cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3568455.v1
title: Appendix A. Eleven additional figures showing the fit of each element of the model to the empirical data available (e.g., bagworm dispersal, male and female emergence phenology, life span, and fecundity).

description: Eleven additional figures showing the fit of each element of the model to the empirical data available (e.g., bagworm dispersal, male and female emergence phenology, life span, and fecundity).
DOI: 10.6084/m9.figshare.3568452
title: Appendix A. Detailed solution to the two-state example problem.

description: Detailed solution to the two-state example problem.
DOI: 10.6084/m9.figshare.3568452.v1
title: Appendix A. Detailed solution to the two-state example problem.

description: Detailed solution to the two-state example problem.
DOI: 10.6084/m9.figshare.3568449
title: Appendix B. Solving a linear system in order to predict mass loss from a decomposition network.

description: Solving a linear system in order to predict mass loss from a decomposition network.
DOI: 10.6084/m9.figshare.3568446
title: Appendix C. Extrapolating the discrete network to the continuum.

description: Extrapolating the discrete network to the continuum.
DOI: 10.6084/m9.figshare.3568446.v1
title: Appendix C. Extrapolating the discrete network to the continuum.

description: Extrapolating the discrete network to the continuum.
DOI: 10.6084/m9.figshare.3568443
title: Appendix D. Monte Carlo method for calculating r(k) from a network with heterogeneous states and distributed rates.

description: Monte Carlo method for calculating r(k) from a network with heterogeneous states and distributed rates.
DOI: 10.6084/m9.figshare.3568443.v1
title: Appendix D. Monte Carlo method for calculating r(k) from a network with heterogeneous states and distributed rates.

description: Monte Carlo method for calculating r(k) from a network with heterogeneous states and distributed rates.
DOI: 10.6084/m9.figshare.3568440
title: Appendix E. Proof that constraints on v are sufficient to guarantee dg/dt &lt; 0.

description: Proof that constraints on v are sufficient to guarantee dg/dt &lt; 0.
DOI: 10.6084/m9.figshare.3568440.v1
title: Appendix E. Proof that constraints on v are sufficient to guarantee dg/dt &lt; 0.

description: Proof that constraints on v are sufficient to guarantee dg/dt &lt; 0.
DOI: 10.6084/m9.figshare.3568437
title: Supplement 1. Matlab codes for the inversion algorithm and the heterogeneous CENTURY model.

description: File List ReguILTv.m (MD5: cfc11d6c4e0ee77da1654507be85b19f) ReguILTv.readme (MD5: 3472dcd6ce11cb1ca3184bd1b5e0b206) CenturyMonteCarlo.m (MD5: e39ea2e9e33fe5ab2d2802861879a5ab) CenturyMonteCarlo.readme (MD5: 5b164105cef994982f23302ccc883f32) README (MD5: edd12c825a2664bebb919b803f7ccfaf) Description The code ReguILT.m identifies the constrained regularized inverse Laplace transform of a decay time series g(t). The exit rate function is constrained such that mass cannot increase over time. Please see the help file ReguILT.README for its use and an example. The code CenturyMonteCarlo.m calculates the exit rate function v(ln k) associated with the Century model with heterogeneous pools. Please see the help file CenturyMonteCarlo.README for its use and an example. The general help file README contains this information.
DOI: 10.6084/m9.figshare.3568437.v1
title: Supplement 1. Matlab codes for the inversion algorithm and the heterogeneous CENTURY model.

description: File List ReguILTv.m (MD5: cfc11d6c4e0ee77da1654507be85b19f) ReguILTv.readme (MD5: 3472dcd6ce11cb1ca3184bd1b5e0b206) CenturyMonteCarlo.m (MD5: e39ea2e9e33fe5ab2d2802861879a5ab) CenturyMonteCarlo.readme (MD5: 5b164105cef994982f23302ccc883f32) README (MD5: edd12c825a2664bebb919b803f7ccfaf) Description The code ReguILT.m identifies the constrained regularized inverse Laplace transform of a decay time series g(t). The exit rate function is constrained such that mass cannot increase over time. Please see the help file ReguILT.README for its use and an example. The code CenturyMonteCarlo.m calculates the exit rate function v(ln k) associated with the Century model with heterogeneous pools. Please see the help file CenturyMonteCarlo.README for its use and an example. The general help file README contains this information.
DOI: 10.6084/m9.figshare.3568434
title: Full Archive

description: Full Archive
DOI: 10.6084/m9.figshare.3568434.v1
title: Full Archive

description: Full Archive
DOI: 10.6084/m9.figshare.3568431
title: Appendix A. Time series and wavelet spectra for sockeye salmon populations not shown in Fig. 1.

description: Time series and wavelet spectra for sockeye salmon populations not shown in Fig. 1.
DOI: 10.6084/m9.figshare.3568431.v1
title: Appendix A. Time series and wavelet spectra for sockeye salmon populations not shown in Fig. 1.

description: Time series and wavelet spectra for sockeye salmon populations not shown in Fig. 1.
DOI: 10.6084/m9.figshare.3568425
title: Appendix A. A binomial product model can incorporate spatial aggregation for quadrat sampling.

description: A binomial product model can incorporate spatial aggregation for quadrat sampling.
DOI: 10.6084/m9.figshare.3568422
title: Appendix B. Rarefaction and extrapolation for species richness (abundance data).

description: Rarefaction and extrapolation for species richness (abundance data).
DOI: 10.6084/m9.figshare.3568419
title: Appendix C. Rarefaction and extrapolation for species richness (incidence data).

description: Rarefaction and extrapolation for species richness (incidence data).
DOI: 10.6084/m9.figshare.3568416
title: Appendix D. Proof details for some formulas (Eqs. 5, 8, 9b, 11a, and 11b of the main text) and a replication principle.

description: Proof details for some formulas (Eqs. 5, 8, 9b, 11a, and 11b of the main text) and a replication principle.
DOI: 10.6084/m9.figshare.3568413
title: Appendix E. Extrapolation formulas for Hill numbers of q = 1 and q ≥ 2 based on abundance data.

description: Extrapolation formulas for Hill numbers of q = 1 and q ≥ 2 based on abundance data.
DOI: 10.6084/m9.figshare.3568410
title: Appendix F. Using simulation to test the proposed analytic estimators.

description: Using simulation to test the proposed analytic estimators.
DOI: 10.6084/m9.figshare.3568407
title: Appendix G. A bootstrap method to construct an unconditional variance estimator for any interpolated or extrapolated estimator.

description: A bootstrap method to construct an unconditional variance estimator for any interpolated or extrapolated estimator.
DOI: 10.6084/m9.figshare.3568404
title: Appendix H. Rarefaction and extrapolation of Hill numbers for incidence data.

description: Rarefaction and extrapolation of Hill numbers for incidence data.
DOI: 10.6084/m9.figshare.3568401
title: Appendix I. Hill numbers and Hurlbert’s indices.

description: Hill numbers and Hurlbert’s indices.
DOI: 10.6084/m9.figshare.3568398
title: Appendix J. An example: sample-size- and coverage-based Shannon diversity curves may exhibit inconsistent patterns.

description: An example: sample-size- and coverage-based Shannon diversity curves may exhibit inconsistent patterns.
DOI: 10.6084/m9.figshare.3568395
title: Appendix K. Probability of an Interspecific Encounter (PIE) and rarefaction.

description: Probability of an Interspecific Encounter (PIE) and rarefaction.
DOI: 10.6084/m9.figshare.3568392
title: Supplement 1. R code for the analysis of individual-based (abundance) and sample-based (incidence) species diversity data.

description: File List Main_for_iNEXT.r (MD5: 95671409a75dbaecd2fb6a9e09286b11) Subroutine for iNEXT.r (MD5: 52caa10adebb26e92f43d8c2c2870d3f) Description Main_for_iNEXT.r – R code for analysis of individual-based (abundance) and sample-based (incidence) species diversity data Subroutine_for_iNEXT.r – R subroutine for data analysis
DOI: 10.6084/m9.figshare.3568389
title: Appendix A. An illustrative ultrametric tree.

description: An illustrative ultrametric tree.
DOI: 10.6084/m9.figshare.3568389.v1
title: Appendix A. An illustrative ultrametric tree.

description: An illustrative ultrametric tree.
DOI: 10.6084/m9.figshare.3568386
title: Appendix B. Diversity profile and strong replication principle for Hill numbers and phylogenetic Hill numbers.

description: Diversity profile and strong replication principle for Hill numbers and phylogenetic Hill numbers.
DOI: 10.6084/m9.figshare.3568383
title: Appendix C. Diversity decomposition and related properties.

description: Diversity decomposition and related properties.
DOI: 10.6084/m9.figshare.3568383.v1
title: Appendix C. Diversity decomposition and related properties.

description: Diversity decomposition and related properties.
DOI: 10.6084/m9.figshare.3568380
title: Appendix D. Derivation of four classes of similarity measures and related properties.

description: Derivation of four classes of similarity measures and related properties.
DOI: 10.6084/m9.figshare.3568380.v1
title: Appendix D. Derivation of four classes of similarity measures and related properties.

description: Derivation of four classes of similarity measures and related properties.
DOI: 10.6084/m9.figshare.3568377
title: Appendix E. Mathematical flaws in the traditional additive approach based on generalized entropy excess or phylogenetic generalized entropy excess.

description: Mathematical flaws in the traditional additive approach based on generalized entropy excess or phylogenetic generalized entropy excess.
DOI: 10.6084/m9.figshare.3568377.v1
title: Appendix E. Mathematical flaws in the traditional additive approach based on generalized entropy excess or phylogenetic generalized entropy excess.

description: Mathematical flaws in the traditional additive approach based on generalized entropy excess or phylogenetic generalized entropy excess.
DOI: 10.6084/m9.figshare.3568374
title: Appendix F. A simple hypothetical tree with completely distinct lineages.

description: A simple hypothetical tree with completely distinct lineages.
DOI: 10.6084/m9.figshare.3568374.v1
title: Appendix F. A simple hypothetical tree with completely distinct lineages.

description: A simple hypothetical tree with completely distinct lineages.
DOI: 10.6084/m9.figshare.3568371
title: Appendix G. Additional analysis of Examples 2 and 3.

description: Additional analysis of Examples 2 and 3.
DOI: 10.6084/m9.figshare.3568371.v1
title: Appendix G. Additional analysis of Examples 2 and 3.

description: Additional analysis of Examples 2 and 3.
DOI: 10.6084/m9.figshare.3568368
title: Appendix A. Site coordinates, sampling information, and F:P ratios across sites.

description: Site coordinates, sampling information, and F:P ratios across sites.
DOI: 10.6084/m9.figshare.3568368.v1
title: Appendix A. Site coordinates, sampling information, and F:P ratios across sites.

description: Site coordinates, sampling information, and F:P ratios across sites.
DOI: 10.6084/m9.figshare.3568365
title: Appendix B. Phylogenetic trees of Leptodontidium and Mortierella OTUs.

description: Phylogenetic trees of Leptodontidium and Mortierella OTUs.
DOI: 10.6084/m9.figshare.3568362
title: Appendix C. Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations.

description: Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations.
DOI: 10.6084/m9.figshare.3568362.v1
title: Appendix C. Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations.

description: Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations.
DOI: 10.6084/m9.figshare.3568359
title: Supplement 1. Three files containing BLAST identifications for fungal OTUs and abundances across samples.

description: File List Blast_IDs.csv (MD5: 62e5100c20160c284f4d0c0d7e966652) OTU_by_site_matrix.csv (MD5: fd8cb6e0180fda1c17b283fb1bb9de0e) Phyla_Guild_Assignments.csv (MD5: 835a54ac9732fb782bc6756fd8e10fa6) Description Blast_IDs is a comma-delimited spreadsheet with a row for each OTU encountered in this study. The columns are as follows: Rank = the relative abundance of that OTU across the entire dataset. Rank #1 was the most abundant OTU (in terms of number of clone sequences falling into that OTU). Operational Taxonomic Unit = the code assigned to that OTU when the sequences were clustered using Cap3. Representative Clone = the code for the original clone sequence that was chosen to represent that OTU. Best Match GenBank Accession = the accession number for the sequence in GenBank with the highest bit score when the OTU representative sequence was blasted against our in-house database. Best Match Description = edited text from the title of the top GenBank blast hit meant to convey the putative identity. Percent Identity = the percent of identical bases over the region of the query and hit that were sufficiently similar to be aligned by BLAST. Length of Overlap = the length of the region that was sufficiently similar to be aligned by BLAST. Bit Score = the quality of the match assigned by BLAST. Quality of Top Match = the taxonomic level to which the query sequence could be identified based on a set of rules involving percent identity combined with overlap length, as described in the text of the article. OTU_by_site_matrix is a comma-delimited spreadsheet providing OUT abundances. Counts of clones belonging to a particular OTU in each sample (site × year × horizon combination) are given. Each row represents one OTU. The site is designated by the first number (e.g., '109'), the horizon by M = mineral and O = organic and the sampling year by 4 = 2004 and 5 = 2005. The first column gives the OTU designation, the second column gives the rank of that OTU and subsequent columns give the clone counts in each sample. The last column provides a cumulative total clone count for each OTU. Phyla_Guild_Assignments is a comma-delimited spreadsheet showing the guilds that were assigned to particular fungal OTUs. The first five columns are identical to those described above for the file Blast_IDs. The next columns, labeled “Phylum or Subphylum” and “Order” give the corresponding GenBank taxonomy designations for the top BLAST match. The last column, labeled “Guild”, provides our best estimate of the trophic guild to which the OTU belongs. ECM = ectomycorrhizal; sap = saprotrophic (typically wood or litter decay); lichen = lichen; ?? = unknown. We only attempted to define guild for a subset of well-defined OTUs.
DOI: 10.6084/m9.figshare.3568359.v1
title: Supplement 1. Three files containing BLAST identifications for fungal OTUs and abundances across samples.

description: File List Blast_IDs.csv (MD5: 62e5100c20160c284f4d0c0d7e966652) OTU_by_site_matrix.csv (MD5: fd8cb6e0180fda1c17b283fb1bb9de0e) Phyla_Guild_Assignments.csv (MD5: 835a54ac9732fb782bc6756fd8e10fa6) Description Blast_IDs is a comma-delimited spreadsheet with a row for each OTU encountered in this study. The columns are as follows: Rank = the relative abundance of that OTU across the entire dataset. Rank #1 was the most abundant OTU (in terms of number of clone sequences falling into that OTU). Operational Taxonomic Unit = the code assigned to that OTU when the sequences were clustered using Cap3. Representative Clone = the code for the original clone sequence that was chosen to represent that OTU. Best Match GenBank Accession = the accession number for the sequence in GenBank with the highest bit score when the OTU representative sequence was blasted against our in-house database. Best Match Description = edited text from the title of the top GenBank blast hit meant to convey the putative identity. Percent Identity = the percent of identical bases over the region of the query and hit that were sufficiently similar to be aligned by BLAST. Length of Overlap = the length of the region that was sufficiently similar to be aligned by BLAST. Bit Score = the quality of the match assigned by BLAST. Quality of Top Match = the taxonomic level to which the query sequence could be identified based on a set of rules involving percent identity combined with overlap length, as described in the text of the article. OTU_by_site_matrix is a comma-delimited spreadsheet providing OUT abundances. Counts of clones belonging to a particular OTU in each sample (site × year × horizon combination) are given. Each row represents one OTU. The site is designated by the first number (e.g., '109'), the horizon by M = mineral and O = organic and the sampling year by 4 = 2004 and 5 = 2005. The first column gives the OTU designation, the second column gives the rank of that OTU and subsequent columns give the clone counts in each sample. The last column provides a cumulative total clone count for each OTU. Phyla_Guild_Assignments is a comma-delimited spreadsheet showing the guilds that were assigned to particular fungal OTUs. The first five columns are identical to those described above for the file Blast_IDs. The next columns, labeled “Phylum or Subphylum” and “Order” give the corresponding GenBank taxonomy designations for the top BLAST match. The last column, labeled “Guild”, provides our best estimate of the trophic guild to which the OTU belongs. ECM = ectomycorrhizal; sap = saprotrophic (typically wood or litter decay); lichen = lichen; ?? = unknown. We only attempted to define guild for a subset of well-defined OTUs.
DOI: 10.6084/m9.figshare.3568356
title: Appendix A. Description of statistical tests and related methods.

description: Description of statistical tests and related methods.
DOI: 10.6084/m9.figshare.3568353
title: Appendix B. Example showing how data simulated from groups with equal centroids but different variances in Euclidean space can yield groups with unequal centroids in Bray-Curtis space.

description: Example showing how data simulated from groups with equal centroids but different variances in Euclidean space can yield groups with unequal centroids in Bray-Curtis space.
DOI: 10.6084/m9.figshare.3568353.v1
title: Appendix B. Example showing how data simulated from groups with equal centroids but different variances in Euclidean space can yield groups with unequal centroids in Bray-Curtis space.

description: Example showing how data simulated from groups with equal centroids but different variances in Euclidean space can yield groups with unequal centroids in Bray-Curtis space.
DOI: 10.6084/m9.figshare.3568347
title: Appendix C. Description of datasets (Ekofisk and Norwegian continental shelf) and simulation methods used to compare the power of statistical tests to detect real changes in multivariate ecological assemblages.

description: Description of datasets (Ekofisk and Norwegian continental shelf) and simulation methods used to compare the power of statistical tests to detect real changes in multivariate ecological assemblages.
DOI: 10.6084/m9.figshare.3568344
title: Appendix D. Additional figures showing empirical power of multivariate tests for comparisons of groups based on the Ekofisk data.

description: Additional figures showing empirical power of multivariate tests for comparisons of groups based on the Ekofisk data.
DOI: 10.6084/m9.figshare.3568344.v1
title: Appendix D. Additional figures showing empirical power of multivariate tests for comparisons of groups based on the Ekofisk data.

description: Additional figures showing empirical power of multivariate tests for comparisons of groups based on the Ekofisk data.
DOI: 10.6084/m9.figshare.3568341
title: Appendix E. Additional figure showing empirical power of multivariate tests for comparisons of groups based on the Norwegian continental shelf data.

description: Additional figure showing empirical power of multivariate tests for comparisons of groups based on the Norwegian continental shelf data.
DOI: 10.6084/m9.figshare.3568323
title: Appendix A. Tables and figures providing statistical support including representation of the differences between the regional and site level protocols and of model bias, correlation, and variability statistics.

description: Tables and figures providing statistical support including representation of the differences between the regional and site level protocols and of model bias, correlation, and variability statistics.
DOI: 10.6084/m9.figshare.3568323.v1
title: Appendix A. Tables and figures providing statistical support including representation of the differences between the regional and site level protocols and of model bias, correlation, and variability statistics.

description: Tables and figures providing statistical support including representation of the differences between the regional and site level protocols and of model bias, correlation, and variability statistics.
DOI: 10.6084/m9.figshare.3568320
title: Appendix B. Tables and figures providing a statistical representation of the observed flux tower carbon fluxes grouped by the plant function type of the site locations.

description: Tables and figures providing a statistical representation of the observed flux tower carbon fluxes grouped by the plant function type of the site locations.
DOI: 10.6084/m9.figshare.3568320.v1
title: Appendix B. Tables and figures providing a statistical representation of the observed flux tower carbon fluxes grouped by the plant function type of the site locations.

description: Tables and figures providing a statistical representation of the observed flux tower carbon fluxes grouped by the plant function type of the site locations.
DOI: 10.6084/m9.figshare.3568317
title: Appendix A. A figure illustrating 30 years of cliff swallow colony-size frequency distributions.

description: A figure illustrating 30 years of cliff swallow colony-size frequency distributions.
DOI: 10.6084/m9.figshare.3568317.v1
title: Appendix A. A figure illustrating 30 years of cliff swallow colony-size frequency distributions.

description: A figure illustrating 30 years of cliff swallow colony-size frequency distributions.
DOI: 10.6084/m9.figshare.3568314
title: Appendix A. Expanded explanation of the calculations of size-corrected growth rates.

description: Expanded explanation of the calculations of size-corrected growth rates.
DOI: 10.6084/m9.figshare.3568314.v1
title: Appendix A. Expanded explanation of the calculations of size-corrected growth rates.

description: Expanded explanation of the calculations of size-corrected growth rates.
DOI: 10.6084/m9.figshare.3568311
title: Appendix B. Phenological data used to simulate larval hatching dates.

description: Phenological data used to simulate larval hatching dates.
DOI: 10.6084/m9.figshare.3568308
title: Appendix C. Results from species-specific ANOVAs.

description: Results from species-specific ANOVAs.
DOI: 10.6084/m9.figshare.3568311.v1
title: Appendix B. Phenological data used to simulate larval hatching dates.

description: Phenological data used to simulate larval hatching dates.
DOI: 10.6084/m9.figshare.3568308.v1
title: Appendix C. Results from species-specific ANOVAs.

description: Results from species-specific ANOVAs.