cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3551562
title: Appendix D. Simulation results.

description: Simulation results.
DOI: 10.6084/m9.figshare.3551562.v1
title: Appendix D. Simulation results.

description: Simulation results.
DOI: 10.6084/m9.figshare.3551559
title: Appendix E. Additional example application for experimental data with known occupancy probability.

description: Additional example application for experimental data with known occupancy probability.
DOI: 10.6084/m9.figshare.3551556
title: Supplement 1. Examples of R code to fit models.

description: File List FalsePositiveLikelihoods.R<br> FPdatasets.Rdata Description The FalsePositiveLikelihoods.R file contains scripts for R (ver 2.12.1) to calculate each of the basic likelihoods presented in the paper. The script calls the example datasets FPdatasets.Rdata which give examples fitting the same data set using each of the models. The script also gives an example for estimating occupancy when detection is a function of a covariate (dist).
DOI: 10.6084/m9.figshare.3551559.v1
title: Appendix E. Additional example application for experimental data with known occupancy probability.

description: Additional example application for experimental data with known occupancy probability.
DOI: 10.6084/m9.figshare.3551553
title: Appendix A. The negative binomial distribution viewed as a hierarchical Poisson–gamma model.

description: The negative binomial distribution viewed as a hierarchical Poisson–gamma model.
DOI: 10.6084/m9.figshare.3551550
title: Appendix B. A figure showing two-dimensional profile likelihoods of ω and θ.

description: A figure showing two-dimensional profile likelihoods of ω and θ.
DOI: 10.6084/m9.figshare.3551547
title: Appendix C. A figure with observed vs. fitted mean–variance relationships.

description: A figure with observed vs. fitted mean–variance relationships.
DOI: 10.6084/m9.figshare.3551547.v1
title: Appendix C. A figure with observed vs. fitted mean–variance relationships.

description: A figure with observed vs. fitted mean–variance relationships.
DOI: 10.6084/m9.figshare.3551544
title: Appendix D. A table with parameter estimates and standard errors of fitted models.

description: A table with parameter estimates and standard errors of fitted models.
DOI: 10.6084/m9.figshare.3551541
title: Supplement 1. MATLAB code for the log-likelihood.

description: File List nbinll.m nbinll.doc [note that ESA cannot guarantee the forward migration of this file format] Description The file nbinll.m contains MATLAB code for a function returning the log-likelihood of a set of parameters. The likelihood is based on the assumption that the given count data (DATA) is negatively binomially distributed around predefined expectations (X), with the overdispersion parameters ω (OMEGA) and θ (THETA). The file itself contains MATLAB style user instructions/help. The file nbinll.doc is basically the same information as in previous file but in MS-Word format. This file is visually more appealing for viewing the code outside the MATLAB editor.
DOI: 10.6084/m9.figshare.3551541.v1
title: Supplement 1. MATLAB code for the log-likelihood.

description: File List nbinll.m nbinll.doc [note that ESA cannot guarantee the forward migration of this file format] Description The file nbinll.m contains MATLAB code for a function returning the log-likelihood of a set of parameters. The likelihood is based on the assumption that the given count data (DATA) is negatively binomially distributed around predefined expectations (X), with the overdispersion parameters ω (OMEGA) and θ (THETA). The file itself contains MATLAB style user instructions/help. The file nbinll.doc is basically the same information as in previous file but in MS-Word format. This file is visually more appealing for viewing the code outside the MATLAB editor.
DOI: 10.6084/m9.figshare.3551538
title: Supplement 2. Count data on migrating woodlarks at Hanko bird observatory.

description: File List Woodlark_data.txt Description The file Woodlark_data.txt is a tab-delimited ASCII file, containing count data on migrating woodlarks at Hanko bird observatory, during autumns 2007–2009. The migration period considered ranges from 1st September (day-of-year 245) to 10th of November (day-of-year 315). The first row is a heading line. Column definitions: Column 1, title DOY. The time of migration season expressed as day-of-year, from 1st September (day 245) to 10th of November (day 315). Checksum for DOY = 19880. Column 2, title Y07. Day specific number of observed migrating woodlarks in autumn 2007. Checksum for Y07 = 323. Column 3, title Y08. Day specific number of observed migrating woodlarks in autumn 2008. Checksum for Y08 = 361. Column 4, title Y09. Day specific number of observed migrating woodlarks in autumn 2009. Checksum for Y09 = 217.
DOI: 10.6084/m9.figshare.3551535
title: Appendix A. A description of the studied ecosystem and site, including Baltic Sea map, and figures depicting herring recruitment and Bosmina abundance, model statistics, and model results.

description: A description of the studied ecosystem and site, including Baltic Sea map, and figures depicting herring recruitment and Bosmina abundance, model statistics, and model results.
DOI: 10.6084/m9.figshare.3551532
title: Appendix A. Description of the experimental design and of successional pathways on experimental panels.

description: Description of the experimental design and of successional pathways on experimental panels.
DOI: 10.6084/m9.figshare.3551532.v1
title: Appendix A. Description of the experimental design and of successional pathways on experimental panels.

description: Description of the experimental design and of successional pathways on experimental panels.
DOI: 10.6084/m9.figshare.3551529
title: Appendix B. List of the species included in the multivariate analysis.

description: List of the species included in the multivariate analysis.
DOI: 10.6084/m9.figshare.3551529.v1
title: Appendix B. List of the species included in the multivariate analysis.

description: List of the species included in the multivariate analysis.
DOI: 10.6084/m9.figshare.3551526
title: Appendix C. Tables of statistical analyses.

description: Tables of statistical analyses.
DOI: 10.6084/m9.figshare.3551526.v1
title: Appendix C. Tables of statistical analyses.

description: Tables of statistical analyses.
DOI: 10.6084/m9.figshare.3551523
title: Appendix A. Supporting fertilization scheme, statistical results, graphs, and species information.

description: Supporting fertilization scheme, statistical results, graphs, and species information.
DOI: 10.6084/m9.figshare.3551523.v1
title: Appendix A. Supporting fertilization scheme, statistical results, graphs, and species information.

description: Supporting fertilization scheme, statistical results, graphs, and species information.
DOI: 10.6084/m9.figshare.3551520
title: Appendix B. A table showing species names, life forms, and trends in the experimental plots.

description: A table showing species names, life forms, and trends in the experimental plots.
DOI: 10.6084/m9.figshare.3551520.v1
title: Appendix B. A table showing species names, life forms, and trends in the experimental plots.

description: A table showing species names, life forms, and trends in the experimental plots.
DOI: 10.6084/m9.figshare.3551517
title: Appendix A. Yield per plot vs. number of species for the Biodepth Ireland experiment.

description: Yield per plot vs. number of species for the Biodepth Ireland experiment.
DOI: 10.6084/m9.figshare.3551514
title: Appendix B. Detail of the construction of the matrices of phylogenetic distances used for the species in the two experiments.

description: Detail of the construction of the matrices of phylogenetic distances used for the species in the two experiments.
DOI: 10.6084/m9.figshare.3551514.v1
title: Appendix B. Detail of the construction of the matrices of phylogenetic distances used for the species in the two experiments.

description: Detail of the construction of the matrices of phylogenetic distances used for the species in the two experiments.
DOI: 10.6084/m9.figshare.3551511
title: Appendix C. Calculation of the standard deviation of the variable CD across all communities at a given level of richness.

description: Calculation of the standard deviation of the variable CD across all communities at a given level of richness.
DOI: 10.6084/m9.figshare.3551511.v1
title: Appendix C. Calculation of the standard deviation of the variable CD across all communities at a given level of richness.

description: Calculation of the standard deviation of the variable CD across all communities at a given level of richness.
DOI: 10.6084/m9.figshare.3551508
title: Supplement 1. Detailed description of how the methods are applied to data, including SAS and R code and data from two experiments.

description: File List Jena_dataset.pdf Worked example of model fitting for the Jena_dataset.pdf Jena_dataset.sas SAS code for analysis of Jena_dataset.sas Jena_dataset.r R code for analysis of Jena_dataset.r Jena_data.csv Jena data Ireland_site_biodepth.csv Data for Ireland_site_Biodepth.csv Description The supplements are designed to assist the reader to implement the methods using the statistical packages SAS and R. The first supplement (Worked example of model fitting for theJena_dataset.pdf) provides a detailed description of the application and interpretation of a range of models using the Jena dataset. The second and third supplements (SAS code for analysis of Jena_dataset.sas) and (R code for analysis of Jena_dataset.r) provide SAS and R code to implement the method using the Jena dataset. The data for the two sites is provided in Jena_data.csv and Ireland_site_biodepth.csv. Hash values for supplements Jena_data.csv and Ireland_site_biodepth.csv calculated by HASHCALC: MD5 hash value for Jena_data.csv 6b86c280a15bbd4aae08b5b4c91363ee MD5 hash value for Ireland_site_biodepth.csv 9b60c32ceca9259e47d7ee42b9ae5f16
DOI: 10.6084/m9.figshare.3551508.v1
title: Supplement 1. Detailed description of how the methods are applied to data, including SAS and R code and data from two experiments.

description: File List Jena_dataset.pdf Worked example of model fitting for the Jena_dataset.pdf Jena_dataset.sas SAS code for analysis of Jena_dataset.sas Jena_dataset.r R code for analysis of Jena_dataset.r Jena_data.csv Jena data Ireland_site_biodepth.csv Data for Ireland_site_Biodepth.csv Description The supplements are designed to assist the reader to implement the methods using the statistical packages SAS and R. The first supplement (Worked example of model fitting for theJena_dataset.pdf) provides a detailed description of the application and interpretation of a range of models using the Jena dataset. The second and third supplements (SAS code for analysis of Jena_dataset.sas) and (R code for analysis of Jena_dataset.r) provide SAS and R code to implement the method using the Jena dataset. The data for the two sites is provided in Jena_data.csv and Ireland_site_biodepth.csv. Hash values for supplements Jena_data.csv and Ireland_site_biodepth.csv calculated by HASHCALC: MD5 hash value for Jena_data.csv 6b86c280a15bbd4aae08b5b4c91363ee MD5 hash value for Ireland_site_biodepth.csv 9b60c32ceca9259e47d7ee42b9ae5f16
DOI: 10.6084/m9.figshare.3551505
title: Full Archive

description: Full Archive
DOI: 10.6084/m9.figshare.3551502
title: Appendix A. Summaries of mass, body length, abundance and functional group classifications.

description: Summaries of mass, body length, abundance and functional group classifications.
DOI: 10.6084/m9.figshare.3551502.v1
title: Appendix A. Summaries of mass, body length, abundance and functional group classifications.

description: Summaries of mass, body length, abundance and functional group classifications.
DOI: 10.6084/m9.figshare.3551499
title: Appendix B. Summary statistics for regression analyses and model selection.

description: Summary statistics for regression analyses and model selection.
DOI: 10.6084/m9.figshare.3551499.v1
title: Appendix B. Summary statistics for regression analyses and model selection.

description: Summary statistics for regression analyses and model selection.
DOI: 10.6084/m9.figshare.3551496
title: Appendix C. Graphs of functional group changes over time in biomass and abundance.

description: Graphs of functional group changes over time in biomass and abundance.
DOI: 10.6084/m9.figshare.3551493
title: Appendix D. Graphs showing temporal comparison of energy use for functional group members.

description: Graphs showing temporal comparison of energy use for functional group members.
DOI: 10.6084/m9.figshare.3551496.v1
title: Appendix C. Graphs of functional group changes over time in biomass and abundance.

description: Graphs of functional group changes over time in biomass and abundance.
DOI: 10.6084/m9.figshare.3551493.v1
title: Appendix D. Graphs showing temporal comparison of energy use for functional group members.

description: Graphs showing temporal comparison of energy use for functional group members.
DOI: 10.6084/m9.figshare.3551490
title: Appendix E. Graphs of species-specific changes over time in energy use.

description: Graphs of species-specific changes over time in energy use.
DOI: 10.6084/m9.figshare.3551487
title: Appendix A. Individual plant shoot and root biomass responses to soil feedback and herbivory.

description: Individual plant shoot and root biomass responses to soil feedback and herbivory.
DOI: 10.6084/m9.figshare.3551490.v1
title: Appendix E. Graphs of species-specific changes over time in energy use.

description: Graphs of species-specific changes over time in energy use.
DOI: 10.6084/m9.figshare.3551487.v1
title: Appendix A. Individual plant shoot and root biomass responses to soil feedback and herbivory.

description: Individual plant shoot and root biomass responses to soil feedback and herbivory.
DOI: 10.6084/m9.figshare.3551484
title: Appendix A. Description of vegetation inventory data sets used in this study.

description: Description of vegetation inventory data sets used in this study.
DOI: 10.6084/m9.figshare.3551484.v1
title: Appendix A. Description of vegetation inventory data sets used in this study.

description: Description of vegetation inventory data sets used in this study.
DOI: 10.6084/m9.figshare.3551481
title: Appendix B. Tree species ≥ 10 cm DBH and their abundance in old-growth and second-growth study areas described in Appendix A.

description: Tree species ≥ 10 cm DBH and their abundance in old-growth and second-growth study areas described in Appendix A.
DOI: 10.6084/m9.figshare.3551478
title: Appendix C. The effect of undetected species on estimated species frequencies.

description: The effect of undetected species on estimated species frequencies.
DOI: 10.6084/m9.figshare.3551475
title: Appendix D. Testing for specialization under the multinomial model, using a super-majority threshold.

description: Testing for specialization under the multinomial model, using a super-majority threshold.
DOI: 10.6084/m9.figshare.3551472
title: Appendix E. Classifications of 78 bird species surveyed by Baker et al. (2002) in woodland and heath plots in southeastern Australia.

description: Classifications of 78 bird species surveyed by Baker et al. (2002) in woodland and heath plots in southeastern Australia.
DOI: 10.6084/m9.figshare.3551469
title: Appendix F. Comparison of results of Indicator Species Analysis, equalized and non-equalized abundance-based phi correlation analysis and multinomial classification of 359 tree species using super-majority threshold and simple-majority threshold using P = 0.05 or P = 0.005.

description: Comparison of results of Indicator Species Analysis, equalized and non-equalized abundance-based phi correlation analysis and multinomial classification of 359 tree species using super-majority threshold and simple-majority threshold using P = 0.05 or P = 0.005.
DOI: 10.6084/m9.figshare.3551469.v1
title: Appendix F. Comparison of results of Indicator Species Analysis, equalized and non-equalized abundance-based phi correlation analysis and multinomial classification of 359 tree species using super-majority threshold and simple-majority threshold using P = 0.05 or P = 0.005.

description: Comparison of results of Indicator Species Analysis, equalized and non-equalized abundance-based phi correlation analysis and multinomial classification of 359 tree species using super-majority threshold and simple-majority threshold using P = 0.05 or P = 0.005.
DOI: 10.6084/m9.figshare.3551466
title: Appendix G. A user's guide for program CLAM, with instructions and a link for downloading the program.

description: A user's guide for program CLAM, with instructions and a link for downloading the program.
DOI: 10.6084/m9.figshare.3551463
title: Appendix A. Supplemental methods: a detailed description of climate data and statistical models compared for model fit.

description: Supplemental methods: a detailed description of climate data and statistical models compared for model fit.
DOI: 10.6084/m9.figshare.3551460
title: Appendix B. Supplemental figures showing relationships between climate variables.

description: Supplemental figures showing relationships between climate variables.
DOI: 10.6084/m9.figshare.3551457
title: Appendix A. Methodological details: site description, propagule pressure indices, and germination rates.

description: Methodological details: site description, propagule pressure indices, and germination rates.
DOI: 10.6084/m9.figshare.3551457.v1
title: Appendix A. Methodological details: site description, propagule pressure indices, and germination rates.

description: Methodological details: site description, propagule pressure indices, and germination rates.
DOI: 10.6084/m9.figshare.3551454
title: Appendix B. Invasibility calculations.

description: Invasibility calculations.
DOI: 10.6084/m9.figshare.3551454.v1
title: Appendix B. Invasibility calculations.

description: Invasibility calculations.
DOI: 10.6084/m9.figshare.3551451
title: Appendix A. Molecular methods in detail.

description: Molecular methods in detail.
DOI: 10.6084/m9.figshare.3551451.v1
title: Appendix A. Molecular methods in detail.

description: Molecular methods in detail.
DOI: 10.6084/m9.figshare.3551448
title: Appendix B. Mean percent root length colonization of each AMF when inoculated alone and the mean number of LSU copies detected by qPCR of each AMF when co-inoculated.

description: Mean percent root length colonization of each AMF when inoculated alone and the mean number of LSU copies detected by qPCR of each AMF when co-inoculated.
DOI: 10.6084/m9.figshare.3551448.v1
title: Appendix B. Mean percent root length colonization of each AMF when inoculated alone and the mean number of LSU copies detected by qPCR of each AMF when co-inoculated.

description: Mean percent root length colonization of each AMF when inoculated alone and the mean number of LSU copies detected by qPCR of each AMF when co-inoculated.
DOI: 10.6084/m9.figshare.3551445
title: Appendix A. GPS coordinates, harvest dates, soil temperature measured, and PCR (polymerase chain reaction) success of the five geothermal and three nonthermal sites.

description: GPS coordinates, harvest dates, soil temperature measured, and PCR (polymerase chain reaction) success of the five geothermal and three nonthermal sites.
DOI: 10.6084/m9.figshare.3551445.v1
title: Appendix A. GPS coordinates, harvest dates, soil temperature measured, and PCR (polymerase chain reaction) success of the five geothermal and three nonthermal sites.

description: GPS coordinates, harvest dates, soil temperature measured, and PCR (polymerase chain reaction) success of the five geothermal and three nonthermal sites.
DOI: 10.6084/m9.figshare.3551442
title: Appendix B. Plant species observed within the three nonthermal grasslands.

description: Plant species observed within the three nonthermal grasslands.
DOI: 10.6084/m9.figshare.3551442.v1
title: Appendix B. Plant species observed within the three nonthermal grasslands.

description: Plant species observed within the three nonthermal grasslands.
DOI: 10.6084/m9.figshare.3551439
title: Appendix C. Ribotype name, their closest BLASTN match, fragment sizes with Mbo1 and Hinf1 digestion, and accession numbers.

description: Ribotype name, their closest BLASTN match, fragment sizes with Mbo1 and Hinf1 digestion, and accession numbers.
DOI: 10.6084/m9.figshare.3551439.v1
title: Appendix C. Ribotype name, their closest BLASTN match, fragment sizes with Mbo1 and Hinf1 digestion, and accession numbers.

description: Ribotype name, their closest BLASTN match, fragment sizes with Mbo1 and Hinf1 digestion, and accession numbers.
DOI: 10.6084/m9.figshare.3551436
title: Appendix D. Presence of RFLP types in the five geothermal and three nonthermal grasslands sampled.

description: Presence of RFLP types in the five geothermal and three nonthermal grasslands sampled.
DOI: 10.6084/m9.figshare.3551436.v1
title: Appendix D. Presence of RFLP types in the five geothermal and three nonthermal grasslands sampled.

description: Presence of RFLP types in the five geothermal and three nonthermal grasslands sampled.
DOI: 10.6084/m9.figshare.3551433
title: Appendix E. RFLP species accumulation curves for the geothermal and non-thermal grasslands.

description: RFLP species accumulation curves for the geothermal and non-thermal grasslands.
DOI: 10.6084/m9.figshare.3551433.v1
title: Appendix E. RFLP species accumulation curves for the geothermal and non-thermal grasslands.

description: RFLP species accumulation curves for the geothermal and non-thermal grasslands.
DOI: 10.6084/m9.figshare.3551430
title: Appendix F. Phylogenetic tree of Glomus group A based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Glomus group A based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551430.v1
title: Appendix F. Phylogenetic tree of Glomus group A based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Glomus group A based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551427
title: Appendix G. Phylogenetic tree of Scutellospora based on 18S.

description: Phylogenetic tree of Scutellospora based on 18S.
DOI: 10.6084/m9.figshare.3551427.v1
title: Appendix G. Phylogenetic tree of Scutellospora based on 18S.

description: Phylogenetic tree of Scutellospora based on 18S.
DOI: 10.6084/m9.figshare.3551424
title: Appendix H. Phylogenetic tree of Acaulospora based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Acaulospora based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551424.v1
title: Appendix H. Phylogenetic tree of Acaulospora based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Acaulospora based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551421
title: Appendix I. Phylogenetic tree of Archaeospora based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Archaeospora based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551421.v1
title: Appendix I. Phylogenetic tree of Archaeospora based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Archaeospora based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551418
title: Appendix J. Phylogenetic tree of Paraglomus based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Paraglomus based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551415
title: Appendix A. Diagram of hierarchical sampling scheme.

description: Diagram of hierarchical sampling scheme.
DOI: 10.6084/m9.figshare.3551418.v1
title: Appendix J. Phylogenetic tree of Paraglomus based on ITS 1, 5.85 rDNA, and ITS 2.

description: Phylogenetic tree of Paraglomus based on ITS 1, 5.85 rDNA, and ITS 2.
DOI: 10.6084/m9.figshare.3551415.v1
title: Appendix A. Diagram of hierarchical sampling scheme.

description: Diagram of hierarchical sampling scheme.
DOI: 10.6084/m9.figshare.3551412
title: Appendix B. Assessment of model fit.

description: Assessment of model fit.
DOI: 10.6084/m9.figshare.3551412.v1
title: Appendix B. Assessment of model fit.

description: Assessment of model fit.