cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3528272
title: Supplement 1. Visual Basic source code containing the algorithms described in this paper.

description: File List <i>All files at once</i> BBridgeCode.zip -- zip file containing Visual Basic executable, source code, and example input file. <i>Individual files</i> BrownianBridgeExecutable.exe – Executable Visual Basic program<br> ProjBrownianBridge.vbp.txt – Source code for Visual Basic program<br> ProjBrownianBridge.vbw.txt – Source code for Visual Basic program<br> FrmBBAnalysis.frm.txt – Source code for Visual Basic program<br> FrmGridExtent.frm.txt – Source code for Visual Basic program<br> FrmOpenFileBB.frm.txt – Source code for Visual Basic program<br> FrmSaveASBrownBridge.txt – Source code for Visual Basic program<br> Mod1DMinimization.bas.txt – Source code for Visual Basic program<br> ModFileManagement.bas.txt – Source code for Visual Basic program<br> ModPublicVariablesBB.bas.txt – Source code for Visual Basic program<br> ExampleInput.txt – Example input file<br> Description BrownianBridgeExeecutable.exe calculates the utilization distribution (i.e., probability function) based on temporally explicit location data. Algorithms are described in the original paper. The user loads a location file containing tab-delimited columns representing the <i>x</i>-coordinate, <i>y</i>-coordinate, and time of each location. The input file should have column headings such as “<i>x</i>-coordinate”, “<i>y</i>-coordinate” and “RunningClock”. An example input data file, ExampleInput.txt, is available from the file list. Output grid is a text file containing <i>x</i> and <i>y</i> coordinates of the grid along with associated probability-of-occurrence at that grid location.
DOI: 10.6084/m9.figshare.3528269
title: Appendix A. Tables of life-history parameters associated with population models depicted in Figs. 1 and 2.

description: Tables of life-history parameters associated with population models depicted in Figs. 1 and 2.
DOI: 10.6084/m9.figshare.3528269.v1
title: Appendix A. Tables of life-history parameters associated with population models depicted in Figs. 1 and 2.

description: Tables of life-history parameters associated with population models depicted in Figs. 1 and 2.
DOI: 10.6084/m9.figshare.3528266
title: Appendix B. Algorithm for calculating the lineage-extinction probability.

description: Algorithm for calculating the lineage-extinction probability.
DOI: 10.6084/m9.figshare.3528266.v1
title: Appendix B. Algorithm for calculating the lineage-extinction probability.

description: Algorithm for calculating the lineage-extinction probability.
DOI: 10.6084/m9.figshare.3528263
title: Appendix C. Method for transforming a value of the extinction-effective population index into the corresponding value of stage size.

description: Method for transforming a value of the extinction-effective population index into the corresponding value of stage size.
DOI: 10.6084/m9.figshare.3528263.v1
title: Appendix C. Method for transforming a value of the extinction-effective population index into the corresponding value of stage size.

description: Method for transforming a value of the extinction-effective population index into the corresponding value of stage size.
DOI: 10.6084/m9.figshare.3528260
title: Supplement 1. MATLAB source codes used to calculate lineage extinction probability.

description: File List BranchProcess.m.txt -- MATLAB source codes for calculating the lineage-extinction probability Description Matlab source codes used to calculate lineage-extinction probability. By removing the file name extension ".txt", it becomes a source code that runs under Matlab (MathWorks 2001). Please see MathWorks (2001. MATLAB. Version 7.0, release 14. MathWorks, Natick, Massachusetts, USA) for how to run source codes.
DOI: 10.6084/m9.figshare.3528260.v1
title: Supplement 1. MATLAB source codes used to calculate lineage extinction probability.

description: File List BranchProcess.m.txt -- MATLAB source codes for calculating the lineage-extinction probability Description Matlab source codes used to calculate lineage-extinction probability. By removing the file name extension ".txt", it becomes a source code that runs under Matlab (MathWorks 2001). Please see MathWorks (2001. MATLAB. Version 7.0, release 14. MathWorks, Natick, Massachusetts, USA) for how to run source codes.
DOI: 10.6084/m9.figshare.3528257
title: Appendix A. A table showing the different matrices used in the calculation of the different scenarios and how they were parameterized.

description: A table showing the different matrices used in the calculation of the different scenarios and how they were parameterized.
DOI: 10.6084/m9.figshare.3528257.v1
title: Appendix A. A table showing the different matrices used in the calculation of the different scenarios and how they were parameterized.

description: A table showing the different matrices used in the calculation of the different scenarios and how they were parameterized.
DOI: 10.6084/m9.figshare.3528254
title: Appendix B. A description of how matrix elements were modified to allow for variation among years in the 11 different types of disturbance matrices.

description: A description of how matrix elements were modified to allow for variation among years in the 11 different types of disturbance matrices.
DOI: 10.6084/m9.figshare.3528254.v1
title: Appendix B. A description of how matrix elements were modified to allow for variation among years in the 11 different types of disturbance matrices.

description: A description of how matrix elements were modified to allow for variation among years in the 11 different types of disturbance matrices.
DOI: 10.6084/m9.figshare.3528251
title: Appendix A. Summary of meta-analytical techniques applied in this paper.

description: Summary of meta-analytical techniques applied in this paper.
DOI: 10.6084/m9.figshare.3528251.v1
title: Appendix A. Summary of meta-analytical techniques applied in this paper.

description: Summary of meta-analytical techniques applied in this paper.
DOI: 10.6084/m9.figshare.3528248
title: Appendix B. Tables summarizing the canopy cover and tree density inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.

description: Tables summarizing the canopy cover and tree density inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.
DOI: 10.6084/m9.figshare.3528248.v1
title: Appendix B. Tables summarizing the canopy cover and tree density inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.

description: Tables summarizing the canopy cover and tree density inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.
DOI: 10.6084/m9.figshare.3528245
title: Appendix C. Understory variables measured inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.

description: Understory variables measured inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.
DOI: 10.6084/m9.figshare.3528245.v1
title: Appendix C. Understory variables measured inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.

description: Understory variables measured inside and outside livestock exclosures at five sites in northern Arizona in 1941 and 2004.
DOI: 10.6084/m9.figshare.3528242
title: Appendix A. Size of canopy seed banks for serotinous species at four shrubland sites near Eneabba, southwestern Australia.

description: Size of canopy seed banks for serotinous species at four shrubland sites near Eneabba, southwestern Australia.
DOI: 10.6084/m9.figshare.3528239
title: Appendix B. Spatial autocorrelation analyses for soil seed bank species at four shrubland sites near Eneabba, southwestern Australia, by site and species attributes for scales 1–10 m.

description: Spatial autocorrelation analyses for soil seed bank species at four shrubland sites near Eneabba, southwestern Australia, by site and species attributes for scales 1–10 m.
DOI: 10.6084/m9.figshare.3528239.v1
title: Appendix B. Spatial autocorrelation analyses for soil seed bank species at four shrubland sites near Eneabba, southwestern Australia, by site and species attributes for scales 1–10 m.

description: Spatial autocorrelation analyses for soil seed bank species at four shrubland sites near Eneabba, southwestern Australia, by site and species attributes for scales 1–10 m.
DOI: 10.6084/m9.figshare.3528236
title: Appendix C. Analysis of covariance model for the relationship between mode of regeneration, taxonomic family, and extant density of plant species, with estimated canopy seed store size per plant as covariate, for four high-diversity shrubland sites near Eneabba, southwestern Australia.

description: Analysis of covariance model for the relationship between mode of regeneration, taxonomic family, and extant density of plant species, with estimated canopy seed store size per plant as covariate, for four high-diversity shrubland sites near Eneabba, southwestern Australia.
DOI: 10.6084/m9.figshare.3528236.v1
title: Appendix C. Analysis of covariance model for the relationship between mode of regeneration, taxonomic family, and extant density of plant species, with estimated canopy seed store size per plant as covariate, for four high-diversity shrubland sites near Eneabba, southwestern Australia.

description: Analysis of covariance model for the relationship between mode of regeneration, taxonomic family, and extant density of plant species, with estimated canopy seed store size per plant as covariate, for four high-diversity shrubland sites near Eneabba, southwestern Australia.
DOI: 10.6084/m9.figshare.3528233
title: Appendix A. A description of the model PHENOFIT.

description: A description of the model PHENOFIT.
DOI: 10.6084/m9.figshare.3528233.v1
title: Appendix A. A description of the model PHENOFIT.

description: A description of the model PHENOFIT.
DOI: 10.6084/m9.figshare.3528230
title: Appendix B. A descriptive figure of PHENOFIT.

description: A descriptive figure of PHENOFIT.
DOI: 10.6084/m9.figshare.3528230.v1
title: Appendix B. A descriptive figure of PHENOFIT.

description: A descriptive figure of PHENOFIT.
DOI: 10.6084/m9.figshare.3528227
title: Appendix A. Annual percentage mortality rates and 95% confidence intervals for paired and unpaired species in wet and dry plots, in the Tapajós National Forest, east-central Brazilian Amazon.

description: Annual percentage mortality rates and 95% confidence intervals for paired and unpaired species in wet and dry plots, in the Tapajós National Forest, east-central Brazilian Amazon.
DOI: 10.6084/m9.figshare.3528224
title: Appendix A. Life history characteristics and population parameters of 16 species of Myristicaceae in the 25-ha Yasuní forest dynamics plot.

description: Life history characteristics and population parameters of 16 species of Myristicaceae in the 25-ha Yasuní forest dynamics plot.
DOI: 10.6084/m9.figshare.3528224.v1
title: Appendix A. Life history characteristics and population parameters of 16 species of Myristicaceae in the 25-ha Yasuní forest dynamics plot.

description: Life history characteristics and population parameters of 16 species of Myristicaceae in the 25-ha Yasuní forest dynamics plot.
DOI: 10.6084/m9.figshare.3528221
title: Appendix B. Topographic map of the 25-ha Yasuní forest dynamics plot, showing locations of the 30 nested 20×20 m seedling plots.

description: Topographic map of the 25-ha Yasuní forest dynamics plot, showing locations of the 30 nested 20×20 m seedling plots.
DOI: 10.6084/m9.figshare.3528221.v1
title: Appendix B. Topographic map of the 25-ha Yasuní forest dynamics plot, showing locations of the 30 nested 20×20 m seedling plots.

description: Topographic map of the 25-ha Yasuní forest dynamics plot, showing locations of the 30 nested 20×20 m seedling plots.
DOI: 10.6084/m9.figshare.3528218
title: Appendix C. Survival of seedlings of 15 Myristicaceae species in 30 seedling plots within the Yasuní forest dynamics plot over three years.

description: Survival of seedlings of 15 Myristicaceae species in 30 seedling plots within the Yasuní forest dynamics plot over three years.
DOI: 10.6084/m9.figshare.3528218.v1
title: Appendix C. Survival of seedlings of 15 Myristicaceae species in 30 seedling plots within the Yasuní forest dynamics plot over three years.

description: Survival of seedlings of 15 Myristicaceae species in 30 seedling plots within the Yasuní forest dynamics plot over three years.
DOI: 10.6084/m9.figshare.3528215
title: Appendix D. Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: community test.

description: Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: community test.
DOI: 10.6084/m9.figshare.3528215.v1
title: Appendix D. Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: community test.

description: Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: community test.
DOI: 10.6084/m9.figshare.3528212
title: Appendix E. Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: habitat test.

description: Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: habitat test.
DOI: 10.6084/m9.figshare.3528212.v1
title: Appendix E. Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: habitat test.

description: Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: habitat test.
DOI: 10.6084/m9.figshare.3528209
title: Appendix F. Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: light availability test.

description: Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: light availability test.
DOI: 10.6084/m9.figshare.3528209.v1
title: Appendix F. Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: light availability test.

description: Summary of observed regression slopes of seedling survival on adult tree abundance or seedling density: light availability test.
DOI: 10.6084/m9.figshare.3528206
title: Appendix G. Community compensatory trend (CCT) analysis for each individual seedling plot and three different areas of surrounding adult trees.

description: Community compensatory trend (CCT) analysis for each individual seedling plot and three different areas of surrounding adult trees.
DOI: 10.6084/m9.figshare.3528206.v1
title: Appendix G. Community compensatory trend (CCT) analysis for each individual seedling plot and three different areas of surrounding adult trees.

description: Community compensatory trend (CCT) analysis for each individual seedling plot and three different areas of surrounding adult trees.
DOI: 10.6084/m9.figshare.3528203
title: Appendix H. Habitat associations of 15 species of Myristicaceae seedlings on the Yasuní forest dynamics plot.

description: Habitat associations of 15 species of Myristicaceae seedlings on the Yasuní forest dynamics plot.
DOI: 10.6084/m9.figshare.3528203.v1
title: Appendix H. Habitat associations of 15 species of Myristicaceae seedlings on the Yasuní forest dynamics plot.

description: Habitat associations of 15 species of Myristicaceae seedlings on the Yasuní forest dynamics plot.
DOI: 10.6084/m9.figshare.3528200
title: Appendix I. Comparison of analysis of deviance models for the proportion of seedling survivors of species in each quarter 20×20 m seedling plot.

description: Comparison of analysis of deviance models for the proportion of seedling survivors of species in each quarter 20×20 m seedling plot.
DOI: 10.6084/m9.figshare.3528200.v1
title: Appendix I. Comparison of analysis of deviance models for the proportion of seedling survivors of species in each quarter 20×20 m seedling plot.

description: Comparison of analysis of deviance models for the proportion of seedling survivors of species in each quarter 20×20 m seedling plot.
DOI: 10.6084/m9.figshare.3528197
title: Appendix A. The theory behind the formulas.

description: The theory behind the formulas.
DOI: 10.6084/m9.figshare.3528194
title: Appendix B. Statistical methods for estimating cov(E,C).

description: Statistical methods for estimating cov(E,C).
DOI: 10.6084/m9.figshare.3528197.v1
title: Appendix A. The theory behind the formulas.

description: The theory behind the formulas.
DOI: 10.6084/m9.figshare.3528191
title: Appendix C. An example with simulated data.

description: An example with simulated data.
DOI: 10.6084/m9.figshare.3528191.v1
title: Appendix C. An example with simulated data.

description: An example with simulated data.
DOI: 10.6084/m9.figshare.3528188
title: Supplement 1. R code for assessing covariance between environment and competition.

description: File List Readme.txt Assessing_CovEC.r Example_data.txt all_files.zip Description This supplement contains an R program that does the calcuations listed in the text. This program is provided for convenience. The formulae are relatively straight forward to use and program. Bootstrap <i>P</i> value correction is a little more complex, but again would not be difficult for users to program in a language of their choice. The code (Assessing_CovEC.r), as written, analyzes the data from Appendix C, with no user inputs. These data are in the file Example_data.txt. To use this program for your own data, you need to substitute your own data file name. This file must be an ascii file with two columns, the first for the removal and the second for the control, with rows corresponding to blocks in the experiment. Users must also supply as input variables, nbl, the number of blocks in the experiment, theta, the error variance ratio, and reps, the number of bootstrap replicates to be used. The code provided has these values in the first section labeled "user inputs." To run the program with your own data, all you need to do is modify the values in this section of the code for yourself. The program is not provided as compiled code as it much simpler just to modify the first section of the source code for your own purposes.
DOI: 10.6084/m9.figshare.3528188.v1
title: Supplement 1. R code for assessing covariance between environment and competition.

description: File List Readme.txt Assessing_CovEC.r Example_data.txt all_files.zip Description This supplement contains an R program that does the calcuations listed in the text. This program is provided for convenience. The formulae are relatively straight forward to use and program. Bootstrap <i>P</i> value correction is a little more complex, but again would not be difficult for users to program in a language of their choice. The code (Assessing_CovEC.r), as written, analyzes the data from Appendix C, with no user inputs. These data are in the file Example_data.txt. To use this program for your own data, you need to substitute your own data file name. This file must be an ascii file with two columns, the first for the removal and the second for the control, with rows corresponding to blocks in the experiment. Users must also supply as input variables, nbl, the number of blocks in the experiment, theta, the error variance ratio, and reps, the number of bootstrap replicates to be used. The code provided has these values in the first section labeled "user inputs." To run the program with your own data, all you need to do is modify the values in this section of the code for yourself. The program is not provided as compiled code as it much simpler just to modify the first section of the source code for your own purposes.
DOI: 10.6084/m9.figshare.3528185
title: Appendix A. A description of the site characteristics data sets.

description: A description of the site characteristics data sets.
DOI: 10.6084/m9.figshare.3528185.v1
title: Appendix A. A description of the site characteristics data sets.

description: A description of the site characteristics data sets.
DOI: 10.6084/m9.figshare.3528182
title: Appendix B. A correlation plot for annual mean urchin GI and the coastal anomaly index at all smoothing scales.

description: A correlation plot for annual mean urchin GI and the coastal anomaly index at all smoothing scales.
DOI: 10.6084/m9.figshare.3528182.v1
title: Appendix B. A correlation plot for annual mean urchin GI and the coastal anomaly index at all smoothing scales.

description: A correlation plot for annual mean urchin GI and the coastal anomaly index at all smoothing scales.
DOI: 10.6084/m9.figshare.3528179
title: Appendix C. The semivariogram of the annual mean urchin gonadal indices.

description: The semivariogram of the annual mean urchin gonadal indices.
DOI: 10.6084/m9.figshare.3528179.v1
title: Appendix C. The semivariogram of the annual mean urchin gonadal indices.

description: The semivariogram of the annual mean urchin gonadal indices.
DOI: 10.6084/m9.figshare.3528176
title: Appendix D. The multiple-regression model of the small- and large-scale coastal anomaly indices predicting annual mean urchin GI.

description: The multiple-regression model of the small- and large-scale coastal anomaly indices predicting annual mean urchin GI.
DOI: 10.6084/m9.figshare.3528176.v1
title: Appendix D. The multiple-regression model of the small- and large-scale coastal anomaly indices predicting annual mean urchin GI.

description: The multiple-regression model of the small- and large-scale coastal anomaly indices predicting annual mean urchin GI.
DOI: 10.6084/m9.figshare.3528173
title: Appendix A. Maps showing the location of recruitment experiment in San Juan de la Costa, Mexico.

description: Maps showing the location of recruitment experiment in San Juan de la Costa, Mexico.
DOI: 10.6084/m9.figshare.3528170
title: Appendix B. A photograph of the Sargassum bed in the natural fringe.

description: A photograph of the Sargassum bed in the natural fringe.
DOI: 10.6084/m9.figshare.3528170.v1
title: Appendix B. A photograph of the Sargassum bed in the natural fringe.

description: A photograph of the Sargassum bed in the natural fringe.
DOI: 10.6084/m9.figshare.3528167
title: Appendix C. Design of the artificial Sargassum structure.

description: Design of the artificial Sargassum structure.
DOI: 10.6084/m9.figshare.3528167.v1
title: Appendix C. Design of the artificial Sargassum structure.

description: Design of the artificial Sargassum structure.
DOI: 10.6084/m9.figshare.3528164
title: Appendix D. A general methodology used for Sargassum biomass estimation.

description: A general methodology used for Sargassum biomass estimation.
DOI: 10.6084/m9.figshare.3528164.v1
title: Appendix D. A general methodology used for Sargassum biomass estimation.

description: A general methodology used for Sargassum biomass estimation.
DOI: 10.6084/m9.figshare.3528161
title: Appendix A. The species (zooplankton) or genera (phytoplankton) belonging to each of the defined functional groups.

description: The species (zooplankton) or genera (phytoplankton) belonging to each of the defined functional groups.
DOI: 10.6084/m9.figshare.3528158
title: Appendix B. ANOVA tables for TP, chlorophyll a, and periphyton growth.

description: ANOVA tables for TP, chlorophyll a, and periphyton growth.
DOI: 10.6084/m9.figshare.3528161.v1
title: Appendix A. The species (zooplankton) or genera (phytoplankton) belonging to each of the defined functional groups.

description: The species (zooplankton) or genera (phytoplankton) belonging to each of the defined functional groups.
DOI: 10.6084/m9.figshare.3528158.v1
title: Appendix B. ANOVA tables for TP, chlorophyll a, and periphyton growth.

description: ANOVA tables for TP, chlorophyll a, and periphyton growth.
DOI: 10.6084/m9.figshare.3528155
title: Appendix C. The methods and results of the primary production experiment.

description: The methods and results of the primary production experiment.
DOI: 10.6084/m9.figshare.3528155.v1
title: Appendix C. The methods and results of the primary production experiment.

description: The methods and results of the primary production experiment.