cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3528935
title: Supplement 1. WinBUGS model code.

description: File List Byers_WinBUGS_code.txt -- WinBUGS code Description The file "Byers_WinBUGS_code.txt" contains the code for fitting our hierarchical spatial model. To execute the code, the text must be pasted into a document window in WinBugs. <i>Note</i>: WinBUGS parameterizes the normal distribution in terms of the precision parameter "tau" which is the reciprocal of the variance parameter.
DOI: 10.6084/m9.figshare.3528935.v1
title: Supplement 1. WinBUGS model code.

description: File List Byers_WinBUGS_code.txt -- WinBUGS code Description The file "Byers_WinBUGS_code.txt" contains the code for fitting our hierarchical spatial model. To execute the code, the text must be pasted into a document window in WinBugs. <i>Note</i>: WinBUGS parameterizes the normal distribution in terms of the precision parameter "tau" which is the reciprocal of the variance parameter.
DOI: 10.6084/m9.figshare.3528932
title: Appendix A. Results from ANOVA testing effects of the predator richness and identity treatments on juvenile oyster survival, oyster recruitment, and percentage organic matter.

description: Results from ANOVA testing effects of the predator richness and identity treatments on juvenile oyster survival, oyster recruitment, and percentage organic matter.
DOI: 10.6084/m9.figshare.3528932.v1
title: Appendix A. Results from ANOVA testing effects of the predator richness and identity treatments on juvenile oyster survival, oyster recruitment, and percentage organic matter.

description: Results from ANOVA testing effects of the predator richness and identity treatments on juvenile oyster survival, oyster recruitment, and percentage organic matter.
DOI: 10.6084/m9.figshare.3528929
title: Appendix B. Results from ANOVA testing planned comparisons of different combinations of predators with and without blue crabs on juvenile oyster survival, oyster recruitment, and organic matter.

description: Results from ANOVA testing planned comparisons of different combinations of predators with and without blue crabs on juvenile oyster survival, oyster recruitment, and organic matter.
DOI: 10.6084/m9.figshare.3528926
title: Appendix C. Results from ANOVA testing effects of removing different combinations of species of predator with and without compensation for the loss of biomass on juvenile oyster survival, oyster recruitment, and organic matter.

description: Results from ANOVA testing effects of removing different combinations of species of predator with and without compensation for the loss of biomass on juvenile oyster survival, oyster recruitment, and organic matter.
DOI: 10.6084/m9.figshare.3528926.v1
title: Appendix C. Results from ANOVA testing effects of removing different combinations of species of predator with and without compensation for the loss of biomass on juvenile oyster survival, oyster recruitment, and organic matter.

description: Results from ANOVA testing effects of removing different combinations of species of predator with and without compensation for the loss of biomass on juvenile oyster survival, oyster recruitment, and organic matter.
DOI: 10.6084/m9.figshare.3528923
title: Appendix A. Figures showing the survival and growth of Bugula neritina colonies.

description: Figures showing the survival and growth of Bugula neritina colonies.
DOI: 10.6084/m9.figshare.3528923.v1
title: Appendix A. Figures showing the survival and growth of Bugula neritina colonies.

description: Figures showing the survival and growth of Bugula neritina colonies.
DOI: 10.6084/m9.figshare.3528920
title: Appendix A. A table showing the locations of study populations of Senecio vulgaris.

description: A table showing the locations of study populations of Senecio vulgaris.
DOI: 10.6084/m9.figshare.3528920.v1
title: Appendix A. A table showing the locations of study populations of Senecio vulgaris.

description: A table showing the locations of study populations of Senecio vulgaris.
DOI: 10.6084/m9.figshare.3528917
title: Appendix B. A summary of hierarchical mixed-model ANOVA in growth and reproductive traits of Senecio vulgaris.

description: A summary of hierarchical mixed-model ANOVA in growth and reproductive traits of Senecio vulgaris.
DOI: 10.6084/m9.figshare.3528917.v1
title: Appendix B. A summary of hierarchical mixed-model ANOVA in growth and reproductive traits of Senecio vulgaris.

description: A summary of hierarchical mixed-model ANOVA in growth and reproductive traits of Senecio vulgaris.
DOI: 10.6084/m9.figshare.3528914
title: Appendix C. A summary of hierarchical analysis of molecular variance (AMOVA) for 249 Senecio vulgaris individuals representing 24 populations from three regions: North America, Europe (Switzerland), and Australia.

description: A summary of hierarchical analysis of molecular variance (AMOVA) for 249 Senecio vulgaris individuals representing 24 populations from three regions: North America, Europe (Switzerland), and Australia.
DOI: 10.6084/m9.figshare.3528914.v1
title: Appendix C. A summary of hierarchical analysis of molecular variance (AMOVA) for 249 Senecio vulgaris individuals representing 24 populations from three regions: North America, Europe (Switzerland), and Australia.

description: A summary of hierarchical analysis of molecular variance (AMOVA) for 249 Senecio vulgaris individuals representing 24 populations from three regions: North America, Europe (Switzerland), and Australia.
DOI: 10.6084/m9.figshare.3528911
title: Appendix A. A table showing means and error per treatment and tissue type in Nicotiana tabacum damaged by foliar and root herbivores.

description: A table showing means and error per treatment and tissue type in Nicotiana tabacum damaged by foliar and root herbivores.
DOI: 10.6084/m9.figshare.3528911.v1
title: Appendix A. A table showing means and error per treatment and tissue type in Nicotiana tabacum damaged by foliar and root herbivores.

description: A table showing means and error per treatment and tissue type in Nicotiana tabacum damaged by foliar and root herbivores.
DOI: 10.6084/m9.figshare.3528908
title: Appendix B. MANOVA table for the effects of root herbivory (nematodes), shoot herbivory (generalist and specialist caterpillars), and their interaction on above- and belowground secondary chemistry in Nicotiana tabacum.

description: MANOVA table for the effects of root herbivory (nematodes), shoot herbivory (generalist and specialist caterpillars), and their interaction on above- and belowground secondary chemistry in Nicotiana tabacum.
DOI: 10.6084/m9.figshare.3528908.v1
title: Appendix B. MANOVA table for the effects of root herbivory (nematodes), shoot herbivory (generalist and specialist caterpillars), and their interaction on above- and belowground secondary chemistry in Nicotiana tabacum.

description: MANOVA table for the effects of root herbivory (nematodes), shoot herbivory (generalist and specialist caterpillars), and their interaction on above- and belowground secondary chemistry in Nicotiana tabacum.
DOI: 10.6084/m9.figshare.3528905
title: Appendix C. A table showing effect sizes and variances used in meta-analysis of root herbivory on aboveground secondary chemistry of Nicotiana tabacum by biosynthetic site.

description: A table showing effect sizes and variances used in meta-analysis of root herbivory on aboveground secondary chemistry of Nicotiana tabacum by biosynthetic site.
DOI: 10.6084/m9.figshare.3528902
title: Appendix D. A table showing plants and secondary chemicals used for comparison of constitutive defenses between leaves and roots.

description: A table showing plants and secondary chemicals used for comparison of constitutive defenses between leaves and roots.
DOI: 10.6084/m9.figshare.3528902.v1
title: Appendix D. A table showing plants and secondary chemicals used for comparison of constitutive defenses between leaves and roots.

description: A table showing plants and secondary chemicals used for comparison of constitutive defenses between leaves and roots.
DOI: 10.6084/m9.figshare.3528899
title: Appendix E. A table showing effect sizes and variances used in meta-analysis of induced defenses elicited and expressed in leaves and roots.

description: A table showing effect sizes and variances used in meta-analysis of induced defenses elicited and expressed in leaves and roots.
DOI: 10.6084/m9.figshare.3528896
title: Appendix F. Publications used for analyses of constitutive and induced defenses.

description: Publications used for analyses of constitutive and induced defenses.
DOI: 10.6084/m9.figshare.3528896.v1
title: Appendix F. Publications used for analyses of constitutive and induced defenses.

description: Publications used for analyses of constitutive and induced defenses.
DOI: 10.6084/m9.figshare.12905711
title: Data for Plastome phylogenomics enables biogeographic analysis and a new subtribal classification of the Andropogoneae (Poaceae – Panicoideae)

description: File is composed of four directories. <br>Alignments Andropogoneae_Biogeo_Final_Alignment.fsa--Full plastome alignment. Andropogoneae_Biogeo_Final_Alignment_Gblocks.fsa--Gblocks alignment (gaps removed).BEAST2_Analysis Andropogoneae_Biogeo_25run_analysis.txt--Log file analysis for all runs. Andropogoneae_Biogeography_20KBurnin_forAnnotator.trees_results_keep--MCC tree made from all data.<br> Andropogoneae_Biogeography_20KBurnin_forAnnotator.trees_results_mean--MCC tree made from mean of node heights.<br> Andropogoneae_Biogeography_20KBurnin_forAnnotator.trees_results_median--MCC tree made median of node heights.Maximum_Likelihood_Phylogenies Full_Alignment--Standard output files for RAxML run using full alignment. Gblocks_Alignment--Standard output files for RAxML run using Gblocks alignment.RASP_Analysis<br> SDIVA_8states--Output files for SDIVA run using RASP. Andro_DEC_8states--Output files for DEC run using RASP. BBM_8stats--Output files for BBM run using RASP.
DOI: 10.6084/m9.figshare.12905711.v1
title: Data for Plastome phylogenomics enables biogeographic analysis and a new subtribal classification of the Andropogoneae (Poaceae – Panicoideae)

description: File is composed of four directories. <br>Alignments Andropogoneae_Biogeo_Final_Alignment.fsa--Full plastome alignment. Andropogoneae_Biogeo_Final_Alignment_Gblocks.fsa--Gblocks alignment (gaps removed).BEAST2_Analysis Andropogoneae_Biogeo_25run_analysis.txt--Log file analysis for all runs. Andropogoneae_Biogeography_20KBurnin_forAnnotator.trees_results_keep--MCC tree made from all data.<br> Andropogoneae_Biogeography_20KBurnin_forAnnotator.trees_results_mean--MCC tree made from mean of node heights.<br> Andropogoneae_Biogeography_20KBurnin_forAnnotator.trees_results_median--MCC tree made median of node heights.Maximum_Likelihood_Phylogenies Full_Alignment--Standard output files for RAxML run using full alignment. Gblocks_Alignment--Standard output files for RAxML run using Gblocks alignment.RASP_Analysis<br> SDIVA_8states--Output files for SDIVA run using RASP. Andro_DEC_8states--Output files for DEC run using RASP. BBM_8stats--Output files for BBM run using RASP.
DOI: 10.6084/m9.figshare.3528893
title: Appendix A. Study statistics and site variables used in the meta-analysis, including biome classification, climate, latitude, and statistics calculated for the analysis, with references.

description: Study statistics and site variables used in the meta-analysis, including biome classification, climate, latitude, and statistics calculated for the analysis, with references.
DOI: 10.6084/m9.figshare.3528890
title: Appendix B. Effect of fertilizer form and method of aboveground net primary productivity on R.

description: Effect of fertilizer form and method of aboveground net primary productivity on R.
DOI: 10.6084/m9.figshare.3528890.v1
title: Appendix B. Effect of fertilizer form and method of aboveground net primary productivity on R.

description: Effect of fertilizer form and method of aboveground net primary productivity on R.
DOI: 10.6084/m9.figshare.3528887
title: Supplement 1. Matlab m-code used to obtain values of mean annual temperature and mean annual precipitation at a point nearest to the study site from the New et al. (2000) 10' climatology when local data were not available.

description: File List GlobalClimate.m -- Matlab code Description This code returns the mean annual temperature (MAT) and mean annual precipitation (MAP) for any terrestrial lat × long coordinates using the data set described in New et al (2000). Input (at prompt): latitude and longitude (in decimal degrees with N and E &gt; 0 and W and S &lt;0) Output: mean annual precipitation MAP (mm y-1) and mean annual temperature MAT, (degrees C) References: New, Mark, David Lister, Mike Hulme, and Ian Makin. 2002. A high resolution data set of surface climate over global land areas. Climate Research 21:1–25. Required data files (should be renamed after downloading): Tglobal10min.mat: http://www.cru.uea.ac.uk/cru/data/tmc.htm/grid_10min_pre.dat.gz Pglobal10min.mat: http://www.cru.uea.ac.uk/cru/data/tmc.htm/grid_10min_tmp.dat.gz
DOI: 10.6084/m9.figshare.3528887.v1
title: Supplement 1. Matlab m-code used to obtain values of mean annual temperature and mean annual precipitation at a point nearest to the study site from the New et al. (2000) 10' climatology when local data were not available.

description: File List GlobalClimate.m -- Matlab code Description This code returns the mean annual temperature (MAT) and mean annual precipitation (MAP) for any terrestrial lat × long coordinates using the data set described in New et al (2000). Input (at prompt): latitude and longitude (in decimal degrees with N and E &gt; 0 and W and S &lt;0) Output: mean annual precipitation MAP (mm y-1) and mean annual temperature MAT, (degrees C) References: New, Mark, David Lister, Mike Hulme, and Ian Makin. 2002. A high resolution data set of surface climate over global land areas. Climate Research 21:1–25. Required data files (should be renamed after downloading): Tglobal10min.mat: http://www.cru.uea.ac.uk/cru/data/tmc.htm/grid_10min_pre.dat.gz Pglobal10min.mat: http://www.cru.uea.ac.uk/cru/data/tmc.htm/grid_10min_tmp.dat.gz
DOI: 10.6084/m9.figshare.3528884
title: Appendix A. A description of the individual-based model (IBM) and fitting to egg drift data.

description: A description of the individual-based model (IBM) and fitting to egg drift data.
DOI: 10.6084/m9.figshare.3528884.v1
title: Appendix A. A description of the individual-based model (IBM) and fitting to egg drift data.

description: A description of the individual-based model (IBM) and fitting to egg drift data.
DOI: 10.6084/m9.figshare.3528881
title: Appendix B. A description and justification of the parameters used for the IBM of salmon spawning.

description: A description and justification of the parameters used for the IBM of salmon spawning.
DOI: 10.6084/m9.figshare.3528881.v1
title: Appendix B. A description and justification of the parameters used for the IBM of salmon spawning.

description: A description and justification of the parameters used for the IBM of salmon spawning.
DOI: 10.6084/m9.figshare.3528878
title: Appendix C. A description and table of the details of the bioenergetics modeling.

description: A description and table of the details of the bioenergetics modeling.
DOI: 10.6084/m9.figshare.3528878.v1
title: Appendix C. A description and table of the details of the bioenergetics modeling.

description: A description and table of the details of the bioenergetics modeling.
DOI: 10.6084/m9.figshare.3528875
title: Appendix D. A figure showing observed and predicted seasonal egg production in streams.

description: A figure showing observed and predicted seasonal egg production in streams.
DOI: 10.6084/m9.figshare.3528875.v1
title: Appendix D. A figure showing observed and predicted seasonal egg production in streams.

description: A figure showing observed and predicted seasonal egg production in streams.
DOI: 10.6084/m9.figshare.3528872
title: Appendix E. Estimated parameters comparing model predictions of egg drift and observed egg drift.

description: Estimated parameters comparing model predictions of egg drift and observed egg drift.
DOI: 10.6084/m9.figshare.3528872.v1
title: Appendix E. Estimated parameters comparing model predictions of egg drift and observed egg drift.

description: Estimated parameters comparing model predictions of egg drift and observed egg drift.
DOI: 10.6084/m9.figshare.3528869
title: Appendix F. Model fits (by AICc) and parameter values for competing models that described the relationship between salmon density and observed egg drift.

description: Model fits (by AICc) and parameter values for competing models that described the relationship between salmon density and observed egg drift.
DOI: 10.6084/m9.figshare.3528869.v1
title: Appendix F. Model fits (by AICc) and parameter values for competing models that described the relationship between salmon density and observed egg drift.

description: Model fits (by AICc) and parameter values for competing models that described the relationship between salmon density and observed egg drift.
DOI: 10.6084/m9.figshare.3528866
title: Appendix G. Model fits for competing models that described the relationship between salmon density and egg consumption by grayling and rainbow trout in Hidden Lake Creek, Alaska, 2000–2005.

description: Model fits for competing models that described the relationship between salmon density and egg consumption by grayling and rainbow trout in Hidden Lake Creek, Alaska, 2000–2005.
DOI: 10.6084/m9.figshare.3528866.v1
title: Appendix G. Model fits for competing models that described the relationship between salmon density and egg consumption by grayling and rainbow trout in Hidden Lake Creek, Alaska, 2000–2005.

description: Model fits for competing models that described the relationship between salmon density and egg consumption by grayling and rainbow trout in Hidden Lake Creek, Alaska, 2000–2005.
DOI: 10.6084/m9.figshare.3528863
title: Appendix A. Image of a mesocosm used in the experiment.

description: Image of a mesocosm used in the experiment.
DOI: 10.6084/m9.figshare.3528863.v1
title: Appendix A. Image of a mesocosm used in the experiment.

description: Image of a mesocosm used in the experiment.
DOI: 10.6084/m9.figshare.3528860
title: Appendix B. Description of prey assemblage.

description: Description of prey assemblage.
DOI: 10.6084/m9.figshare.3528860.v1
title: Appendix B. Description of prey assemblage.

description: Description of prey assemblage.
DOI: 10.6084/m9.figshare.3528857
title: Appendix C. Calculation of resource capture efficiency.

description: Calculation of resource capture efficiency.
DOI: 10.6084/m9.figshare.3528857.v1
title: Appendix C. Calculation of resource capture efficiency.

description: Calculation of resource capture efficiency.
DOI: 10.6084/m9.figshare.3528854
title: Appendix D. Total resource capture rate within all treatments.

description: Total resource capture rate within all treatments.
DOI: 10.6084/m9.figshare.3528854.v1
title: Appendix D. Total resource capture rate within all treatments.

description: Total resource capture rate within all treatments.
DOI: 10.6084/m9.figshare.3528851
title: Appendix E. Analysis of predator diversity and density effects.

description: Analysis of predator diversity and density effects.
DOI: 10.6084/m9.figshare.3528851.v1
title: Appendix E. Analysis of predator diversity and density effects.

description: Analysis of predator diversity and density effects.
DOI: 10.6084/m9.figshare.3528848
title: Appendix F. Analysis of species-specific resource consumption.

description: Analysis of species-specific resource consumption.
DOI: 10.6084/m9.figshare.3528845
title: Appendix G. Comparison of prey consumption patterns.

description: Comparison of prey consumption patterns.
DOI: 10.6084/m9.figshare.3528848.v1
title: Appendix F. Analysis of species-specific resource consumption.

description: Analysis of species-specific resource consumption.
DOI: 10.6084/m9.figshare.3528845.v1
title: Appendix G. Comparison of prey consumption patterns.

description: Comparison of prey consumption patterns.
DOI: 10.6084/m9.figshare.3528842
title: Appendix A. Stability of the logistic semi-discrete model.

description: Stability of the logistic semi-discrete model.
DOI: 10.6084/m9.figshare.3528839
title: Supplement 1. Mathematica code to calculate the overcompensation and consumer–resource stability boundaries of the semi-discrete model.

description: File List StabilityAnalysisSemi-DiscreteLogistic.nb - Mathematica code <br> StabilityAnalysisSemi-DiscreteLogistic.pdf - PDF of the code Description Mathematica (version 5) code to calculate the overcompensation and consumer-resource stability boundaries of the semi-discrete model as a function of mu and alpha, for different values of rho. The analysis is decsribed in Appendix A. The code calculates the stability boundaries in sections.<br> data1 - bottom part of the consumer-resource boundary (heavy solid line in Fig. 2a of the main text);<br> data2 - top part of the consumer-resource boundary (dotted line in Fig. 2a);<br> data3 - top of the left arm of the overcompensation boundary (dashed line in Fig. 2a) until it crosses the consumer-resource boundary;<br> data4 - bottom of the left arm of the overcompensation boundary (dashed line in Fig. 2a) until the minimum of the boundary;<br> data5 - right arm of the overcompensation boundary (dashed line in Fig. 2a). Some parameter definitions:<br> J11, J12, J21, J22 - elements of the Jacobian from the linear stability analysis of the model.<br> Cond1 - condition for existence of a positive equilibrium;<br> Cond2 - transition from stability to overcompensation cycles;<br> Cond3 - transition from stability to consumer - resource cycles;<br> Period - period of population cycles on the consumer - resource stability boundary (for a discussion of caclulating boundary conditions and the period see Gurney, W. S. C., and R. M. Nisbet. 1998. Ecological Dynamics. Oxford University Press, New York, New York, USA)
DOI: 10.6084/m9.figshare.3528836
title: Appendix A. A table of ecosystem functions to which the Price Equation does or does not apply.

description: A table of ecosystem functions to which the Price Equation does or does not apply.
DOI: 10.6084/m9.figshare.3528836.v1
title: Appendix A. A table of ecosystem functions to which the Price Equation does or does not apply.

description: A table of ecosystem functions to which the Price Equation does or does not apply.
DOI: 10.6084/m9.figshare.3528833
title: Appendix B. A derivation of a generalization of the Price Equation partition to non-nested sets of species, showing that relaxing the assumption of strict nestedness is possible, but that the resulting generalization of the Price Equation partition is of limited utility.

description: A derivation of a generalization of the Price Equation partition to non-nested sets of species, showing that relaxing the assumption of strict nestedness is possible, but that the resulting generalization of the Price Equation partition is of limited utility.
DOI: 10.6084/m9.figshare.3528833.v1
title: Appendix B. A derivation of a generalization of the Price Equation partition to non-nested sets of species, showing that relaxing the assumption of strict nestedness is possible, but that the resulting generalization of the Price Equation partition is of limited utility.

description: A derivation of a generalization of the Price Equation partition to non-nested sets of species, showing that relaxing the assumption of strict nestedness is possible, but that the resulting generalization of the Price Equation partition is of limited utility.
DOI: 10.6084/m9.figshare.3528830
title: Appendix A. Tables with parameter values and equations used for the physiologically structured population model of perch (Perca fluviatilis) and its resource.

description: Tables with parameter values and equations used for the physiologically structured population model of perch (Perca fluviatilis) and its resource.