cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3552549
title: Appendix A. The conditions for extinction and persistence in a model with linear functional responses, the parameter space leading to alternative equilibria in this linear response model, and the responses of populations and yields to harvesting in models with type-2 functional responses.

description: The conditions for extinction and persistence in a model with linear functional responses, the parameter space leading to alternative equilibria in this linear response model, and the responses of populations and yields to harvesting in models with type-2 functional responses.
DOI: 10.6084/m9.figshare.3552549.v1
title: Appendix A. The conditions for extinction and persistence in a model with linear functional responses, the parameter space leading to alternative equilibria in this linear response model, and the responses of populations and yields to harvesting in models with type-2 functional responses.

description: The conditions for extinction and persistence in a model with linear functional responses, the parameter space leading to alternative equilibria in this linear response model, and the responses of populations and yields to harvesting in models with type-2 functional responses.
DOI: 10.6084/m9.figshare.3552546
title: Appendix A. Examples from past climate transitions.

description: Examples from past climate transitions.
DOI: 10.6084/m9.figshare.3552543
title: Appendix B. Deviations in the performance of leading indicators when measured in time series due to methodological issues.

description: Deviations in the performance of leading indicators when measured in time series due to methodological issues.
DOI: 10.6084/m9.figshare.3552540
title: Appendix C. Reliability in identification of increasing trends in variance and autocorrelation.

description: Reliability in identification of increasing trends in variance and autocorrelation.
DOI: 10.6084/m9.figshare.3552540.v1
title: Appendix C. Reliability in identification of increasing trends in variance and autocorrelation.

description: Reliability in identification of increasing trends in variance and autocorrelation.
DOI: 10.6084/m9.figshare.3552537
title: Appendix A. An adaptive Metropolis-Hastings scheme.

description: An adaptive Metropolis-Hastings scheme.
DOI: 10.6084/m9.figshare.3552534
title: Supplement 1. R code for fitting the random-walk state-space model using particle filter MCMC.

description: File List adaptiveMH.r (md5: 1c7f3697e28dca0aceda63360930e29f)<br> adaptiveMHfuns.r (md5: cabc33a60ab779b954d853816c9e3cce)<br> PF.r (md5: eff6f6611833c86c1d1a8e8135af7e04) Description adaptiveMH.r – Contains a script for fitting a random-walk model with drift for Kangaroo population dynamics on the log-scale using particle filtering Metropolis Hastings with an initial adaptive phase. adaptiveMHfuns.r – Contains functions that are used for estimating and handling the normal mixture proposals. PF.r – Contains functions that perform the particle filtering and define the model.
DOI: 10.6084/m9.figshare.3552531
title: Appendix A. Model selection.

description: Model selection.
DOI: 10.6084/m9.figshare.3552528
title: Appendix B. Posterior predictive checks.

description: Posterior predictive checks.
DOI: 10.6084/m9.figshare.3552531.v1
title: Appendix A. Model selection.

description: Model selection.
DOI: 10.6084/m9.figshare.3552525
title: Appendix C. Posterior distributions of the CR-SEM parameters (conditional on the covariates being in the model).

description: Posterior distributions of the CR-SEM parameters (conditional on the covariates being in the model).
DOI: 10.6084/m9.figshare.3552525.v1
title: Appendix C. Posterior distributions of the CR-SEM parameters (conditional on the covariates being in the model).

description: Posterior distributions of the CR-SEM parameters (conditional on the covariates being in the model).
DOI: 10.6084/m9.figshare.3552522
title: Supplement 1. BUGS code to implement the CR-SEM approach.

description: File List BUGScodes.txt (md5: 065a902fc724b73a8db114ad6c8875ae) Description BUGS codes for fitting SEM-CR models to the blackbird and blue tits data.
DOI: 10.6084/m9.figshare.3552522.v1
title: Supplement 1. BUGS code to implement the CR-SEM approach.

description: File List BUGScodes.txt (md5: 065a902fc724b73a8db114ad6c8875ae) Description BUGS codes for fitting SEM-CR models to the blackbird and blue tits data.
DOI: 10.6084/m9.figshare.3552519
title: Appendix A. An alternate version of Fig. 2, assuming random-split starting trees with Grafen branch lengths, and a figure showing the relationship between K and tree size.

description: An alternate version of Fig. 2, assuming random-split starting trees with Grafen branch lengths, and a figure showing the relationship between K and tree size.
DOI: 10.6084/m9.figshare.3552516
title: Supplement 1. R function to thin terminal polytomies.

description: File List thin_terminal_polytomies.R (md5: e5971814a64f86b1e0968186a7cdb120) Description thin_terminal_polytomies.R is an R function to thin terminal polytomies.
DOI: 10.6084/m9.figshare.3552519.v1
title: Appendix A. An alternate version of Fig. 2, assuming random-split starting trees with Grafen branch lengths, and a figure showing the relationship between K and tree size.

description: An alternate version of Fig. 2, assuming random-split starting trees with Grafen branch lengths, and a figure showing the relationship between K and tree size.
DOI: 10.6084/m9.figshare.3552516.v1
title: Supplement 1. R function to thin terminal polytomies.

description: File List thin_terminal_polytomies.R (md5: e5971814a64f86b1e0968186a7cdb120) Description thin_terminal_polytomies.R is an R function to thin terminal polytomies.
DOI: 10.6084/m9.figshare.3552513
title: Appendix A. Patch characteristics, tree age model, and the lichen survey.

description: Patch characteristics, tree age model, and the lichen survey.
DOI: 10.6084/m9.figshare.3552507
title: Appendix B. Modeling colonization probability and connectivity.

description: Modeling colonization probability and connectivity.
DOI: 10.6084/m9.figshare.3552507.v1
title: Appendix B. Modeling colonization probability and connectivity.

description: Modeling colonization probability and connectivity.
DOI: 10.6084/m9.figshare.3552504
title: Appendix C. Model building and prior and posterior distributions of model parameters.

description: Model building and prior and posterior distributions of model parameters.
DOI: 10.6084/m9.figshare.3552504.v1
title: Appendix C. Model building and prior and posterior distributions of model parameters.

description: Model building and prior and posterior distributions of model parameters.
DOI: 10.6084/m9.figshare.3552501
title: Supplement 1. Model code and data structure for fitting the general model using OpenBUGS.

description: File List OpenBUGS_code.txt (md5: 90849493aeb5943ad41b2f14bfdf3ef0) Description The OpenBUGS_code.txt gives the model code and data structure for fitting the general model using OpenBUGS.
DOI: 10.6084/m9.figshare.3552501.v1
title: Supplement 1. Model code and data structure for fitting the general model using OpenBUGS.

description: File List OpenBUGS_code.txt (md5: 90849493aeb5943ad41b2f14bfdf3ef0) Description The OpenBUGS_code.txt gives the model code and data structure for fitting the general model using OpenBUGS.
DOI: 10.6084/m9.figshare.3552492
title: Appendix A. Plant-species traits that affect ecosystem functioning.

description: Plant-species traits that affect ecosystem functioning.
DOI: 10.6084/m9.figshare.3552492.v1
title: Appendix A. Plant-species traits that affect ecosystem functioning.

description: Plant-species traits that affect ecosystem functioning.
DOI: 10.6084/m9.figshare.3552489
title: Appendix B. Example of construction of a trait richness gradient.

description: Example of construction of a trait richness gradient.
DOI: 10.6084/m9.figshare.3552489.v1
title: Appendix B. Example of construction of a trait richness gradient.

description: Example of construction of a trait richness gradient.
DOI: 10.6084/m9.figshare.3552486
title: Appendix C. Correlation coefficient among traits.

description: Correlation coefficient among traits.
DOI: 10.6084/m9.figshare.3552486.v1
title: Appendix C. Correlation coefficient among traits.

description: Correlation coefficient among traits.
DOI: 10.6084/m9.figshare.3552483
title: Appendix A. Site information and field methods.

description: Site information and field methods.
DOI: 10.6084/m9.figshare.3552480
title: Appendix B. Radiocarbon dating and age-depth models.

description: Radiocarbon dating and age-depth models.
DOI: 10.6084/m9.figshare.3552483.v1
title: Appendix A. Site information and field methods.

description: Site information and field methods.
DOI: 10.6084/m9.figshare.3552477
title: Appendix C. Testate amoeba assemblages and water-table depth reconstructions.

description: Testate amoeba assemblages and water-table depth reconstructions.
DOI: 10.6084/m9.figshare.3552477.v1
title: Appendix C. Testate amoeba assemblages and water-table depth reconstructions.

description: Testate amoeba assemblages and water-table depth reconstructions.
DOI: 10.6084/m9.figshare.3552474
title: Data Paper. Data Paper

description: File List The zip file contains the entire data set as a single downloadable archive. All files contain 4028 records, including an initial header row and 4027 data records, and each is in tab-delimited ASCII text format. Clark_tropical_trees_1983_2010.zip<br> Crown_positions_1983_2010.txt<br> Crowns_above_1983_2010.txt<br> Dates_1983_2010.txt<br> Diameter_1983_2010.txt<br> Diameter_growth_1983_2010.txt<br> Habitats_1983_2010.txt<br> Heights_1983_2010.txt<br> Height_growth_1983_2010.txt<br> How_measured_1983_2010.txt<br> Location_descriptions_1983_2010.txt<br> POM_heights_1983_2010.txt<br> Stem_condition_1983_2010.txt<br> DescriptionTree species richness in tropical rain forest typically exceeds several hundred species over mesoscale landscapes. There is no generally accepted ecological theory that accounts for the coexistence of so many species with the same general morphologies and the same basic requirements of light, nutrients, water, and physical space. In part this lack of theory rests on the lack of understanding of the post-establishment ecology for the vast majority of tropical tree species. Of even more immediate concern is the lack of data on tree performance in relation to climate; such data are critical to project effects of global climate change on tropical forests. Here we present data on the post-establishment ecology of 10 species of tropical wet forest trees selected to span a range of predicted life history patterns. The study site was terra firme old-growth tropical wet forest at the La Selva Biological Station in Costa Rica. Particular emphasis has been placed on evaluating the precision of measurements, metadata development, and annual measurements of all individuals; the annual time step is a temporal interval that captures the scale of climate and microhabitat variations and the responses of trees to this variation in tropical rain forest. We present data on survivorship, growth, and microhabitat for 4027 individuals from established seedling to canopy-level individuals measured annually between 1983 and 2010 (the study is ongoing and complete through 2011), thus adding 10 years’ data and &gt;600 new individuals to the data set published in <i>Ecological Archives</i> in 2006. The data set is unique in its scope (number of years of continuous annual measurements, number of monitored individuals) as well as in the degree of metadata documentation and unrestricted access to the raw data (data sets published in 2000, 2006, this paper). The data have been used to study life history patterns, relations with microhabitats including edaphic factors and crown light environments, relations among ecophysiology, morphology, and performance, the relation of tree performance to climate variation both at local and global scales, and in a variety of remote-sensing studies. <i>Key words: Costa Rica; emergents; global change; La Selva; life history strategies; physical damage; tree demography; tropical rain forest; tropical trees.</i>
DOI: 10.6084/m9.figshare.3552474.v1
title: Data Paper. Data Paper

description: File List The zip file contains the entire data set as a single downloadable archive. All files contain 4028 records, including an initial header row and 4027 data records, and each is in tab-delimited ASCII text format. Clark_tropical_trees_1983_2010.zip<br> Crown_positions_1983_2010.txt<br> Crowns_above_1983_2010.txt<br> Dates_1983_2010.txt<br> Diameter_1983_2010.txt<br> Diameter_growth_1983_2010.txt<br> Habitats_1983_2010.txt<br> Heights_1983_2010.txt<br> Height_growth_1983_2010.txt<br> How_measured_1983_2010.txt<br> Location_descriptions_1983_2010.txt<br> POM_heights_1983_2010.txt<br> Stem_condition_1983_2010.txt<br> DescriptionTree species richness in tropical rain forest typically exceeds several hundred species over mesoscale landscapes. There is no generally accepted ecological theory that accounts for the coexistence of so many species with the same general morphologies and the same basic requirements of light, nutrients, water, and physical space. In part this lack of theory rests on the lack of understanding of the post-establishment ecology for the vast majority of tropical tree species. Of even more immediate concern is the lack of data on tree performance in relation to climate; such data are critical to project effects of global climate change on tropical forests. Here we present data on the post-establishment ecology of 10 species of tropical wet forest trees selected to span a range of predicted life history patterns. The study site was terra firme old-growth tropical wet forest at the La Selva Biological Station in Costa Rica. Particular emphasis has been placed on evaluating the precision of measurements, metadata development, and annual measurements of all individuals; the annual time step is a temporal interval that captures the scale of climate and microhabitat variations and the responses of trees to this variation in tropical rain forest. We present data on survivorship, growth, and microhabitat for 4027 individuals from established seedling to canopy-level individuals measured annually between 1983 and 2010 (the study is ongoing and complete through 2011), thus adding 10 years’ data and &gt;600 new individuals to the data set published in <i>Ecological Archives</i> in 2006. The data set is unique in its scope (number of years of continuous annual measurements, number of monitored individuals) as well as in the degree of metadata documentation and unrestricted access to the raw data (data sets published in 2000, 2006, this paper). The data have been used to study life history patterns, relations with microhabitats including edaphic factors and crown light environments, relations among ecophysiology, morphology, and performance, the relation of tree performance to climate variation both at local and global scales, and in a variety of remote-sensing studies. <i>Key words: Costa Rica; emergents; global change; La Selva; life history strategies; physical damage; tree demography; tropical rain forest; tropical trees.</i>
DOI: 10.6084/m9.figshare.3552471
title: Appendix A. Mapped stand used for demographic inference.

description: Mapped stand used for demographic inference.
DOI: 10.6084/m9.figshare.3552468
title: Appendix B. Parameters and state variables included in the models.

description: Parameters and state variables included in the models.
DOI: 10.6084/m9.figshare.3552471.v1
title: Appendix A. Mapped stand used for demographic inference.

description: Mapped stand used for demographic inference.
DOI: 10.6084/m9.figshare.3552468.v1
title: Appendix B. Parameters and state variables included in the models.

description: Parameters and state variables included in the models.
DOI: 10.6084/m9.figshare.3552465
title: Appendix C. Selection of priors.

description: Selection of priors.
DOI: 10.6084/m9.figshare.3552462
title: Appendix D. Model evaluation.

description: Model evaluation.
DOI: 10.6084/m9.figshare.3552465.v1
title: Appendix C. Selection of priors.

description: Selection of priors.
DOI: 10.6084/m9.figshare.3552459
title: Appendix A. Simple linear regressions of total population woody growth, reproductive biomass, and percent population woody growth and reproductive biomass as functions of precipitation for each year.

description: Simple linear regressions of total population woody growth, reproductive biomass, and percent population woody growth and reproductive biomass as functions of precipitation for each year.
DOI: 10.6084/m9.figshare.3552462.v1
title: Appendix D. Model evaluation.

description: Model evaluation.
DOI: 10.6084/m9.figshare.3552456
title: Appendix B. Conceptual figure describing the calculation of a, b, c1, and c2.

description: Conceptual figure describing the calculation of a, b, c1, and c2.
DOI: 10.6084/m9.figshare.3552456.v1
title: Appendix B. Conceptual figure describing the calculation of a, b, c1, and c2.

description: Conceptual figure describing the calculation of a, b, c1, and c2.
DOI: 10.6084/m9.figshare.3552453
title: Appendix C. Tabular results for female and male growth as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.

description: Tabular results for female and male growth as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.
DOI: 10.6084/m9.figshare.3552453.v1
title: Appendix C. Tabular results for female and male growth as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.

description: Tabular results for female and male growth as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.
DOI: 10.6084/m9.figshare.3552450
title: Appendix D. Tabular results for female reproductive biomass as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.

description: Tabular results for female reproductive biomass as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.
DOI: 10.6084/m9.figshare.3552450.v1
title: Appendix D. Tabular results for female reproductive biomass as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.

description: Tabular results for female reproductive biomass as a function of mass from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.
DOI: 10.6084/m9.figshare.3552447
title: Appendix E. Tabular results for female reproductive allocation as a function of relative growth rate from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.

description: Tabular results for female reproductive allocation as a function of relative growth rate from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.
DOI: 10.6084/m9.figshare.3552447.v1
title: Appendix E. Tabular results for female reproductive allocation as a function of relative growth rate from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.

description: Tabular results for female reproductive allocation as a function of relative growth rate from log–log transformed ordinary least squares, ordinary least squares bisector and reduced major axis regressions.
DOI: 10.6084/m9.figshare.3552444
title: Appendix A. A scheme of the labeling facility.

description: A scheme of the labeling facility.
DOI: 10.6084/m9.figshare.3552444.v1
title: Appendix A. A scheme of the labeling facility.

description: A scheme of the labeling facility.
DOI: 10.6084/m9.figshare.3552441
title: Appendix B. Sources of error in the estimation of relative photosynthesis rate (RPR).

description: Sources of error in the estimation of relative photosynthesis rate (RPR).
DOI: 10.6084/m9.figshare.3552441.v1
title: Appendix B. Sources of error in the estimation of relative photosynthesis rate (RPR).

description: Sources of error in the estimation of relative photosynthesis rate (RPR).
DOI: 10.6084/m9.figshare.3552438
title: Appendix C. Environmental parameters in labeling chambers.

description: Environmental parameters in labeling chambers.
DOI: 10.6084/m9.figshare.3552435
title: Appendix D. The evolution of the δ13C of shoots vs. time and vs. cumulative photosynthetic active radiation (PAR) during several labeling experiments.

description: The evolution of the δ13C of shoots vs. time and vs. cumulative photosynthetic active radiation (PAR) during several labeling experiments.
DOI: 10.6084/m9.figshare.3552438.v1
title: Appendix C. Environmental parameters in labeling chambers.

description: Environmental parameters in labeling chambers.
DOI: 10.6084/m9.figshare.3552435.v1
title: Appendix D. The evolution of the δ13C of shoots vs. time and vs. cumulative photosynthetic active radiation (PAR) during several labeling experiments.

description: The evolution of the δ13C of shoots vs. time and vs. cumulative photosynthetic active radiation (PAR) during several labeling experiments.
DOI: 10.6084/m9.figshare.3552432
title: Appendix E. A model to assess the role of tracer residence in shoot metabolic pools, tracer partitioning belowground, and tracer use in shoot respiration in determining the fraction of assimilated tracer lost from the shoot (flost) during steady state labeling.

description: A model to assess the role of tracer residence in shoot metabolic pools, tracer partitioning belowground, and tracer use in shoot respiration in determining the fraction of assimilated tracer lost from the shoot (flost) during steady state labeling.
DOI: 10.6084/m9.figshare.3552432.v1
title: Appendix E. A model to assess the role of tracer residence in shoot metabolic pools, tracer partitioning belowground, and tracer use in shoot respiration in determining the fraction of assimilated tracer lost from the shoot (flost) during steady state labeling.

description: A model to assess the role of tracer residence in shoot metabolic pools, tracer partitioning belowground, and tracer use in shoot respiration in determining the fraction of assimilated tracer lost from the shoot (flost) during steady state labeling.
DOI: 10.6084/m9.figshare.3552429
title: Appendix F. Tracer respired belowground (soil + roots) over the initial six hours after a labeling pulse, as a proportion of total tracer respired during the complete chase period.

description: Tracer respired belowground (soil + roots) over the initial six hours after a labeling pulse, as a proportion of total tracer respired during the complete chase period.
DOI: 10.6084/m9.figshare.3552429.v1
title: Appendix F. Tracer respired belowground (soil + roots) over the initial six hours after a labeling pulse, as a proportion of total tracer respired during the complete chase period.

description: Tracer respired belowground (soil + roots) over the initial six hours after a labeling pulse, as a proportion of total tracer respired during the complete chase period.
DOI: 10.6084/m9.figshare.3552426
title: Appendix A. Implementation of conditional permutation.

description: Implementation of conditional permutation.
DOI: 10.6084/m9.figshare.3552423
title: Appendix B. Derivation of Eq. 6.

description: Derivation of Eq. 6.