using the Plotting simulations.R script, which then has code for creating Figure 3. 

Complete pronghorn case studyThe GPS collar data for the pronghorn case study are formatted into encounter histories (data/eh.rds). The encounter histories record each day that the pronghorn was alive (1) and dead (0). Fate data are included are formatted to record each animalID and cause of mortality (for each collared (data/fates.rds). Covariate data include daily covariate values for each animalID (data/covariatedata.rds). The code to format encounter histories, fate, and encounter histories is found in R/Pronghorn case study.R. "R/Pronghorn case study.R" has code to prepare data for and run the SHQ analysis. This script also includes the code to create Figures 4, 5, and 6 from those results.
DOI: 10.5281/zenodo.15225029
title: Survival and Habitat Quality (SHQ) analysis data and code

description: This archive contains the source code and data required for reproducing the analyses and figures from the manuscript "A lifetime of experiences: Modeling habitat quality through cumulative effects on individual survival", accepted for publication by the journal Methods in Ecology and Evolution on 2025-04-07. Code and data are included to:



Perform SHQ on simulated dataThe code to simulate data for SHQ is in Appendix C; the model code to run SHQ is in Appendix A (both are published as online supplemental material with the article and here in the folder "appendices"). The MCMC results from running SHQ on simulated datasets with and without missing values are in the results folder under "SHQsim_withNAs" and "SHQsim_noNAs". These results files can be read into R using the Plotting simulations.R script in the zip file, which then has code for creating Figure 2. 

Compare known fate vs. SHQThe model code to run known fate survival analysis is in Appendix B. The NIMBLE results from running SHQ and known fate survival analysis on the same simulated dataset are saved as .RDS files in the folder "KFvsSHQ" in the results folder. These results files can be read into R using the Plotting simulations.R script in the zip file, which then has code for creating Figure 3. 

Complete pronghorn case studyThe GPS collar data for the pronghorn case study are formatted into encounter histories (data/eh.rds). The encounter histories record each day that the pronghorn was alive (1) and dead (0). Fate data are included are formatted to record each animalID and cause of mortality (for each collared (data/fates.rds). Covariate data include daily covariate values for each animalID (data/covariatedata.rds). The code to format encounter histories, fate, and encounter histories is found in R/Pronghorn case study.R. "R/Pronghorn case study.R" has code to prepare data for and run the SHQ analysis. This script also includes the code to create Figures 4, 5, and 6 from those results.
DOI: 10.5281/zenodo.15242216
title: Survival and Habitat Quality (SHQ) analysis data and code

description: This archive contains the source code and data required for reproducing the analyses and figures from the manuscript "A lifetime of experiences: Modeling habitat quality through cumulative effects on individual survival", accepted for publication by the journal Methods in Ecology and Evolution on 2025-04-07. Code and data are included to:



Perform SHQ on simulated dataThe code to simulate data for SHQ is in R/Simulate data.R. The model code to run SHQ is in models/SHQ.txt. The MCMC results from running SHQ on simulated datasets with and without missing values are in the results folder under "SHQsim_withNAs" and "SHQsim_noNAs". These results files can be read into R using the Plotting simulations.R script, which then has code for creating Figure 2. 

Compare known fate vs. SHQCode to simulate data for known fate survival analysis is in R/Simulate data.R. The model code to run known fate survival analysis is in models/Known_fate.txt. The MCMC results from running SHQ and known fate survival analysis on the same simulated dataset are saved as .RDS files in the folder "KFvsSHQ" in the results folder. These results files can be read into R using the Plotting simulations.R script, which then has code for creating Figure 3. 

Complete pronghorn case studyThe GPS collar data for the pronghorn case study are formatted into encounter histories (data/eh.rds). The encounter histories record each day that the pronghorn was alive (1) and dead (0). Fate data are included are formatted to record each animalID and cause of mortality (for each collared (data/fates.rds). Covariate data include daily covariate values for each animalID (data/covariatedata.rds). The code to format encounter histories, fate, and encounter histories is found in R/Pronghorn case study.R. "R/Pronghorn case study.R" has code to prepare data for and run the SHQ analysis. This script also includes the code to create Figures 4, 5, and 6 from those results.
DOI: 10.14288/1.0423139
title: X-ray fluorescence microimaging of single leaf and root subsamples from quillay (Quillaja saponaria Molina) and espino (Vachellia caven (Molina) Seigler & Ebinger), grown with (100 μM) and without (0 μM) added Cu

description: X-ray fluorescence microimaging of single leaf and root subsamples from quillay (Quillaja saponaria Molina) and espino (Vachellia caven (Molina) Seigler & Ebinger), grown with (100 μM) and without (0 μM) added Cu, at the Canadian Light Source Synchrotron facility (Saskatoon, SK).
DOI: 10.15468/dl.vnn8hy
title: Occurrence Download

description: A dataset containing 35127443 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Mexico"
 ]
}

 The dataset includes 35127443 records from 3875 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012129-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.au7hs5
title: Occurrence Download

description: A dataset containing 5917 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Peltula Nyl."
 ]
}

 The dataset includes 5917 records from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013024-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15480582
title: Testing Zenodo Embargo
DOI: 10.15468/dl.33vurn
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is one of (Indonesia, Malaysia, Thailand)",
 "TaxonKey is Albizia julibrissin Durazz."
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008289-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15268478
title: RadField3D: Validation Dataset

description: Validation dataset for the paper: "RadField3D: A Data Generator and Data Format for Deep Learning in Radiation-Protection Dosimetry for Medical Applications"

Simulated and Measured data in the .rf3 files are in relative units, only! In order to retrieve the actual doses from it, one needs the specific calibration factor for the energy range and the montitor chamber.The measured .csv files are containing the raw chamber currents from the monitor chamber. For easier comparisions, the CSV files were additionally converted to .rf3 files (RadFiled3D format) just like the simulation results. Those files contain only a single "Measurement" channel containing a "Doserate" layer where all voxels are zero except for the voxels that overlap a measurement point.

 

Used equipment:    120kV facility of the Physikalisch-Technische Bundesanstalt in Brunswiek.    Monitor chamber: PTW TK-30 type TM32005

Scatter phantoms:    Measurement series A: Water cylinder (simplified head phantom)    Measurement series B: Alderson phantom torso without head

 

Contained Simulations:   Series A: Water cylinder irradiation with two voxel size resolutions: 1 x 1 x 1 cm^3 and 2 x 2 x 2 cm^3   Series B: Alderson phantom torso irradiation with one file for each rotation of the xray beam (in 10 degree steps) beeing equal                  to a rotation of the alderson phantom itself.

 

For more information please read the corresponding paper.For further questions please contact me: felix.lehner@ptb.de
DOI: 10.5281/zenodo.15268479
title: RadField3D: Validation Dataset

description: Validation dataset for the paper: "RadField3D: A Data Generator and Data Format for Deep Learning in Radiation-Protection Dosimetry for Medical Applications"

Simulated and Measured data in the .rf3 files are in relative units, only! In order to retrieve the actual doses from it, one needs the specific calibration factor for the energy range and the montitor chamber.The measured .csv files are containing the raw chamber currents from the monitor chamber. For easier comparisions, the CSV files were additionally converted to .rf3 files (RadFiled3D format) just like the simulation results. Those files contain only a single "Measurement" channel containing a "Doserate" layer where all voxels are zero except for the voxels that overlap a measurement point.

 

Used equipment:    120kV facility of the Physikalisch-Technische Bundesanstalt in Brunswiek.    Monitor chamber: PTW TK-30 type TM32005

Scatter phantoms:    Measurement series A: Water cylinder (simplified head phantom)    Measurement series B: Alderson phantom torso without head

 

Contained Simulations:   Series A: Water cylinder irradiation with two voxel size resolutions: 1 x 1 x 1 cm^3 and 2 x 2 x 2 cm^3   Series B: Alderson phantom torso irradiation with one file for each rotation of the xray beam (in 10 degree steps) beeing equal                  to a rotation of the alderson phantom itself.

 

For more information please read the corresponding paper.For further questions please contact me: felix.lehner@ptb.de
DOI: 10.15468/dl.byy6hy
title: Occurrence Download

description: A dataset containing 6711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyprinus carpio",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1985",
 "Year is less than or equal to 1989"
 ]
}

 The dataset includes 6711 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010589-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2bnrxr
title: Occurrence Download

description: A dataset containing 8871 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.44.57_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 8871 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010590-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18251507
title: Cardionema DC. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18251508
title: Cardionema DC. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18251509
title: Cardamine L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18251510
title: Cardamine L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.15468/dl.qkxc4r
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.44.58_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010593-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abwtk4
title: Occurrence Download

description: A dataset containing 312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Clerodendrum trichotomum",
 "Year 1970-2000"
 ]
}

 The dataset includes 312 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010596-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bnq5f2
title: Occurrence Download

description: A dataset containing 8450 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ammannia coccinea"
 ]
}

 The dataset includes 8450 records from 360 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010591-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2uguwh
title: Occurrence Download

description: A dataset containing 3846 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ammannia multiflora"
 ]
}

 The dataset includes 3846 records from 134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010595-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6wp6w
title: Occurrence Download

description: A dataset containing 15840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyprinus carpio",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1990",
 "Year is less than or equal to 1994"
 ]
}

 The dataset includes 15840 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010594-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18251513
title: Cardionema ramosissimum (Weinm.) A.Nelson & J.F.Macbr. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18251514
title: Cardionema ramosissimum (Weinm.) A.Nelson & J.F.Macbr. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18251479
title: 5G performance test results

description: This dataset contains 5G performance (uplink/downlink/ping) of 8 different bandwidths across 11 different configuration of receiver and transmitter.
DOI: 10.5281/zenodo.18251480
title: 5G performance test results

description: This dataset contains 5G performance (uplink/downlink/ping) of 8 different bandwidths across 11 different configuration of receiver and transmitter.
DOI: 10.5281/zenodo.18251518
title: Cardiopteridaceae Blume. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.5281/zenodo.18251519
title: Cardiopteridaceae Blume. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:43
DOI: 10.15468/dl.pgfp9y
title: Occurrence Download

description: A dataset containing 4805101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cygnus olor, Columba livia, Pycnonotus sinensis, Leiothrix lutea, Zosterops erythropleurus, Psittacula krameri, Garrulax canorus, Branta canadensis moffitti, Garrulax perspicillatus, Garrulax cineraceus, Colinus virginianus, Garrulax sannio, Pavo cristatus, Branta canadensis, Branta canadensis maxima, Branta leucopsis, Branta ruficollis, Branta sandvicensis, Himantopus mexicanus, Zosterops palpebrosus, Phasianus colchicus karpowi, Pycnonotus cafer, Garrulax leucolophus, Garrulax monileger, Pycnonotus sinensis formosae, Pycnonotus sinensis orii, Zosterops ceylonensis, Branta canadensis fulva, Branta canadensis occidentalis, Branta canadensis parvipes, Branta canadensis interior, Zosterops japonicus simplex)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 1000"
 ]
}

 The dataset includes 4805101 records from 1118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010571-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/ak6-vcz-9h7
title: Lacertidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rje-r7e-6bm
title: Homo sapiens Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pg3-ccp-b33
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0ad-tpe-kvf
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k9a-xew-gl4
title: Laganum Link, 1807

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9xs-9k9-48m
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v2n-2br-sr6
title: †Prolagus Pomel, 1853

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/037-926-and
title: †Prolagus Pomel, 1853

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cwn-g5l-gfp
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lsc-g3f-e85
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aan-fdz-j84
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rsb-26z-t7z
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7e3-9c1-jv5
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rrm-4bx-ws7
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gqh-882-bwk
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vst-m2n-s8z
title: Cervus elaphus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/12g-s7k-848
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5lc-09m-4hj
title: Aves

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fxk-awk-bc5
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2ye-tjr-g7b
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/33y-kmh-7l1
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dmc-lmj-e7h
title: †Nerinea Deshayes, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j5y-53g-c8n
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.