cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3563118.v1
title: Appendix B. An example of applications of the proposed DI metric based on data from various sources.

description: An example of applications of the proposed DI metric based on data from various sources.
DOI: 10.6084/m9.figshare.3563115
title: Appendix A. Detailed description and likelihood function for the Bayesian hierarchical hurdle model.

description: Detailed description and likelihood function for the Bayesian hierarchical hurdle model.
DOI: 10.6084/m9.figshare.3563115.v1
title: Appendix A. Detailed description and likelihood function for the Bayesian hierarchical hurdle model.

description: Detailed description and likelihood function for the Bayesian hierarchical hurdle model.
DOI: 10.6084/m9.figshare.3563112
title: Appendix B. Supplemental figures showing patterns for each forest stand, environmental coefficients, and results from alternative models.

description: Supplemental figures showing patterns for each forest stand, environmental coefficients, and results from alternative models.
DOI: 10.6084/m9.figshare.3563112.v1
title: Appendix B. Supplemental figures showing patterns for each forest stand, environmental coefficients, and results from alternative models.

description: Supplemental figures showing patterns for each forest stand, environmental coefficients, and results from alternative models.
DOI: 10.6084/m9.figshare.3563109
title: Appendix C. Supplemental tables describing environmental variables in each forest stand, tests for phylogenetic trait conservation, and comparisons of native and introduced species.

description: Supplemental tables describing environmental variables in each forest stand, tests for phylogenetic trait conservation, and comparisons of native and introduced species.
DOI: 10.6084/m9.figshare.3563109.v1
title: Appendix C. Supplemental tables describing environmental variables in each forest stand, tests for phylogenetic trait conservation, and comparisons of native and introduced species.

description: Supplemental tables describing environmental variables in each forest stand, tests for phylogenetic trait conservation, and comparisons of native and introduced species.
DOI: 10.6084/m9.figshare.3563106
title: Supplement 1. All python/STAN code, including Bayesian hierarchical model, used in the analysis.

description: File List Supplement_Model_REPORT.txt (MD5: ea2e3f2c6f17b80e7d3b55eff718d9d3) Description Supplement_Model_REPORT.txt contains all Python/STAN code needed to replicate the analysis and hierarchical model.
DOI: 10.6084/m9.figshare.3563106.v1
title: Supplement 1. All python/STAN code, including Bayesian hierarchical model, used in the analysis.

description: File List Supplement_Model_REPORT.txt (MD5: ea2e3f2c6f17b80e7d3b55eff718d9d3) Description Supplement_Model_REPORT.txt contains all Python/STAN code needed to replicate the analysis and hierarchical model.
DOI: 10.6084/m9.figshare.3563103
title: Appendix A. Detailed description of the simulation study.

description: Detailed description of the simulation study.
DOI: 10.6084/m9.figshare.3563100
title: Appendix B. Detailed description of the applications.

description: Detailed description of the applications.
DOI: 10.6084/m9.figshare.3563097
title: Appendix C. Parameter estimates obtained using TMB for models fitted to the ringed seal data.

description: Parameter estimates obtained using TMB for models fitted to the ringed seal data.
DOI: 10.6084/m9.figshare.3563094
title: Supplement 1. R code for fitting Argos data with argosTrack.

description: File List argosTrack.tar.gz (md5: e7e7f6f0e502c42b4cd24ee8f9679e62)<br> argosTrack.R (md5: 7857ead3f7e13ed67ceb16655b546ac6)<br> bsam.R (md5: 2f4b064ef9089a90873b0049fea39b31)<br> crawl.R (md5: f36b3c25fd8e929a3d41cd4867cdfd92)<br> Description argosTrack.tar.gz - Source code for the R package argosTrack. argosTrack.R - Example of how to use the package argosTrack. bsam.R - R code for analysis of the seal data using bsam. crawl.R - R code for analysis of the seal data using crawl. Installing argosTrack on Windows The argosTrack package depends on the package TMB. To install TMB download and unzip the code from: https://github.com/kaskr/adcomp/archive/master.zip. Open R, change the working directory to the unzipped adcomp-master folder, and run source("install_windows.R"). The command will ask to install Rtools which should be accepted. After a successfull installation of TMB, change the working directory to the folder containing argosTrack.tar.gz and install with library(TMB);install.packages("mvtnorm");install.packages("argosTrack.tar.gz",repos=NULL,type="source"). Installing argosTrack on Linux The argosTrack package depends on the package TMB. To install TMB download and unzip the code from: https://github.com/kaskr/adcomp/archive/master.zip. In the terminal, change directory to the unzipped adcomp-master folder, and run make install. After a successfull installation of TMB, change the directory to the folder containing argosTrack.tar.gz, open R, and run install.packages("mvtnorm");install.packages("argosTrack.tar.gz",repos=NULL,type="source"). Installing argosTrack on Mac OS X The argosTrack package depends on the package TMB. To install TMB, install Xcode from the App Store, install gFortran from http://cran.r-project.org/bin/macosx/tools/, and download and unzip the TMB source code from: https://github.com/kaskr/adcomp/archive/master.zip. Open the terminal and change the directory to the unzipped adcomp-master folder. Run the command make install. After a successfull installation of TMB, change the directory to the folder containing argosTrack.tar.gz, open R, and run install.packages("mvtnorm");install.packages("argosTrack.tar.gz",repos=NULL,type="source").
DOI: 10.6084/m9.figshare.3563091
title: Appendix A. Complete specification of mixture t model used for the simulation study and harbor seal analysis.

description: Complete specification of mixture t model used for the simulation study and harbor seal analysis.
DOI: 10.6084/m9.figshare.3563088
title: Appendix B. Full-conditional distributions and Markov chain Monte Carlo algorithm for parameter estimation.

description: Full-conditional distributions and Markov chain Monte Carlo algorithm for parameter estimation.
DOI: 10.6084/m9.figshare.3563085
title: Appendix C. Performance of mixture t model in simulation study.

description: Performance of mixture t model in simulation study.
DOI: 10.6084/m9.figshare.3563082
title: Appendix D. Summary of results for an analysis of harbor seal data near Kodiak Island, Alaska, USA.

description: Summary of results for an analysis of harbor seal data near Kodiak Island, Alaska, USA.
DOI: 10.6084/m9.figshare.3563079
title: Appendix E. Estimated Argos satellite telemetry error by location class.

description: Estimated Argos satellite telemetry error by location class.
DOI: 10.6084/m9.figshare.3563079.v1
title: Appendix E. Estimated Argos satellite telemetry error by location class.

description: Estimated Argos satellite telemetry error by location class.
DOI: 10.6084/m9.figshare.3563076
title: Supplement 1. Source code and data for implementing the MCMC algorithm for the mixture t model.

description: File List script.R (MD5: 57da87fd1e041a03add66cc2af0c8933) constraints.MCMC.R (MD5: c52c9d7c30dcb95fae66d473cc4b25e1) update.mu.cpp (MD5: 8a3185afcf71659dbcfbd21be73a14f2) workspace.Rdata (MD5: 7bd75c148d65bf52ef058b182672fe2b) seal.csv (MD5: 4e8a85f13486610fbab515c2fa04bef9) Description script.R contains R code for loading the data (workspace.Rdata), necessary R packages, subroutines (update.mu.cpp), and MCMC algorithm for model fitting (constraints.MCMC.R); simulating data; fitting the model to simulated data and examining the associated results; and fitting the model to the harbor seal telemetry data used in the case study and examining the associated results. constraints.MCMC.R contains code to implement the MCMC algorithm for model fitting as outlined in Appendix B. update.mu.cpp contains optional C++ code for updating -- IMAGE: Please see in attached file. -- in the MCMC algorithm. Use argument Cpp=TRUE to the constraints.MCMC function to implement this C++ routine. workspace.Rdata contains raster data representing the support of -- IMAGE: Please see in attached file. --, bathymetry, and distance to haul-out site; a design matrix of spatially-reference habitat covariates for the resource selection function; and a spatial object containing the Argos telemetry locations of the harbor seal used in our case study. seal.csv contains the <i>x</i>- and <i>y</i>-coordinates of the telemetry locations for the harbor seal used in our case study (in Albers equal area projection), as well as the associated dates, times, and Argos location classes.
DOI: 10.6084/m9.figshare.3563073
title: Appendix A. Detailed description of the implementation of the model in the kfdnm R package.

description: Detailed description of the implementation of the model in the kfdnm R package.
DOI: 10.6084/m9.figshare.3563073.v1
title: Appendix A. Detailed description of the implementation of the model in the kfdnm R package.

description: Detailed description of the implementation of the model in the kfdnm R package.
DOI: 10.6084/m9.figshare.3563070
title: Appendix B. Results from simulations conducted using OpenBUGS and kfdnm.

description: Results from simulations conducted using OpenBUGS and kfdnm.
DOI: 10.6084/m9.figshare.3563070.v1
title: Appendix B. Results from simulations conducted using OpenBUGS and kfdnm.

description: Results from simulations conducted using OpenBUGS and kfdnm.
DOI: 10.6084/m9.figshare.3563067
title: Appendix C. Results from simulations conducted using JAGS and WinBUGS.

description: Results from simulations conducted using JAGS and WinBUGS.
DOI: 10.6084/m9.figshare.3563067.v1
title: Appendix C. Results from simulations conducted using JAGS and WinBUGS.

description: Results from simulations conducted using JAGS and WinBUGS.
DOI: 10.6084/m9.figshare.3563064
title: Supplement 1. OpenBUGS implementation of the combined known-fate open N-mixture model for the applied wolf survival and recruitment example.

description: File List OpenBUGS_wolf_example.txt (MD5: 0852bb78ec1b990960116c2ddd031ec2) Description The file OpenBUGS_wolf_example.txt contains the OpenBUGS code used for the combined known-fate open <i>N</i>-mixture model in the wolf example. Detailed explanations of model components are provided directly in the code.
DOI: 10.6084/m9.figshare.3563064.v1
title: Supplement 1. OpenBUGS implementation of the combined known-fate open N-mixture model for the applied wolf survival and recruitment example.

description: File List OpenBUGS_wolf_example.txt (MD5: 0852bb78ec1b990960116c2ddd031ec2) Description The file OpenBUGS_wolf_example.txt contains the OpenBUGS code used for the combined known-fate open <i>N</i>-mixture model in the wolf example. Detailed explanations of model components are provided directly in the code.
DOI: 10.6084/m9.figshare.3563061
title: Data Paper. Data Paper

description: File List SIA_N_C_Atlantic_marine_fishes_squids_20150105_v1.csv (MD5: 727079426b7882df65f92a6eeaf5d756) Description Nitrogen and carbon stable isotope data are frequently used to describe the origins and transformations of organic matter. Nitrogen stable isotopes (δ<sup>15</sup>N) in tissue are used to estimate species’ trophic levels, the extent of omnivory, food chain length, and community-wide relationships between body size and trophic level; the latter leading to estimates of predator–prey mass ratios for parameterization, calibration, and validation of food web models. Carbon stable isotopes (δ<sup>13</sup>C) are used to identify pathways linking producers and consumers and for studies of migration and movement. Collectively, δ<sup>15</sup>N and δ<sup>13</sup>C, often with other stable isotopes such as δ<sup>34</sup>S, may be used to define the contribution of different producers and pathways to consumer production, to assess the trophic impacts of invasive species and habitat modification, and to predict past habitat use, movements, and migrations. Stable isotope data often complement dietary data (e.g., from stomach contents) in food web studies, because stable isotope composition is indicative of assimilated diet over months to years, depending on species, size, environment, and tissue type. There are relatively few large-scale compilations of δ<sup>15</sup>N and δ<sup>13</sup>C data for marine species from offshore habitats, but such data facilitate comparative analysis and research into food web structure and function. The data provided comprise 5535 records for individuals of 62 species of fish and squid weighing 0.3 g to 17920 g and sampled from the northeast Atlantic shelf seas (Celtic Sea, North Sea, Irish Sea, Channel) from 2002 to 2010. For every sampled individual the record lists: species name, date of sampling, position of sampling, body mass, percentage nitrogen in muscle tissue, percentage carbon in muscle tissue, and δ<sup>15</sup>N and δ<sup>13</sup>C natural abundance in muscle tissue. Awareness of, and access to, these data should catalyze and facilitate new research with stable isotopes, to improve understanding of marine biology, food web ecology, and human impacts on the environment. <i>Key words</i>: <i>body size; cephalopod; consumer; elasmobranch; food chain; food web; marine; producer; teleost; trophic position; stable isotopes.</i>
DOI: 10.6084/m9.figshare.3563058
title: Appendix A. Additional tables, methods, and results.

description: Additional tables, methods, and results.
DOI: 10.6084/m9.figshare.3563058.v1
title: Appendix A. Additional tables, methods, and results.

description: Additional tables, methods, and results.
DOI: 10.6084/m9.figshare.3563055
title: Supplement 1. Raw data file for statistical analyses of the effects of the presence/absence of invasive toads on counts of lizards, snakes, and crocodiles; and for the influence of declines in monitor lizards on the fledging success of finches.

description: File List data.csv (MD5: 6ffb77913bb9109caa9abdd3f08c760d) Description The year column indicates the year in which the survey was conducted. Survey# refers to the number of the survey within a year (there were five surveys per year). Toads refers to whether toads were absent (a) or present (p). Mean air temp denotes mean air temperature for each survey, calculated as the mean of five temperature taken throughout the day. Mean water temp denotes mean air temperature for each survey, calculated as the mean of five temperature taken throughout the day. Mean temp differential denotes mean temperature differential and refers to the difference between the air and water temperature at a given time (means are then calculated for the five values per survey). Mitchells, mertens, crocs, gilberts, tree snakes, and panoptes refers to counts for each of those species, per survey. The second set of data is to examine the effects of declines in monitor lizards on fledging success of crimson finches. The year column indicates the year of survey. Data for mitchells and mertens are mean counts for the year, and finches refers to fledging success for that year.
DOI: 10.6084/m9.figshare.3563055.v1
title: Supplement 1. Raw data file for statistical analyses of the effects of the presence/absence of invasive toads on counts of lizards, snakes, and crocodiles; and for the influence of declines in monitor lizards on the fledging success of finches.

description: File List data.csv (MD5: 6ffb77913bb9109caa9abdd3f08c760d) Description The year column indicates the year in which the survey was conducted. Survey# refers to the number of the survey within a year (there were five surveys per year). Toads refers to whether toads were absent (a) or present (p). Mean air temp denotes mean air temperature for each survey, calculated as the mean of five temperature taken throughout the day. Mean water temp denotes mean air temperature for each survey, calculated as the mean of five temperature taken throughout the day. Mean temp differential denotes mean temperature differential and refers to the difference between the air and water temperature at a given time (means are then calculated for the five values per survey). Mitchells, mertens, crocs, gilberts, tree snakes, and panoptes refers to counts for each of those species, per survey. The second set of data is to examine the effects of declines in monitor lizards on fledging success of crimson finches. The year column indicates the year of survey. Data for mitchells and mertens are mean counts for the year, and finches refers to fledging success for that year.
DOI: 10.6084/m9.figshare.3563052
title: Appendix A. Details on preliminary experiments, size and biomass of taxa used in the experiments, and information on the interaction calculations.

description: Details on preliminary experiments, size and biomass of taxa used in the experiments, and information on the interaction calculations.
DOI: 10.6084/m9.figshare.3563049
title: Appendix B. Map of the oyster reefs sampled within Pamlico Sound.

description: Map of the oyster reefs sampled within Pamlico Sound.
DOI: 10.6084/m9.figshare.3563049.v1
title: Appendix B. Map of the oyster reefs sampled within Pamlico Sound.

description: Map of the oyster reefs sampled within Pamlico Sound.
DOI: 10.6084/m9.figshare.3563046
title: Appendix C. Detailed results of consumed crabs from experiment 1.

description: Detailed results of consumed crabs from experiment 1.
DOI: 10.6084/m9.figshare.3563043
title: Appendix D. Detailed results from field surveys.

description: Detailed results from field surveys.
DOI: 10.6084/m9.figshare.3563043.v1
title: Appendix D. Detailed results from field surveys.

description: Detailed results from field surveys.
DOI: 10.6084/m9.figshare.3563040
title: Appendix A. Feedback estimates from within-light treatment subsets.

description: Feedback estimates from within-light treatment subsets.
DOI: 10.6084/m9.figshare.3563040.v1
title: Appendix A. Feedback estimates from within-light treatment subsets.

description: Feedback estimates from within-light treatment subsets.
DOI: 10.6084/m9.figshare.3563037
title: Appendix B. The role of Phase I biomass in driving the light x PSF interaction.

description: The role of Phase I biomass in driving the light x PSF interaction.
DOI: 10.6084/m9.figshare.3563037.v1
title: Appendix B. The role of Phase I biomass in driving the light x PSF interaction.

description: The role of Phase I biomass in driving the light x PSF interaction.
DOI: 10.6084/m9.figshare.3563034
title: Appendix A. Detailed methodologies for field surveys and oak wood identification.

description: Detailed methodologies for field surveys and oak wood identification.
DOI: 10.6084/m9.figshare.3563034.v1
title: Appendix A. Detailed methodologies for field surveys and oak wood identification.

description: Detailed methodologies for field surveys and oak wood identification.
DOI: 10.6084/m9.figshare.3563031
title: Appendix B. Additional results from analyses of the plant community.

description: Additional results from analyses of the plant community.
DOI: 10.6084/m9.figshare.3563031.v1
title: Appendix B. Additional results from analyses of the plant community.

description: Additional results from analyses of the plant community.
DOI: 10.6084/m9.figshare.3563028
title: Appendix C. Additional results describing environmental attributes affected by the tree crown and relationships with plant community composition.

description: Additional results describing environmental attributes affected by the tree crown and relationships with plant community composition.
DOI: 10.6084/m9.figshare.3563028.v1
title: Appendix C. Additional results describing environmental attributes affected by the tree crown and relationships with plant community composition.

description: Additional results describing environmental attributes affected by the tree crown and relationships with plant community composition.
DOI: 10.6084/m9.figshare.3563025
title: Appendix A. Detailed methods used for reassigning tanks to density treatments.

description: Detailed methods used for reassigning tanks to density treatments.
DOI: 10.6084/m9.figshare.3563025.v1
title: Appendix A. Detailed methods used for reassigning tanks to density treatments.

description: Detailed methods used for reassigning tanks to density treatments.
DOI: 10.6084/m9.figshare.3563022
title: Appendix A. Table of the effects of soil nutrient concentrations on foliar resorption.

description: Table of the effects of soil nutrient concentrations on foliar resorption.
DOI: 10.6084/m9.figshare.3563019
title: Appendix B. Relationship between soil predictor variables.

description: Relationship between soil predictor variables.
DOI: 10.6084/m9.figshare.3563016
title: Appendix C. Resorption results by species.

description: Resorption results by species.
DOI: 10.6084/m9.figshare.3563013
title: Appendix A. Aboveground wood net primary production (ANPPw) and litter trap leaf area index (LAIt) for all plots prior to and following peak disturbance, the fraction of tree basal area girdled in each plot, and the three most dominant upper canopy tree species with respect to basal area in each plot prior to disturbance.

description: Aboveground wood net primary production (ANPPw) and litter trap leaf area index (LAIt) for all plots prior to and following peak disturbance, the fraction of tree basal area girdled in each plot, and the three most dominant upper canopy tree species with respect to basal area in each plot prior to disturbance.
DOI: 10.6084/m9.figshare.3563010
title: Appendix A. Optical density (800 nm) of phytoplankton species grown in monocultures and the three communities during the time course of the experiment.

description: Optical density (800 nm) of phytoplankton species grown in monocultures and the three communities during the time course of the experiment.
DOI: 10.6084/m9.figshare.3563010.v1
title: Appendix A. Optical density (800 nm) of phytoplankton species grown in monocultures and the three communities during the time course of the experiment.

description: Optical density (800 nm) of phytoplankton species grown in monocultures and the three communities during the time course of the experiment.
DOI: 10.6084/m9.figshare.3563007
title: Appendix B. Results of statistical comparisons between predicted and observed C:P ratios and concentrations of fatty acids in the three different phytoplankton assemblages.

description: Results of statistical comparisons between predicted and observed C:P ratios and concentrations of fatty acids in the three different phytoplankton assemblages.
DOI: 10.6084/m9.figshare.3563007.v1
title: Appendix B. Results of statistical comparisons between predicted and observed C:P ratios and concentrations of fatty acids in the three different phytoplankton assemblages.

description: Results of statistical comparisons between predicted and observed C:P ratios and concentrations of fatty acids in the three different phytoplankton assemblages.
DOI: 10.6084/m9.figshare.3563004
title: Appendix A. Description of the data sets gathered for this study, including external data sources.

description: Description of the data sets gathered for this study, including external data sources.
DOI: 10.6084/m9.figshare.3563004.v1
title: Appendix A. Description of the data sets gathered for this study, including external data sources.

description: Description of the data sets gathered for this study, including external data sources.