cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3567165
title: Supplement 1. Complete insect damage data set from the nine Paleocene–Eocene Bighorn Basin sites described in this paper.

description: File List data.txt Description The complete insect damage data set shown as a list of every identifiable dicot leaf, its size, and the damage types on it. Column definitions: Site: Bighorn fossil plant sites. P = Paleocene, E = Eocene. Site numbers within the Paleocene and Eocene are chronologic, from oldest to youngest. USNM Locality Number: Formal locality number assigned by the National Museum of Natural History, Smithsonian Institution. Sites E2, E3, and E5 consist of multiple localities at the same (or very nearly the same) stratigraphic level, and so each locality was given its own USNM locality number. Collector's Locality Number: Informal, preliminary locality number assigned in the field. EDC = Ellen Currano, SW = Scott Wing, PW = Peter Wilf. LB and DC1 were both collected by Scott Wing. Collections were made at some USNM localities during multiple years; therefore, the fossils collected from different years have different collector's locality numbers, which were written on the specimens. Field Collection Number: Specimen number assigned during field censuses. Specimens with census numbers were collected and are housed in the Department of Paleobiology, National Museum of Natural History, Smithsonian Institution. Those listed as "C" were tallied on the outcrop. Plant species: Full descriptions and photographs of the plant species and morphotypes are available in Appendix B. Size: Laminar size, as defined by Webb (1959): lepto = leptophyll, nano = nanophyll, micro = microphyll, noto = notophyll, meso = mesophyll, macro = macrophyll, mega = megaphyll, frag = fragment. DT: Insect damage morphotypes (DTs) observed on each fossil. P1 and P2 were scored for the presence or absence of each damage type (Wilf et al. 2006). For the other seven sites, the number of occurrences of each DT was recorded and is given in parentheses after the DT. For example, 4(2) means that there are two occurrences of DT 4 on the leaf. Piercing and sucking was scored for presence / absence because of the abundance of occurrences of piercing and sucking scars on individual leaves.
DOI: 10.6084/m9.figshare.3567165.v1
title: Supplement 1. Complete insect damage data set from the nine Paleocene–Eocene Bighorn Basin sites described in this paper.

description: File List data.txt Description The complete insect damage data set shown as a list of every identifiable dicot leaf, its size, and the damage types on it. Column definitions: Site: Bighorn fossil plant sites. P = Paleocene, E = Eocene. Site numbers within the Paleocene and Eocene are chronologic, from oldest to youngest. USNM Locality Number: Formal locality number assigned by the National Museum of Natural History, Smithsonian Institution. Sites E2, E3, and E5 consist of multiple localities at the same (or very nearly the same) stratigraphic level, and so each locality was given its own USNM locality number. Collector's Locality Number: Informal, preliminary locality number assigned in the field. EDC = Ellen Currano, SW = Scott Wing, PW = Peter Wilf. LB and DC1 were both collected by Scott Wing. Collections were made at some USNM localities during multiple years; therefore, the fossils collected from different years have different collector's locality numbers, which were written on the specimens. Field Collection Number: Specimen number assigned during field censuses. Specimens with census numbers were collected and are housed in the Department of Paleobiology, National Museum of Natural History, Smithsonian Institution. Those listed as "C" were tallied on the outcrop. Plant species: Full descriptions and photographs of the plant species and morphotypes are available in Appendix B. Size: Laminar size, as defined by Webb (1959): lepto = leptophyll, nano = nanophyll, micro = microphyll, noto = notophyll, meso = mesophyll, macro = macrophyll, mega = megaphyll, frag = fragment. DT: Insect damage morphotypes (DTs) observed on each fossil. P1 and P2 were scored for the presence or absence of each damage type (Wilf et al. 2006). For the other seven sites, the number of occurrences of each DT was recorded and is given in parentheses after the DT. For example, 4(2) means that there are two occurrences of DT 4 on the leaf. Piercing and sucking was scored for presence / absence because of the abundance of occurrences of piercing and sucking scars on individual leaves.
DOI: 10.6084/m9.figshare.3567162
title: Appendix A. Predator manipulation studies included in the meta-analysis.

description: Predator manipulation studies included in the meta-analysis.
DOI: 10.6084/m9.figshare.3567162.v1
title: Appendix A. Predator manipulation studies included in the meta-analysis.

description: Predator manipulation studies included in the meta-analysis.
DOI: 10.6084/m9.figshare.3567159
title: Appendix B. Two methods to examine the possibility of publication bias in our data set.

description: Two methods to examine the possibility of publication bias in our data set.
DOI: 10.6084/m9.figshare.3567159.v1
title: Appendix B. Two methods to examine the possibility of publication bias in our data set.

description: Two methods to examine the possibility of publication bias in our data set.
DOI: 10.6084/m9.figshare.3567156
title: Appendix A. Details on the decomposition.

description: Details on the decomposition.
DOI: 10.6084/m9.figshare.3567156.v1
title: Appendix A. Details on the decomposition.

description: Details on the decomposition.
DOI: 10.6084/m9.figshare.3567153
title: Appendix B. Report on the whole simulations.

description: Report on the whole simulations.
DOI: 10.6084/m9.figshare.3567153.v1
title: Appendix B. Report on the whole simulations.

description: Report on the whole simulations.
DOI: 10.6084/m9.figshare.3567150
title: Appendix C. Details on the description of butterfly species in chalk grassland communities.

description: Details on the description of butterfly species in chalk grassland communities.
DOI: 10.6084/m9.figshare.3567150.v1
title: Appendix C. Details on the description of butterfly species in chalk grassland communities.

description: Details on the description of butterfly species in chalk grassland communities.
DOI: 10.6084/m9.figshare.3567147
title: Supplement 1. Source code and directions for computing, displaying, and testing the decomposition of trait diversity along a phylogenetic tree, with example data sets provided.

description: File List supfileA.R supfileB.pdf Description The file subfileA.R provides the source code for three functions in the R environment. The functions depend on the ade4 package of R. The function decdiv decomposes trait diversity across the nodes of a phylogenetic tree. It depends on the phylogenetic tree, a data frame (or alternatively a vector) containing the abundances of the species in communities, and trait distances between species. The trait distances might have been computed in R, for instance with the ade4 package where several functions are available (e.g., ‘dist.ktab’, ‘dist.binary’, ‘dist.quant’, ‘dist.prop’). The function plot.decdiv opens a graphics device and displays the phylogeny. It includes an argument that allows the display of circles at nodes whose diameter reflects the contributions of nodes to trait diversity. The function rtest.decdiv computes the “single-node skewness test”, “few-nodes skewness test” and “tips/root node skewness test” (or alternatively tips skewness test and root skewness tests separately by specifying options). The file subfileB.pdf contains directions for using the functions. It also provides examples with data sets contained in the package ade4 of the R environment.
DOI: 10.6084/m9.figshare.3567147.v1
title: Supplement 1. Source code and directions for computing, displaying, and testing the decomposition of trait diversity along a phylogenetic tree, with example data sets provided.

description: File List supfileA.R supfileB.pdf Description The file subfileA.R provides the source code for three functions in the R environment. The functions depend on the ade4 package of R. The function decdiv decomposes trait diversity across the nodes of a phylogenetic tree. It depends on the phylogenetic tree, a data frame (or alternatively a vector) containing the abundances of the species in communities, and trait distances between species. The trait distances might have been computed in R, for instance with the ade4 package where several functions are available (e.g., ‘dist.ktab’, ‘dist.binary’, ‘dist.quant’, ‘dist.prop’). The function plot.decdiv opens a graphics device and displays the phylogeny. It includes an argument that allows the display of circles at nodes whose diameter reflects the contributions of nodes to trait diversity. The function rtest.decdiv computes the “single-node skewness test”, “few-nodes skewness test” and “tips/root node skewness test” (or alternatively tips skewness test and root skewness tests separately by specifying options). The file subfileB.pdf contains directions for using the functions. It also provides examples with data sets contained in the package ade4 of the R environment.
DOI: 10.25345/c5275f
title: MassIVE MSV000086072 - Test original mzML files Test original mzML files
title: No PTMs are included in the dataset No PTMs are included in the dataset No PTMs are included in the dataset
DOI: 10.6084/m9.figshare.3567144
title: Appendix A. One-dimensional functional richness (FRIs).

description: One-dimensional functional richness (FRIs).
DOI: 10.6084/m9.figshare.3567141
title: Appendix B. Multi-dimensional functional richness (FRIm).

description: Multi-dimensional functional richness (FRIm).
DOI: 10.6084/m9.figshare.3567141.v1
title: Appendix B. Multi-dimensional functional richness (FRIm).

description: Multi-dimensional functional richness (FRIm).
DOI: 10.6084/m9.figshare.3567138
title: Appendix C. One-dimensional functional divergence (FDs).

description: One-dimensional functional divergence (FDs).
DOI: 10.6084/m9.figshare.3567135
title: Appendix A. A table showing global echinoderms database details along with the sampling method used to collect samples and to estimate density and biomass, and a figure showing GLODAP bottle data distribution used to estimate the calcite compensation depth (Ω = 1) with depth in Fig. 4.

description: A table showing global echinoderms database details along with the sampling method used to collect samples and to estimate density and biomass, and a figure showing GLODAP bottle data distribution used to estimate the calcite compensation depth (Ω = 1) with depth in Fig. 4.
DOI: 10.6084/m9.figshare.3567135.v1
title: Appendix A. A table showing global echinoderms database details along with the sampling method used to collect samples and to estimate density and biomass, and a figure showing GLODAP bottle data distribution used to estimate the calcite compensation depth (Ω = 1) with depth in Fig. 4.

description: A table showing global echinoderms database details along with the sampling method used to collect samples and to estimate density and biomass, and a figure showing GLODAP bottle data distribution used to estimate the calcite compensation depth (Ω = 1) with depth in Fig. 4.
DOI: 10.6084/m9.figshare.3567132
title: Appendix A. Supplemental methodological information for contaminants sampling, data reduction, and the toxicity experiment.

description: Supplemental methodological information for contaminants sampling, data reduction, and the toxicity experiment.
DOI: 10.6084/m9.figshare.3567132.v1
title: Appendix A. Supplemental methodological information for contaminants sampling, data reduction, and the toxicity experiment.

description: Supplemental methodological information for contaminants sampling, data reduction, and the toxicity experiment.
DOI: 10.6084/m9.figshare.3567126
title: Appendix B. Tables summarizing contaminants, invertebrate abundance, and parasite presence.

description: Tables summarizing contaminants, invertebrate abundance, and parasite presence.
DOI: 10.6084/m9.figshare.3567126.v1
title: Appendix B. Tables summarizing contaminants, invertebrate abundance, and parasite presence.

description: Tables summarizing contaminants, invertebrate abundance, and parasite presence.
DOI: 10.6084/m9.figshare.3567123
title: Appendix C. Summary and photographs of abnormalities to wood frog populations at the Kenai National Wildlife Refuge, Alaska.

description: Summary and photographs of abnormalities to wood frog populations at the Kenai National Wildlife Refuge, Alaska.
DOI: 10.6084/m9.figshare.3567123.v1
title: Appendix C. Summary and photographs of abnormalities to wood frog populations at the Kenai National Wildlife Refuge, Alaska.

description: Summary and photographs of abnormalities to wood frog populations at the Kenai National Wildlife Refuge, Alaska.
DOI: 10.6084/m9.figshare.3567120
title: Appendix D. Supplemental results for predator exclusion and limb amputation experiments.

description: Supplemental results for predator exclusion and limb amputation experiments.
DOI: 10.6084/m9.figshare.3567120.v1
title: Appendix D. Supplemental results for predator exclusion and limb amputation experiments.

description: Supplemental results for predator exclusion and limb amputation experiments.
DOI: 10.6084/m9.figshare.3567114
title: Appendix A. Conditions for muffling or magnifying variance in ecosystems with multiple regime shifts.

description: Conditions for muffling or magnifying variance in ecosystems with multiple regime shifts.
DOI: 10.6084/m9.figshare.3567114.v1
title: Appendix A. Conditions for muffling or magnifying variance in ecosystems with multiple regime shifts.

description: Conditions for muffling or magnifying variance in ecosystems with multiple regime shifts.
DOI: 10.6084/m9.figshare.3567111
title: Appendix A. Descriptions of soil layers and their properties by site.

description: Descriptions of soil layers and their properties by site.
DOI: 10.6084/m9.figshare.3567111.v1
title: Appendix A. Descriptions of soil layers and their properties by site.

description: Descriptions of soil layers and their properties by site.
DOI: 10.6084/m9.figshare.3567105
title: Appendix A. Observed frequency landscapes for 14 bird species breeding at the Holt Research Forest, Arrowsic, Maine, USA, 1983–1987.

description: Observed frequency landscapes for 14 bird species breeding at the Holt Research Forest, Arrowsic, Maine, USA, 1983–1987.
DOI: 10.6084/m9.figshare.3567105.v1
title: Appendix A. Observed frequency landscapes for 14 bird species breeding at the Holt Research Forest, Arrowsic, Maine, USA, 1983–1987.

description: Observed frequency landscapes for 14 bird species breeding at the Holt Research Forest, Arrowsic, Maine, USA, 1983–1987.
DOI: 10.6084/m9.figshare.3567102
title: Appendix B. Frequency distributions of occupied quads based on observed data and various null models and P values from goodness-of-fit tests comparing each distribution to the observed distribution.

description: Frequency distributions of occupied quads based on observed data and various null models and P values from goodness-of-fit tests comparing each distribution to the observed distribution.
DOI: 10.6084/m9.figshare.3567102.v1
title: Appendix B. Frequency distributions of occupied quads based on observed data and various null models and P values from goodness-of-fit tests comparing each distribution to the observed distribution.

description: Frequency distributions of occupied quads based on observed data and various null models and P values from goodness-of-fit tests comparing each distribution to the observed distribution.
DOI: 10.6084/m9.figshare.3567099
title: Appendix C. Results of goodness-of-fit tests between average frequency distributions of quad occupancy generated by site fidelity models with varying strengths of site fidelity and the frequency distributions based on the observed data.

description: Results of goodness-of-fit tests between average frequency distributions of quad occupancy generated by site fidelity models with varying strengths of site fidelity and the frequency distributions based on the observed data.
DOI: 10.6084/m9.figshare.3567099.v1
title: Appendix C. Results of goodness-of-fit tests between average frequency distributions of quad occupancy generated by site fidelity models with varying strengths of site fidelity and the frequency distributions based on the observed data.

description: Results of goodness-of-fit tests between average frequency distributions of quad occupancy generated by site fidelity models with varying strengths of site fidelity and the frequency distributions based on the observed data.
DOI: 10.6084/m9.figshare.3567096
title: Appendix D. Model-averaged parameter estimates of vegetation variables and their associated unconditional standard errors (SE) and relative variable importance (RVI) for habitat models of 20 bird species breeding at the Holt Research Forest, 1983-1987.

description: Model-averaged parameter estimates of vegetation variables and their associated unconditional standard errors (SE) and relative variable importance (RVI) for habitat models of 20 bird species breeding at the Holt Research Forest, 1983-1987.
DOI: 10.6084/m9.figshare.3567096.v1
title: Appendix D. Model-averaged parameter estimates of vegetation variables and their associated unconditional standard errors (SE) and relative variable importance (RVI) for habitat models of 20 bird species breeding at the Holt Research Forest, 1983-1987.

description: Model-averaged parameter estimates of vegetation variables and their associated unconditional standard errors (SE) and relative variable importance (RVI) for habitat models of 20 bird species breeding at the Holt Research Forest, 1983-1987.
DOI: 10.6084/m9.figshare.3567093
title: Appendix E. Frequency landscapes fit by the logistic regression models for 14 bird species breeding at the Holt Research Forest, 1983–1987.

description: Frequency landscapes fit by the logistic regression models for 14 bird species breeding at the Holt Research Forest, 1983–1987.
DOI: 10.6084/m9.figshare.3567093.v1
title: Appendix E. Frequency landscapes fit by the logistic regression models for 14 bird species breeding at the Holt Research Forest, 1983–1987.

description: Frequency landscapes fit by the logistic regression models for 14 bird species breeding at the Holt Research Forest, 1983–1987.
DOI: 10.6084/m9.figshare.3567087
title: Appendix A. Maximum-likelihood tree for the nuclear internal transcribed spacer (ITS) locus for all sequences used in concatenated analysis.

description: Maximum-likelihood tree for the nuclear internal transcribed spacer (ITS) locus for all sequences used in concatenated analysis.
DOI: 10.6084/m9.figshare.3567087.v1
title: Appendix A. Maximum-likelihood tree for the nuclear internal transcribed spacer (ITS) locus for all sequences used in concatenated analysis.

description: Maximum-likelihood tree for the nuclear internal transcribed spacer (ITS) locus for all sequences used in concatenated analysis.
DOI: 10.6084/m9.figshare.3567084
title: Appendix B. Maximum-likelihood tree for the chloroplast trnD-T locus for all sequences used in concatenated analysis.

description: Maximum-likelihood tree for the chloroplast trnD-T locus for all sequences used in concatenated analysis.
DOI: 10.6084/m9.figshare.3567084.v1
title: Appendix B. Maximum-likelihood tree for the chloroplast trnD-T locus for all sequences used in concatenated analysis.

description: Maximum-likelihood tree for the chloroplast trnD-T locus for all sequences used in concatenated analysis.
DOI: 10.6084/m9.figshare.3567081
title: Appendix C. Summary of distance-decay analyses for Inga communities in Madre de Dios using log(geographic distance).

description: Summary of distance-decay analyses for Inga communities in Madre de Dios using log(geographic distance).
DOI: 10.6084/m9.figshare.3567081.v1
title: Appendix C. Summary of distance-decay analyses for Inga communities in Madre de Dios using log(geographic distance).

description: Summary of distance-decay analyses for Inga communities in Madre de Dios using log(geographic distance).
DOI: 10.6084/m9.figshare.3567078
title: Appendix D. Results of habitat-specialization analyses of Inga species in Madre de Dios as per the original morphology-based species delimitations.

description: Results of habitat-specialization analyses of Inga species in Madre de Dios as per the original morphology-based species delimitations.
DOI: 10.6084/m9.figshare.3567078.v1
title: Appendix D. Results of habitat-specialization analyses of Inga species in Madre de Dios as per the original morphology-based species delimitations.

description: Results of habitat-specialization analyses of Inga species in Madre de Dios as per the original morphology-based species delimitations.
DOI: 10.6084/m9.figshare.3567075
title: Appendix E. Results of habitat-specialization analyses of Inga species in Madre de Dios as per the species delimitations revised based on the reciprocal illumination procedure.

description: Results of habitat-specialization analyses of Inga species in Madre de Dios as per the species delimitations revised based on the reciprocal illumination procedure.
DOI: 10.6084/m9.figshare.3567075.v1
title: Appendix E. Results of habitat-specialization analyses of Inga species in Madre de Dios as per the species delimitations revised based on the reciprocal illumination procedure.

description: Results of habitat-specialization analyses of Inga species in Madre de Dios as per the species delimitations revised based on the reciprocal illumination procedure.
DOI: 10.6084/m9.figshare.3567069
title: Appendix A. The bivariate Gaussian log-linear model.

description: The bivariate Gaussian log-linear model.
DOI: 10.6084/m9.figshare.3567069.v1
title: Appendix A. The bivariate Gaussian log-linear model.

description: The bivariate Gaussian log-linear model.
DOI: 10.6084/m9.figshare.3567066
title: Appendix B. Tables showing (1) the Akaike Information Criterion for the standard Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial, and the negative binomial hurdle models and (2) estimates of the linear, (), and quadratic, () coefficients of distance from water (boma), the interaction between distance from water and boma (), and their standard errors for the negative binomial hurdle model.

description: Tables showing (1) the Akaike Information Criterion for the standard Poisson, negative binomial, zero-inflated Poisson, zero-inflated negative binomial, and the negative binomial hurdle models and (2) estimates of the linear, (), and quadratic, () coefficients of distance from water (boma), the interaction between distance from water and boma (), and their standard errors for the negative binomial hurdle model.
DOI: 10.6084/m9.figshare.3567063
title: Index Files

description: Index Files
DOI: 10.6084/m9.figshare.3567063.v1
title: Index Files

description: Index Files
DOI: 10.6084/m9.figshare.3567060
title: Appendix A. Gaussian random field priors and precision hyper-priors.

description: Gaussian random field priors and precision hyper-priors.
DOI: 10.6084/m9.figshare.3567057
title: Supplement 1. WinBUGS code used to generate all of the results presented in the tables.

description: File List programs.txt -- text file containing all of the WinBUGS programs Description The file programs.txt contains the WinBUGS code used to generate all of the results presented in the tables in the main article.
DOI: 10.6084/m9.figshare.3567054
title: Appendix A. Ecosystems and references used in meta-analysis to assess dreissenid impacts.

description: Ecosystems and references used in meta-analysis to assess dreissenid impacts.
DOI: 10.6084/m9.figshare.3567051
title: Appendix A. Flow conditions, upwelling, and bathymetry of study sites.

description: Flow conditions, upwelling, and bathymetry of study sites.
DOI: 10.6084/m9.figshare.3567051.v1
title: Appendix A. Flow conditions, upwelling, and bathymetry of study sites.

description: Flow conditions, upwelling, and bathymetry of study sites.