cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3554517.v1
title: Appendix D. Full results of plant tolerance regressions.

description: Full results of plant tolerance regressions.
DOI: 10.6084/m9.figshare.3554514
title: Appendix A. Graphical model of an HMM for animal movement.

description: Graphical model of an HMM for animal movement.
DOI: 10.6084/m9.figshare.3554511
title: Appendix B. Description of HMM model checking via pseudo-residuals, and plots of pseudo-residuals obtained in the bison application.

description: Description of HMM model checking via pseudo-residuals, and plots of pseudo-residuals obtained in the bison application.
DOI: 10.6084/m9.figshare.3554508
title: Appendix C. Outline of the different types of random walks, and description of how biased random walks can be fitted in the HMM framework.

description: Outline of the different types of random walks, and description of how biased random walks can be fitted in the HMM framework.
DOI: 10.6084/m9.figshare.3554505
title: Appendix D. Plots of movement trajectories simulated from four different types of HMMs.

description: Plots of movement trajectories simulated from four different types of HMMs.
DOI: 10.6084/m9.figshare.3554502
title: Appendix E. Plots of the bison movement paths.

description: Plots of the bison movement paths.
DOI: 10.6084/m9.figshare.3554499
title: Appendix F. Model fitting results, including parameter estimates for the individual-specific models, log-likelihood and AIC values for all considered models, and plots of the fitted state dwell-time distributions in the individual-specific models.

description: Model fitting results, including parameter estimates for the individual-specific models, log-likelihood and AIC values for all considered models, and plots of the fitted state dwell-time distributions in the individual-specific models.
DOI: 10.6084/m9.figshare.3554496
title: Appendix G. Verification of the HMM representation being an approximate representation of the example HSMM given in the section Extensions: Other formulations of the state process.

description: Verification of the HMM representation being an approximate representation of the example HSMM given in the section Extensions: Other formulations of the state process.
DOI: 10.6084/m9.figshare.3554493
title: Supplement 1. R code for fitting the individual-specific HMMs and HSMMs, for computing the HSMM residuals, for fitting the hierarchical HSMM, and observations for one of the bison, as well as an updated more efficient version of the code.

description: File List (Older version) 1_individual_specific_HMMs_and_HSMMs.r (md5: 480705d7fbaa10185b499a13c72dff91) 2_residuals_for_HSMMs.r (md5: f49e03aedde8c09cad8325ce72b87a8b) (Older version) 3_hierarchical_HSMM.r (md5: c5e3234dcbc9a81079411c26e85892d2) 4_obs.txt (md5: b5eea7bba207da7711801939d10da124) <b>Revised, more efficient code. Received and published 5 February 2015:</b> 1_individual_specific_HMMs_and_HSMMs_revised.r.R (MD5: c4ec48927645e403ed9e3c6b7df22f9f) 3_hierarchical_HSMM_revised.r.R (MD5: 5f11bc3831bd8c7a93f7560d304e6f56) Description The supplements give R implementations of the methods described in the paper. The first supplement gives R code for fitting individual-specific HMMs and HSMMs. The second supplement gives R code for computing residuals for fitted HSMMs. The third supplement gives R code for fitting the hierarchical HSMM described in Section 5 of the main manuscript. The fourth supplement gives an example bivariate time series, the step lengths and turning angles for one of the bison considered in the main manuscript, that can be analyzed using the first supplement.
DOI: 10.6084/m9.figshare.3554490
title: Appendix A. Species list of plants and pollinators in this study.

description: Species list of plants and pollinators in this study.
DOI: 10.6084/m9.figshare.3554484
title: Supplement 1. The R source code used to determine aspects of plant– pollinator network structure as described in this paper.

description: File List Supplement_1.r (md5: 8f0f8e567e94eef75ac0aa9f51acf4fb)Description For each of our 10 glades, we used R (version 2.12.1) and associated available packages (vegan and bipartite) to determine aspects of plant–pollinator network structure as described in our manuscript. Supplement_1.r contains scripts for determining the nestedness of plant–pollinator interaction networks at each site, calculating metrics describing the structure of each of the networks, determining the spatial nestedness of plant and pollinator species, and calculating the behavioral specialization of plants and pollinators.
DOI: 10.6084/m9.figshare.3554481
title: Supplement 2. The R source code used in the null model analysis.

description: File List Supplement_2_mgen.r (md5: cded81369c9adb7d94232d74043d8bd7) Supplement_2.r (md5: d0ed7ae9bdec91e191e0200bb03da0c7) Description Supplement_2_mgen.r contains a function to generate simulated interaction matrices. Supplement_2.r contains the scripts to perform the null model simulation.
DOI: 10.6084/m9.figshare.3554478
title: Appendix A. Compositional responses of plant communities, plant community responses in community-weighted mean trait value, a table of species presence or absence in alpine grassland plots associated with the studied treatments, and a figure of phylogenetic relationships among species.

description: Compositional responses of plant communities, plant community responses in community-weighted mean trait value, a table of species presence or absence in alpine grassland plots associated with the studied treatments, and a figure of phylogenetic relationships among species.
DOI: 10.6084/m9.figshare.3554478.v1
title: Appendix A. Compositional responses of plant communities, plant community responses in community-weighted mean trait value, a table of species presence or absence in alpine grassland plots associated with the studied treatments, and a figure of phylogenetic relationships among species.

description: Compositional responses of plant communities, plant community responses in community-weighted mean trait value, a table of species presence or absence in alpine grassland plots associated with the studied treatments, and a figure of phylogenetic relationships among species.
DOI: 10.6084/m9.figshare.3554472
title: Appendix A. A figure showing mean density of total Daphnia following the invasion of Daphnia lumholtzi or Daphnia pulex into mesocosms with and without added cyanobacteria.

description: A figure showing mean density of total Daphnia following the invasion of Daphnia lumholtzi or Daphnia pulex into mesocosms with and without added cyanobacteria.
DOI: 10.6084/m9.figshare.3554472.v1
title: Appendix A. A figure showing mean density of total Daphnia following the invasion of Daphnia lumholtzi or Daphnia pulex into mesocosms with and without added cyanobacteria.

description: A figure showing mean density of total Daphnia following the invasion of Daphnia lumholtzi or Daphnia pulex into mesocosms with and without added cyanobacteria.
DOI: 10.6084/m9.figshare.3554469
title: Appendix B. Daphnia thermal performance curve (TPC) equations.

description: Daphnia thermal performance curve (TPC) equations.
DOI: 10.6084/m9.figshare.3554469.v1
title: Appendix B. Daphnia thermal performance curve (TPC) equations.

description: Daphnia thermal performance curve (TPC) equations.
DOI: 10.6084/m9.figshare.3554466
title: Appendix A. A figure depicting relationships among environmental temperature, warming-chamber temperature manipulations, and hypothesized ant thermal performance curves at the high-latitude (Harvard Forest) and low-latitude (Duke Forest) sites.

description: A figure depicting relationships among environmental temperature, warming-chamber temperature manipulations, and hypothesized ant thermal performance curves at the high-latitude (Harvard Forest) and low-latitude (Duke Forest) sites.
DOI: 10.6084/m9.figshare.3554466.v1
title: Appendix A. A figure depicting relationships among environmental temperature, warming-chamber temperature manipulations, and hypothesized ant thermal performance curves at the high-latitude (Harvard Forest) and low-latitude (Duke Forest) sites.

description: A figure depicting relationships among environmental temperature, warming-chamber temperature manipulations, and hypothesized ant thermal performance curves at the high-latitude (Harvard Forest) and low-latitude (Duke Forest) sites.
DOI: 10.6084/m9.figshare.3554463
title: Appendix B. Methodological and analytical details on the construction and evaluation of models of ant responses to climate warming.

description: Methodological and analytical details on the construction and evaluation of models of ant responses to climate warming.
DOI: 10.6084/m9.figshare.3554460
title: Appendix C. A table summarizing ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative global climate change models.

description: A table summarizing ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative global climate change models.
DOI: 10.6084/m9.figshare.3554460.v1
title: Appendix C. A table summarizing ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative global climate change models.

description: A table summarizing ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative global climate change models.
DOI: 10.6084/m9.figshare.3554457
title: Appendix D. A table presenting thermal indices of current and future climates at Duke and Harvard Forests.

description: A table presenting thermal indices of current and future climates at Duke and Harvard Forests.
DOI: 10.6084/m9.figshare.3554457.v1
title: Appendix D. A table presenting thermal indices of current and future climates at Duke and Harvard Forests.

description: A table presenting thermal indices of current and future climates at Duke and Harvard Forests.
DOI: 10.6084/m9.figshare.3554451
title: Appendix E. A table presenting model summaries of ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative thermal indices.

description: A table presenting model summaries of ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative thermal indices.
DOI: 10.6084/m9.figshare.3554451.v1
title: Appendix E. A table presenting model summaries of ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative thermal indices.

description: A table presenting model summaries of ant responses to climate warming based on thermal tolerance and MaxEnt predictions developed with alternative thermal indices.
DOI: 10.6084/m9.figshare.3554448
title: Appendix F. A figure presenting sample calculations of thermal accumulation slope.

description: A figure presenting sample calculations of thermal accumulation slope.
DOI: 10.6084/m9.figshare.3554448.v1
title: Appendix F. A figure presenting sample calculations of thermal accumulation slope.

description: A figure presenting sample calculations of thermal accumulation slope.
DOI: 10.6084/m9.figshare.3554445
title: Appendix G. A table presenting phylogenetic model summaries, by site, of ant responses to climate warming based on thermal tolerance and MaxEnt predictions.

description: A table presenting phylogenetic model summaries, by site, of ant responses to climate warming based on thermal tolerance and MaxEnt predictions.
DOI: 10.6084/m9.figshare.3554445.v1
title: Appendix G. A table presenting phylogenetic model summaries, by site, of ant responses to climate warming based on thermal tolerance and MaxEnt predictions.

description: A table presenting phylogenetic model summaries, by site, of ant responses to climate warming based on thermal tolerance and MaxEnt predictions.
DOI: 10.6084/m9.figshare.3554442
title: Appendix H. A figure presenting ant worker density as a function of warming treatment at Harvard Forest.

description: A figure presenting ant worker density as a function of warming treatment at Harvard Forest.
DOI: 10.6084/m9.figshare.3554442.v1
title: Appendix H. A figure presenting ant worker density as a function of warming treatment at Harvard Forest.

description: A figure presenting ant worker density as a function of warming treatment at Harvard Forest.
DOI: 10.6084/m9.figshare.3554433
title: Appendix I. A figure presenting regressions of maximal accumulation temperature as functions of thermal tolerance and MaxEnt predictions.

description: A figure presenting regressions of maximal accumulation temperature as functions of thermal tolerance and MaxEnt predictions.
DOI: 10.6084/m9.figshare.3554433.v1
title: Appendix I. A figure presenting regressions of maximal accumulation temperature as functions of thermal tolerance and MaxEnt predictions.

description: A figure presenting regressions of maximal accumulation temperature as functions of thermal tolerance and MaxEnt predictions.
DOI: 10.6084/m9.figshare.3554430
title: Appendix J. A figure showing regressions of thermal accumulation slope (including standard errors) as functions of thermal tolerance and MaxEnt predictions.

description: A figure showing regressions of thermal accumulation slope (including standard errors) as functions of thermal tolerance and MaxEnt predictions.
DOI: 10.6084/m9.figshare.3554430.v1
title: Appendix J. A figure showing regressions of thermal accumulation slope (including standard errors) as functions of thermal tolerance and MaxEnt predictions.

description: A figure showing regressions of thermal accumulation slope (including standard errors) as functions of thermal tolerance and MaxEnt predictions.
DOI: 10.6084/m9.figshare.3554421
title: Data Paper. Data Paper

description: File List DaPhnE_01.zip -- contains all four data files described below. [d93c96544d106a7ce37f99c7a631ecbc] DaPhnE_01_Synonymy.txt -- tab-delimited ASCII file containing the list of the binomials used by the German, British, the Netherlands, and Swiss source databases and the respective binomials used in DaPhnE. [0785c354ec81a96b0453bcf36de29a65] DaPhnE_01.tre -- ASCII file of the phylogeny in Newick format. [1ecfc21ba9c8a754ac8c784768cb1fb3] DaPhnE_01_nodes_with_references.txt -- tab-delimited ASCII file containing 1212 lines listing nodes with either a reference for the partial phylogenies used to construct the supertree or to the node ages. [abcd006cd50353dcc3839f703c68401d] DaPhnE_01_reference_list.txt -- tab-delimited ASCII file containing 738 references for phylogenies and node dates given in DaPhnE_01_nodes_with_references.txt. [01e130037c617d0f6e392497a9af4177] Description This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, the Netherlands, and Switzerland, totalling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogenetic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a large taxon of European plant species. It can readily be used in phylogenetic analysis tools like ape, phytools, picante, or MESQUITE. <i>BIOLFLOR; British flora; German flora; macroecology; Netherlands flora; phylogeny; PLANTATT; supertree; Swiss flora; vascular plants.</i>
DOI: 10.6084/m9.figshare.3554418
title: Appendix A. Two example analyses using the multinomial diversity model (MDM).

description: Two example analyses using the multinomial diversity model (MDM).
DOI: 10.6084/m9.figshare.3554418.v1
title: Appendix A. Two example analyses using the multinomial diversity model (MDM).

description: Two example analyses using the multinomial diversity model (MDM).
DOI: 10.6084/m9.figshare.3554415
title: Appendix B. Comparison of weighted Shannon diversity and diversity for q ≠ 1.

description: Comparison of weighted Shannon diversity and diversity for q ≠ 1.
DOI: 10.6084/m9.figshare.3554415.v1
title: Appendix B. Comparison of weighted Shannon diversity and diversity for q ≠ 1.

description: Comparison of weighted Shannon diversity and diversity for q ≠ 1.
DOI: 10.6084/m9.figshare.3554412
title: Appendix A. Details of methods used for molecular identification of ectomycorrhizal fungi.

description: Details of methods used for molecular identification of ectomycorrhizal fungi.
DOI: 10.6084/m9.figshare.3554412.v1
title: Appendix A. Details of methods used for molecular identification of ectomycorrhizal fungi.

description: Details of methods used for molecular identification of ectomycorrhizal fungi.
DOI: 10.6084/m9.figshare.3554409
title: Appendix B. Photographs of native Pinus radiata populations on Guadalupe and Cedros Islands, which are located in the Pacific Ocean off the west coast of Baja California, Mexico.

description: Photographs of native Pinus radiata populations on Guadalupe and Cedros Islands, which are located in the Pacific Ocean off the west coast of Baja California, Mexico.
DOI: 10.6084/m9.figshare.3554409.v1
title: Appendix B. Photographs of native Pinus radiata populations on Guadalupe and Cedros Islands, which are located in the Pacific Ocean off the west coast of Baja California, Mexico.

description: Photographs of native Pinus radiata populations on Guadalupe and Cedros Islands, which are located in the Pacific Ocean off the west coast of Baja California, Mexico.
DOI: 10.6084/m9.figshare.3554406
title: Appendix C. Figures showing a sample-based species accumulation curve for ectomycorrhizal fungal OTUs in each of the five soils and the frequency of ectomycorrhizal fungal OTUs on seedlings across the entire study, and a table showing the frequencies of each fungal OTU in each of the five soils along with Genbank best matches and accession numbers for each fungal OTU.

description: Figures showing a sample-based species accumulation curve for ectomycorrhizal fungal OTUs in each of the five soils and the frequency of ectomycorrhizal fungal OTUs on seedlings across the entire study, and a table showing the frequencies of each fungal OTU in each of the five soils along with Genbank best matches and accession numbers for each fungal OTU.
DOI: 10.6084/m9.figshare.3554406.v1
title: Appendix C. Figures showing a sample-based species accumulation curve for ectomycorrhizal fungal OTUs in each of the five soils and the frequency of ectomycorrhizal fungal OTUs on seedlings across the entire study, and a table showing the frequencies of each fungal OTU in each of the five soils along with Genbank best matches and accession numbers for each fungal OTU.

description: Figures showing a sample-based species accumulation curve for ectomycorrhizal fungal OTUs in each of the five soils and the frequency of ectomycorrhizal fungal OTUs on seedlings across the entire study, and a table showing the frequencies of each fungal OTU in each of the five soils along with Genbank best matches and accession numbers for each fungal OTU.
DOI: 10.6084/m9.figshare.3554403
title: Supplement 1. Soil and climate data for each of the five sampled native populations of Pinus radiata.

description: File List Supp1.csv (md5: fc6e602dc38313157b1b03173781f378) Description Soil data (columns 5–16) are from analysis of a single soil sample from each site comprised of 20 bulked subsamples from that site. Soil analyses were performed by the University of California Davis Analytical Laboratory. Bioclimatic variables (bio1–bio19) were obtained from the WorldClim database using centroid latitude and longitude coordinates for each plant population. These bioclimatic variables were calculated from monthly temperature and rainfall data from 1950–2000, interpolated at 1-km resolution (see http://www.worldclim.org/ and Hijmans et al. 2005). Temperatures are expressed in degrees Celsius × 10, and precipitation levels are expressed in millimeters. BIO1 = Annual Mean Temperature (degrees C × 10)<br> BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp))<br> BIO3 = Isothermality (P2/P7) ( × 100)<br> BIO4 = Temperature Seasonality (standard deviation × 100)<br> BIO5 = Max Temperature of Warmest Month<br> BIO6 = Min Temperature of Coldest Month<br> BIO7 = Temperature Annual Range (P5-P6)<br> BIO8 = Mean Temperature of Wettest Quarter<br> BIO9 = Mean Temperature of Driest Quarter<br> BIO10 = Mean Temperature of Warmest Quarter<br> BIO11 = Mean Temperature of Coldest Quarter<br> BIO12 = Annual Precipitation (mm)<br> BIO13 = Precipitation of Wettest Month<br> BIO14 = Precipitation of Driest Month<br> BIO15 = Precipitation Seasonality (Coefficient of Variation)<br> BIO16 = Precipitation of Wettest Quarter<br> BIO17 = Precipitation of Driest Quarter<br> BIO18 = Precipitation of Warmest Quarter<br> BIO19 = Precipitation of Coldest Quarter <br>
DOI: 10.6084/m9.figshare.3554403.v1
title: Supplement 1. Soil and climate data for each of the five sampled native populations of Pinus radiata.

description: File List Supp1.csv (md5: fc6e602dc38313157b1b03173781f378) Description Soil data (columns 5–16) are from analysis of a single soil sample from each site comprised of 20 bulked subsamples from that site. Soil analyses were performed by the University of California Davis Analytical Laboratory. Bioclimatic variables (bio1–bio19) were obtained from the WorldClim database using centroid latitude and longitude coordinates for each plant population. These bioclimatic variables were calculated from monthly temperature and rainfall data from 1950–2000, interpolated at 1-km resolution (see http://www.worldclim.org/ and Hijmans et al. 2005). Temperatures are expressed in degrees Celsius × 10, and precipitation levels are expressed in millimeters. BIO1 = Annual Mean Temperature (degrees C × 10)<br> BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp))<br> BIO3 = Isothermality (P2/P7) ( × 100)<br> BIO4 = Temperature Seasonality (standard deviation × 100)<br> BIO5 = Max Temperature of Warmest Month<br> BIO6 = Min Temperature of Coldest Month<br> BIO7 = Temperature Annual Range (P5-P6)<br> BIO8 = Mean Temperature of Wettest Quarter<br> BIO9 = Mean Temperature of Driest Quarter<br> BIO10 = Mean Temperature of Warmest Quarter<br> BIO11 = Mean Temperature of Coldest Quarter<br> BIO12 = Annual Precipitation (mm)<br> BIO13 = Precipitation of Wettest Month<br> BIO14 = Precipitation of Driest Month<br> BIO15 = Precipitation Seasonality (Coefficient of Variation)<br> BIO16 = Precipitation of Wettest Quarter<br> BIO17 = Precipitation of Driest Quarter<br> BIO18 = Precipitation of Warmest Quarter<br> BIO19 = Precipitation of Coldest Quarter <br>
DOI: 10.6084/m9.figshare.3554400
title: Appendix A. Validation of the mathematical framework proposed.

description: Validation of the mathematical framework proposed.
DOI: 10.6084/m9.figshare.3554400.v1
title: Appendix A. Validation of the mathematical framework proposed.

description: Validation of the mathematical framework proposed.
DOI: 10.6084/m9.figshare.3554397
title: Appendix B. Results for different levels of species pool miss-estimation.

description: Results for different levels of species pool miss-estimation.
DOI: 10.6084/m9.figshare.3554397.v1
title: Appendix B. Results for different levels of species pool miss-estimation.

description: Results for different levels of species pool miss-estimation.
DOI: 10.6084/m9.figshare.3554394
title: Appendix C. Empirical test: species pool estimation and results for phylogenetic diversity.

description: Empirical test: species pool estimation and results for phylogenetic diversity.