cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.drdwh7
title: Occurrence Download

description: A dataset containing 11015 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acipenseriformes, Albuliformes, Anguilliformes, Ateleopodiformes, Atheriniformes, Aulopiformes, Beloniformes, Beryciformes, Clupeiformes, Cypriniformes, Cyprinodontiformes, Elopiformes, Gadiformes, Gasterosteiformes, Gonorynchiformes, Lampriformes, Lophiiformes, Mugiliformes, Myctophiformes, Ophidiiformes, Perciformes, Pleuronectiformes, Polymixiiformes, Osmeriformes, Salmoniformes, Scorpaeniformes, Siluriformes, Stephanoberyciformes, Stomiiformes, Synbranchiformes, Tetraodontiformes, Zeiformes, Petromyzontiformes, Myxiniformes, Carcharhiniformes, Heterodontiformes, Hexanchiformes, Lamniformes, Myliobatiformes, Orectolobiformes, Pristiophoriformes, Rajiformes, Rhinopristiformes, Squaliformes, Squatiniformes, Torpediniformes, Chimaeriformes, Syngnathiformes, Osteoglossiformes, Characiformes, Esociformes, Lepisosteiformes, Batrachoidiformes, Amiiformes, Polypteriformes, Gymnotiformes, Ceratodontiformes, Coelacanthiformes, Percopsiformes, Saccopharyngiformes)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 "Year is greater than or equal to 1970",
 "CoordinateUncertaintyInMeters is less than 3000"
 ]
}

 The dataset includes 11015 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021353-250402121839773/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.3568740
title: Appendix F. Across-area supplementary results: model selection tables.

description: Across-area supplementary results: model selection tables.
DOI: 10.6084/m9.figshare.3568740.v1
title: Appendix F. Across-area supplementary results: model selection tables.

description: Across-area supplementary results: model selection tables.
DOI: 10.6084/m9.figshare.3568737
title: Appendix G. Within vs. among individual supplementary results: result descriptions.

description: Within vs. among individual supplementary results: result descriptions.
DOI: 10.6084/m9.figshare.3568737.v1
title: Appendix G. Within vs. among individual supplementary results: result descriptions.

description: Within vs. among individual supplementary results: result descriptions.
DOI: 10.6084/m9.figshare.3568734
title: Supplement 1. Detailed worked tutorials of analyses performed in this paper, including R code for mixed effects models and example data.

description: File List S1_tutorial.pdf (MD5: b9ce89e5e69463afbfc055a2943824e6) -- worked examples for the analysis of growth variation within and among individuals and populations S2_R_code.txt (MD5: 6028e6cddbdf1473a4eef0faa8bd310a) -- R code to perform analyses in S1 S3_within_zone_example_data.csv (MD5: ab86c1dd8ca7bcd2115f23a14b746bd8) -- within-zone fish growth data S4_among_zone_example_data.csv (MD5: d601bea4192d1f1c4c513fac34e39306) -- among-zone fish growth data S5_example_temperature.csv (MD5: f7ae18b64af07ec4b4d7ff94966bbf46) -- temperature data used in among-zone analyses Description These supplements are designed to assist the reader to implement hierarchical growth models using the statistical software R. The first supplement (S1_tutorial.pdf) provides detailed model descriptions, formulations and analytical steps used in the paper, complementing models presented in Table 3. The second supplement (S2_R_code.txt) provides executable R code for analyses in S1. The third, fourth, and fifth supplements (S3_within_zone_example_data.csv, S4_among_zone_example_data.csv, and S5_example_temperature.csv) are example data sets. Our analyses rely heavily on the R packages lme4, AICcmodavg, effects, lattice and plyr, all available on the comprehensive R archive network (CRAN; cran.r-project.org). Each row in S3_within_zone_example_data.csv and S4_among_zone_example_data.csv represents a measurement of growth in mm (Increment). These observations are associated with an Age (in years) and belong to a fish (FishID) of a given sex (M or F). Each fish has an age-at-capture (ACC, in years). Associated with each Increment is its year of deposition (Year) and the annual bottom temperature (Temp) experienced by the individual at this time. In addition, the S4_among_zone_example_data.csv and S5_example_temperature.csv files contain a variable called zone that assigns each fish to a fictitious fishing area. See Table 2 for additional descriptions of these parameters.
DOI: 10.6084/m9.figshare.3568731
title: Appendix A. A map illustrating location of 39 stream fragments and 448 fish community samples included in analysis of fish community structure across the Great Plains.

description: A map illustrating location of 39 stream fragments and 448 fish community samples included in analysis of fish community structure across the Great Plains.
DOI: 10.6084/m9.figshare.3568728
title: Appendix B. A table showing species included in review of 448 fish collections from the Great Plains as well as reproductive guild and body size classifications.

description: A table showing species included in review of 448 fish collections from the Great Plains as well as reproductive guild and body size classifications.
DOI: 10.6084/m9.figshare.3568728.v1
title: Appendix B. A table showing species included in review of 448 fish collections from the Great Plains as well as reproductive guild and body size classifications.

description: A table showing species included in review of 448 fish collections from the Great Plains as well as reproductive guild and body size classifications.
DOI: 10.6084/m9.figshare.3568722
title: Appendix C. A table showing details and rankings of candidate generalized linear models included in the information theoretic approach used to predict probability of occurrence for fish reproductive guilds in the Great Plains.

description: A table showing details and rankings of candidate generalized linear models included in the information theoretic approach used to predict probability of occurrence for fish reproductive guilds in the Great Plains.
DOI: 10.6084/m9.figshare.3568722.v1
title: Appendix C. A table showing details and rankings of candidate generalized linear models included in the information theoretic approach used to predict probability of occurrence for fish reproductive guilds in the Great Plains.

description: A table showing details and rankings of candidate generalized linear models included in the information theoretic approach used to predict probability of occurrence for fish reproductive guilds in the Great Plains.
DOI: 10.6084/m9.figshare.3568719
title: Supplement 1. Raw community data for 448 fish collections made among 39 stream fragments in the Great Plains.

description: File List Ecological_Archive_Fish_Data_Great_Plains.txt (MD5: 184771856be1471e87d1f73d7a8b0b51) Description This file contains the raw occurrence data for fish collections taken from Great Plains rivers during 1993–2013. Fragment number used in analysis, location (latitude and longitude), year of collection, and the original source of the data are provided. Species occurrences are listed as present (1) or absent (0) from each collection.
DOI: 10.6084/m9.figshare.3568719.v1
title: Supplement 1. Raw community data for 448 fish collections made among 39 stream fragments in the Great Plains.

description: File List Ecological_Archive_Fish_Data_Great_Plains.txt (MD5: 184771856be1471e87d1f73d7a8b0b51) Description This file contains the raw occurrence data for fish collections taken from Great Plains rivers during 1993–2013. Fragment number used in analysis, location (latitude and longitude), year of collection, and the original source of the data are provided. Species occurrences are listed as present (1) or absent (0) from each collection.
DOI: 10.6084/m9.figshare.3568716
title: Appendix A. Figures showing variation of the boundary layer height (m) in the Ukrainian and Belarusian contaminated forests between 2002 and 2010, continental distribution of BA, TC, and TPM for Europe from the GFED3 database, forest tree-cover from Kempeneers et al. (2011) database at 1 km resolution and aggregated at 0.5° resolution for comparison with the GFED3 database, forest cover change around the ChNPP derived from Landsat images from 1987 and 2010 and forest-cover change over the...

description: Figures showing variation of the boundary layer height (m) in the Ukrainian and Belarusian contaminated forests between 2002 and 2010, continental distribution of BA, TC, and TPM for Europe from the GFED3 database, forest tree-cover from Kempeneers et al. (2011) database at 1 km resolution and aggregated at 0.5° resolution for comparison with the GFED3 database, forest cover change around the ChNPP derived from Landsat images from 1987 and 2010 and forest-cover change over the ChNPP from Hansen et al. (2013), biomass burning in Chernobyl as seen from PKU-FUEL model of the Peking University, and prediction of the litter carbon stock and fire occurrence until 2100 calculated from the LPJmL-SPITFIRE model for Europe, Belarus, and Chernobyl.
DOI: 10.6084/m9.figshare.3568716.v1
title: Appendix A. Figures showing variation of the boundary layer height (m) in the Ukrainian and Belarusian contaminated forests between 2002 and 2010, continental distribution of BA, TC, and TPM for Europe from the GFED3 database, forest tree-cover from Kempeneers et al. (2011) database at 1 km resolution and aggregated at 0.5° resolution for comparison with the GFED3 database, forest cover change around the ChNPP derived from Landsat images from 1987 and 2010 and forest-cover change over the...

description: Figures showing variation of the boundary layer height (m) in the Ukrainian and Belarusian contaminated forests between 2002 and 2010, continental distribution of BA, TC, and TPM for Europe from the GFED3 database, forest tree-cover from Kempeneers et al. (2011) database at 1 km resolution and aggregated at 0.5° resolution for comparison with the GFED3 database, forest cover change around the ChNPP derived from Landsat images from 1987 and 2010 and forest-cover change over the ChNPP from Hansen et al. (2013), biomass burning in Chernobyl as seen from PKU-FUEL model of the Peking University, and prediction of the litter carbon stock and fire occurrence until 2100 calculated from the LPJmL-SPITFIRE model for Europe, Belarus, and Chernobyl.
DOI: 10.6084/m9.figshare.3568713
title: Appendix A. Details on the modeling approach.

description: Details on the modeling approach.
DOI: 10.6084/m9.figshare.3568713.v1
title: Appendix A. Details on the modeling approach.

description: Details on the modeling approach.
DOI: 10.6084/m9.figshare.3568710
title: Appendix B. Example of the Ecopath model of the Prince William Sound (1994–1996).

description: Example of the Ecopath model of the Prince William Sound (1994–1996).
DOI: 10.6084/m9.figshare.3568710.v1
title: Appendix B. Example of the Ecopath model of the Prince William Sound (1994–1996).

description: Example of the Ecopath model of the Prince William Sound (1994–1996).
DOI: 10.6084/m9.figshare.3568707
title: Appendix C. Overview of the 101 selected Ecopath models.

description: Overview of the 101 selected Ecopath models.
DOI: 10.6084/m9.figshare.3568707.v1
title: Appendix C. Overview of the 101 selected Ecopath models.

description: Overview of the 101 selected Ecopath models.
DOI: 10.6084/m9.figshare.3568704
title: Supplement 1. Text files of the input data for the 101 Ecopath models and R code for Spearman correlation tests.

description: File List InputData.rar (MD5: 76904b277839a2de9ae118f3e82fbd2b) 101 Text files of the input data for the 101 Ecopath models Rcode.R (MD5: e34088e54b07e6dda9496041d1d0aa15) R code for Spearman correlation tests Description In the first supplement (InputData.rar), for each Ecopath model, identified with its model number in EcoBase (see Appendix C for the metadata and references of the models), one Text file provides the input data: group number (<i>No</i>); group name (<i>GroupName</i>); trophic level of the group (<i>TrophicLevel</i>); biomass of the group (<i>Biomass</i>); and matrix of the mixed trophic impact, with the impacted groups in columns and the impacting groups in rows, both identified with their group numbers. Non-living groups were removed, and mixed trophic impact values of the groups on themselves were replaced by NA. The second supplement (Rcode.R) provides the R code used to run the Spearman rank correlation tests.
DOI: 10.6084/m9.figshare.3568704.v1
title: Supplement 1. Text files of the input data for the 101 Ecopath models and R code for Spearman correlation tests.

description: File List InputData.rar (MD5: 76904b277839a2de9ae118f3e82fbd2b) 101 Text files of the input data for the 101 Ecopath models Rcode.R (MD5: e34088e54b07e6dda9496041d1d0aa15) R code for Spearman correlation tests Description In the first supplement (InputData.rar), for each Ecopath model, identified with its model number in EcoBase (see Appendix C for the metadata and references of the models), one Text file provides the input data: group number (<i>No</i>); group name (<i>GroupName</i>); trophic level of the group (<i>TrophicLevel</i>); biomass of the group (<i>Biomass</i>); and matrix of the mixed trophic impact, with the impacted groups in columns and the impacting groups in rows, both identified with their group numbers. Non-living groups were removed, and mixed trophic impact values of the groups on themselves were replaced by NA. The second supplement (Rcode.R) provides the R code used to run the Spearman rank correlation tests.
DOI: 10.6084/m9.figshare.3568701
title: Supplement 1. Data and code for implementing model selection approaches for occupancy model.

description: File List occ.aux.mcmc.R (MD5: 9d685abe2f0c8f99f7070f9b77b95fe2) section.3.script.R (MD5: 12312816b70fb311b311fe193f705c96) section.4.c.script.R (MD5: 9fc45f466660b8223d7d157b23b86740) section.4.g.script.R (MD5: 9d8448444db1e44336e4b0f9ed999b55) section.5.script.R (MD5: 61ecda7858117325985da1da24261cf9) wt.csv (MD5: fcef00421bb21150fe3b4b9ae15e8333) USGS_Disclaimers.txt (MD5: f9465db5e3077500926435799380311f) Description occ.aux.mcmc.R: Main MCMC algorithm written in R. section.3.script.R: R script for performing analyses in section 3. section.4.c.script.R: R script for performing analyses in section 4c. section.4.g.script.R: R script for performing analyses in section 4g. section.5.script.R: R script for performing analyses in section 5. wt.csv: Willow tit data file. Column definitions y.1, binary variable indicating detection (1) on occasion 1. y.2, binary variable indicating detection (1) on occasion 2. y.3, binary variable indicating detection (1) on occasion 3. elev, continuous variable indicating elevation in meters. forest, continuous variable indicating percent forest cover. Missing values are denoted by NA. USGS_Disclaimers: Required disclaimers from the USGS.
DOI: 10.6084/m9.figshare.3568698
title: Appendix A. Site information, photographs of three land-use type of paddy terraces, and survey design used in this study.

description: Site information, photographs of three land-use type of paddy terraces, and survey design used in this study.
DOI: 10.6084/m9.figshare.3568695
title: Appendix B. Comparisons of mowing frequency among land-use types and relationships between mowing frequency and vegetation height.

description: Comparisons of mowing frequency among land-use types and relationships between mowing frequency and vegetation height.
DOI: 10.6084/m9.figshare.3568692
title: Appendix C. Surrounding landscape information, comparisons of surrounding landscape variables (site slope angle, areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest) among land-use types, and a bi-plot showing the first two PCA axes of surrounding landscape variables (areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest).

description: Surrounding landscape information, comparisons of surrounding landscape variables (site slope angle, areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest) among land-use types, and a bi-plot showing the first two PCA axes of surrounding landscape variables (areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest).
DOI: 10.6084/m9.figshare.3568692.v1
title: Appendix C. Surrounding landscape information, comparisons of surrounding landscape variables (site slope angle, areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest) among land-use types, and a bi-plot showing the first two PCA axes of surrounding landscape variables (areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest).

description: Surrounding landscape information, comparisons of surrounding landscape variables (site slope angle, areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest) among land-use types, and a bi-plot showing the first two PCA axes of surrounding landscape variables (areas of abandoned, traditional, and intensive terrace, residential land, and secondary forest).
DOI: 10.6084/m9.figshare.3568689
title: Appendix D. Photographs of butterflies and orthopteran species and lists of butterfly and orthopteran species, and plant families found in 2011 and 2012.

description: Photographs of butterflies and orthopteran species and lists of butterfly and orthopteran species, and plant families found in 2011 and 2012.
DOI: 10.6084/m9.figshare.3568686
title: Appendix E. Seasonal variation in richness and the inverse Simpson’s index of diversity of butterflies and orthopterans.

description: Seasonal variation in richness and the inverse Simpson’s index of diversity of butterflies and orthopterans.
DOI: 10.6084/m9.figshare.3568686.v1
title: Appendix E. Seasonal variation in richness and the inverse Simpson’s index of diversity of butterflies and orthopterans.

description: Seasonal variation in richness and the inverse Simpson’s index of diversity of butterflies and orthopterans.
DOI: 10.6084/m9.figshare.3568683
title: Appendix F. Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for plant life-history group richness in 2011 and 2012.

description: Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for plant life-history group richness in 2011 and 2012.
DOI: 10.6084/m9.figshare.3568683.v1
title: Appendix F. Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for plant life-history group richness in 2011 and 2012.

description: Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for plant life-history group richness in 2011 and 2012.
DOI: 10.6084/m9.figshare.3568680
title: Appendix G. Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for richness and diversity (the inverse Simpson’s index of diversity) of butterfly and orthopteran groups in 2011 and 2012, and a figure for relationships of herbivorous insect diversity (the inverse Simpson’s index of diversity) of body-size groups, larval-host/mandibular groups, and abundance (No. of individuals) groups with resource of perennial plant variables and mowing frequency.

description: Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for richness and diversity (the inverse Simpson’s index of diversity) of butterfly and orthopteran groups in 2011 and 2012, and a figure for relationships of herbivorous insect diversity (the inverse Simpson’s index of diversity) of body-size groups, larval-host/mandibular groups, and abundance (No. of individuals) groups with resource of perennial plant variables and mowing frequency.
DOI: 10.6084/m9.figshare.3568677
title: Appendix H. Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for richness and diversity (the inverse Simpson’s index of diversity) of butterfly and Orthopteran taxonomic group in 2011 and 2012, and a figure for relationships of species richness of herbivorous insects of taxonomic groups with resource of perennial plant variables and mowing frequency.

description: Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for richness and diversity (the inverse Simpson’s index of diversity) of butterfly and Orthopteran taxonomic group in 2011 and 2012, and a figure for relationships of species richness of herbivorous insects of taxonomic groups with resource of perennial plant variables and mowing frequency.
DOI: 10.6084/m9.figshare.3568677.v1
title: Appendix H. Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for richness and diversity (the inverse Simpson’s index of diversity) of butterfly and Orthopteran taxonomic group in 2011 and 2012, and a figure for relationships of species richness of herbivorous insects of taxonomic groups with resource of perennial plant variables and mowing frequency.

description: Estimated coefficients of explanatory parameters in the best generalized linear mixed model (GLMM) for richness and diversity (the inverse Simpson’s index of diversity) of butterfly and Orthopteran taxonomic group in 2011 and 2012, and a figure for relationships of species richness of herbivorous insects of taxonomic groups with resource of perennial plant variables and mowing frequency.
DOI: 10.6084/m9.figshare.3568674
title: Appendix I. The relationships between productivity and abundances of two herbivorous insect groups in 2011 and 2012.

description: The relationships between productivity and abundances of two herbivorous insect groups in 2011 and 2012.
DOI: 10.6084/m9.figshare.3568671
title: Appendix J. The relationships between species traits and species loss and decline.

description: The relationships between species traits and species loss and decline.
DOI: 10.6084/m9.figshare.3568671.v1
title: Appendix J. The relationships between species traits and species loss and decline.

description: The relationships between species traits and species loss and decline.
DOI: 10.6084/m9.figshare.3568668
title: Supplement 1. Raw data files used for statistical analyses in this study.

description: File List rawdata_AppendixD3.csv (MD5: f3b205e49ec965d1eec907a4c0377ed4) - raw data of appendix rawdata_AppendixD4.csv (MD5: 539014efff86a51e6015b2ab9ac12bbd) - raw data of appendix rawdata_AppendixD5.csv (MD5: 7a756c80a269b48c1779e51cd8d6715c) - raw data of appendix rawdata_butterfly2011.csv (MD5: e1b179477ae438897ba1ce545d4ac695) - raw data for this study rawdata_butterfly2012.csv MD5: 628e9d69afddbff42821f96bf06093bb) - raw data for this study rawdata_orthoptera2011.csv (MD5: 2ce7626b9615d6dcb62f060f81e86cbb) - raw data for this study rawdata_orthoptera2012.csv (MD5: 2b38ac89dfcb8df03ed0a041b5458ed6) - raw data for this study Description These files provide the raw data for all statistical analyses to produce all tables and figures in this study.
DOI: 10.6084/m9.figshare.3568662
title: Appendix A. Hydrograph of the Cinaruco River showing data for two and a half annual flood pulses, and four low-water troughs during the January–April dry season.

description: Hydrograph of the Cinaruco River showing data for two and a half annual flood pulses, and four low-water troughs during the January–April dry season.
DOI: 10.6084/m9.figshare.3568662.v1
title: Appendix A. Hydrograph of the Cinaruco River showing data for two and a half annual flood pulses, and four low-water troughs during the January–April dry season.

description: Hydrograph of the Cinaruco River showing data for two and a half annual flood pulses, and four low-water troughs during the January–April dry season.