cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3552273
title: Supplement 1. R Scripting Language code used for data generation in simulations.

description: File List datgen_defs.R<br> datgen_script.R<br> wedge.R<br> datgen.zip Description datgen_defs.r: This file contains the following functions: xgen() Generates random environmental values given a distribution ID and sample size. mugen() Generates mean values for a negative binomial distribution over a given environmental gradient. ygen() Generates random count data given an environmental gradient, distribution mean, and CV. datgen_script.r: This file generates random datasets as they were in this study. wedge.r: This file contains the following functions: rwedge() Takes random draws from a wedge-shaped pdf. dwedge() Reports the cdf from a wedge-shaped distribution given a quantile. datgen.zip: This zip file contains all the above files.
DOI: 10.6084/m9.figshare.3552273.v1
title: Supplement 1. R Scripting Language code used for data generation in simulations.

description: File List datgen_defs.R<br> datgen_script.R<br> wedge.R<br> datgen.zip Description datgen_defs.r: This file contains the following functions: xgen() Generates random environmental values given a distribution ID and sample size. mugen() Generates mean values for a negative binomial distribution over a given environmental gradient. ygen() Generates random count data given an environmental gradient, distribution mean, and CV. datgen_script.r: This file generates random datasets as they were in this study. wedge.r: This file contains the following functions: rwedge() Takes random draws from a wedge-shaped pdf. dwedge() Reports the cdf from a wedge-shaped distribution given a quantile. datgen.zip: This zip file contains all the above files.
DOI: 10.6084/m9.figshare.3552267
title: Appendix A. Summary statistics for vegetative and reproductive traits of Chromolaena pungens plants following experimental treatments.

description: Summary statistics for vegetative and reproductive traits of Chromolaena pungens plants following experimental treatments.
DOI: 10.6084/m9.figshare.3552267.v1
title: Appendix A. Summary statistics for vegetative and reproductive traits of Chromolaena pungens plants following experimental treatments.

description: Summary statistics for vegetative and reproductive traits of Chromolaena pungens plants following experimental treatments.
DOI: 10.6084/m9.figshare.3552264
title: Appendix B. Summary statistics for multiple-response permutation procedure (MRPP) of herbivore composition among treatments.

description: Summary statistics for multiple-response permutation procedure (MRPP) of herbivore composition among treatments.
DOI: 10.6084/m9.figshare.3552264.v1
title: Appendix B. Summary statistics for multiple-response permutation procedure (MRPP) of herbivore composition among treatments.

description: Summary statistics for multiple-response permutation procedure (MRPP) of herbivore composition among treatments.
DOI: 10.6084/m9.figshare.3552261
title: Full Archive

description: Full Archive
DOI: 10.6084/m9.figshare.3552258
title: Appendix A. Photographs of experimental assembly.

description: Photographs of experimental assembly.
DOI: 10.6084/m9.figshare.3552258.v1
title: Appendix A. Photographs of experimental assembly.

description: Photographs of experimental assembly.
DOI: 10.6084/m9.figshare.3552249
title: Appendix B. Arithmetic treatment means by region.

description: Arithmetic treatment means by region.
DOI: 10.6084/m9.figshare.3552249.v1
title: Appendix B. Arithmetic treatment means by region.

description: Arithmetic treatment means by region.
DOI: 10.6084/m9.figshare.3552246
title: Appendix C. Example of a community that developed without predators (screened treatment) for three months and was then exposed to predation for three days.

description: Example of a community that developed without predators (screened treatment) for three months and was then exposed to predation for three days.
DOI: 10.6084/m9.figshare.3552246.v1
title: Appendix C. Example of a community that developed without predators (screened treatment) for three months and was then exposed to predation for three days.

description: Example of a community that developed without predators (screened treatment) for three months and was then exposed to predation for three days.
DOI: 10.6084/m9.figshare.3552243
title: Data Paper. Data Paper

description: File List MCDB_communities.csv -- 7977 records, not including header row, ASCII text, comma-delimited. MCDB_references.csv -- 186 records, not including header row, ASCII text, comma-delimited. MCDB_sites.csv -- 1,000 records, not including header row, ASCII text, comma-delimited. MCDB_species.csv -- 700 records, not including header row, ASCII text, comma-delimited. MCDB_trapping.csv -- 1,169 records, not including header row, ASCII text, comma-delimited. Description Ecologists have long sought to understand the mechanisms underlying the assembly and structure of communities. Such understanding is relevant to both basic science and conservation-related issues. The macroecological approach to this problem involves asking scientific questions using a large number of communities in order to elucidate generalities in pattern and process. Such analyses are typically conducted using a substantial amount of data from a particular taxonomic group across a diversity of systems. Large community databases are available for a number of taxa, but no publicly available database exists for mammals. Given the logistical challenges of collecting such data de novo, compiling existing information from the literature provides the best avenue for acquiring the necessary data. Here, we provide a data set that includes species lists for 1000 mammal communities, excluding bats, with species-level abundances available for 940 of these communities. All communities found in the literature that included complete, site-specific sampling data, composed of species lists with or without associated abundances, were included in the data set. Most, but not all, sites are limited to species groups that are sampled using a single technique (e.g., small mammals sampled with Sherman traps). The data set consists of 7977 records from 1000 georeferenced sites encompassing a variety of habitats throughout the world, and it includes data on 660 mammal species with sizes ranging from 2 g to &gt;500 kg. <i>Key words: abundance; community; community assembly; community structure; composition; mammals</i>.
DOI: 10.6084/m9.figshare.3552240
title: Appendix A. Models used and fitting of Bayesian piecewise regressions.

description: Models used and fitting of Bayesian piecewise regressions.
DOI: 10.6084/m9.figshare.3552237
title: Appendix B. A summary of fitted models and parameters with figures of estimated scaling exponents.

description: A summary of fitted models and parameters with figures of estimated scaling exponents.
DOI: 10.6084/m9.figshare.3552234
title: Appendix A. A summary table of simulation study results, for all conditions and all parameters.

description: A summary table of simulation study results, for all conditions and all parameters.
DOI: 10.6084/m9.figshare.3552237.v1
title: Appendix B. A summary of fitted models and parameters with figures of estimated scaling exponents.

description: A summary of fitted models and parameters with figures of estimated scaling exponents.
DOI: 10.6084/m9.figshare.3552231
title: Supplement 1. R code for estimating thresholds while accounting for variable detection and data for estimating thresholds for forest birds, Oregon, USA, 2007–2008.

description: File List Supplement_Avian data.csv<br> Supplement_R code.r Description The Supplement_Avian data.csv file contains data on stand-level habitat covariates and visit-specific detections of avian species, Oregon, USA, 2008–2009. Column definitions Stand id Percent cover of conifer species Percent cover of broadleaf species Percent cover of deciduous broadleaf species Percent cover of hardwood species Percent cover of hardwood species in a 2000 m radius circle around each sample stand Elevation (m) of stand Age of stand Year of sampling Visit number Detection of Magnolia Warbler on Visit 1 Detection of Magnolia Warbler on Visit 2 Detection of Orange-crowned Warbler on Visit 1 Detection of Orange-crowned Warbler on Visit 2 Detection of Swainson’s Thrush on Visit 1 Detection of Swainson’s Thrush on Visit 2 Detection of Willow Flycatcher on Visit 1 Detection of Willow Flycatcher on Visit 2 Detection of Wilson’s Warbler on Visit 1 Detection of Wilson’s Warbler on Visit 1 Checksum values are: Column 2 (Percent cover of conifer species – CONIFER): SUM = 5862.83<br> Column 3 (Percent cover of broadleaf species – BROAD): SUM = 7043.17<br> Column 4 (Percent cover of deciduous broadleaf species – DECBROAD): SUM = 5475.17<br> Column 5 (Percent cover of hardwood species – HARDWOOD): SUM = 2151.96<br> Column 6 (Percent cover of hardwood species in a 2000 m radius circle around each sample stand– HWD2000): SUM = 3486.07<br> Column 7 (Stand elevation – ELEVM): SUM = 83240.58<br> Column 8 (Stand age – AGE): SUM = 1537; NA indicates a stand was harvested in 2008<br> Column 9 (Year of sampling – YEAR): SUM = 425792<br> Column 11 (MGWA.1): SUM = 70<br> Column 12 (MGWA.2): SUM = 71<br> Column 13 (OCWA.1): SUM = 121<br> Column 14 (OCWA.2): SUM = 76<br> Column 15 (SWTH.1): SUM = 90<br> Column 16 (SWTH.2): SUM = 95<br> Column 17 (WIFL.1): SUM = 85<br> Column 18 (WIFL.2): SUM = 85<br> Column 19 (WIWA.1): SUM = 36<br> Column 20 (WIWA.2): SUM = 37 The Supplement_R code.r file is R source code for simulation and empirical analyses conducted in Jones et al.
DOI: 10.6084/m9.figshare.3552234.v1
title: Appendix A. A summary table of simulation study results, for all conditions and all parameters.

description: A summary table of simulation study results, for all conditions and all parameters.
DOI: 10.6084/m9.figshare.3552231.v1
title: Supplement 1. R code for estimating thresholds while accounting for variable detection and data for estimating thresholds for forest birds, Oregon, USA, 2007–2008.

description: File List Supplement_Avian data.csv<br> Supplement_R code.r Description The Supplement_Avian data.csv file contains data on stand-level habitat covariates and visit-specific detections of avian species, Oregon, USA, 2008–2009. Column definitions Stand id Percent cover of conifer species Percent cover of broadleaf species Percent cover of deciduous broadleaf species Percent cover of hardwood species Percent cover of hardwood species in a 2000 m radius circle around each sample stand Elevation (m) of stand Age of stand Year of sampling Visit number Detection of Magnolia Warbler on Visit 1 Detection of Magnolia Warbler on Visit 2 Detection of Orange-crowned Warbler on Visit 1 Detection of Orange-crowned Warbler on Visit 2 Detection of Swainson’s Thrush on Visit 1 Detection of Swainson’s Thrush on Visit 2 Detection of Willow Flycatcher on Visit 1 Detection of Willow Flycatcher on Visit 2 Detection of Wilson’s Warbler on Visit 1 Detection of Wilson’s Warbler on Visit 1 Checksum values are: Column 2 (Percent cover of conifer species – CONIFER): SUM = 5862.83<br> Column 3 (Percent cover of broadleaf species – BROAD): SUM = 7043.17<br> Column 4 (Percent cover of deciduous broadleaf species – DECBROAD): SUM = 5475.17<br> Column 5 (Percent cover of hardwood species – HARDWOOD): SUM = 2151.96<br> Column 6 (Percent cover of hardwood species in a 2000 m radius circle around each sample stand– HWD2000): SUM = 3486.07<br> Column 7 (Stand elevation – ELEVM): SUM = 83240.58<br> Column 8 (Stand age – AGE): SUM = 1537; NA indicates a stand was harvested in 2008<br> Column 9 (Year of sampling – YEAR): SUM = 425792<br> Column 11 (MGWA.1): SUM = 70<br> Column 12 (MGWA.2): SUM = 71<br> Column 13 (OCWA.1): SUM = 121<br> Column 14 (OCWA.2): SUM = 76<br> Column 15 (SWTH.1): SUM = 90<br> Column 16 (SWTH.2): SUM = 95<br> Column 17 (WIFL.1): SUM = 85<br> Column 18 (WIFL.2): SUM = 85<br> Column 19 (WIWA.1): SUM = 36<br> Column 20 (WIWA.2): SUM = 37 The Supplement_R code.r file is R source code for simulation and empirical analyses conducted in Jones et al.
DOI: 10.6084/m9.figshare.3552228
title: Appendix A. Additional figures and tables including a map showing study locations, a CAP analysis demonstrating differences in fish communities between locations, and the species lists for Figs. 3B and 4B.

description: Additional figures and tables including a map showing study locations, a CAP analysis demonstrating differences in fish communities between locations, and the species lists for Figs. 3B and 4B.
DOI: 10.6084/m9.figshare.3552228.v1
title: Appendix A. Additional figures and tables including a map showing study locations, a CAP analysis demonstrating differences in fish communities between locations, and the species lists for Figs. 3B and 4B.

description: Additional figures and tables including a map showing study locations, a CAP analysis demonstrating differences in fish communities between locations, and the species lists for Figs. 3B and 4B.
DOI: 10.6084/m9.figshare.3552225
title: Appendix A. Confirmatory tank predation experiments conducted from July 10–20, 2010, on site at the Charles Darwin Research Station, Isla Santa Cruz, Galápagos Islands, Ecuador.

description: Confirmatory tank predation experiments conducted from July 10–20, 2010, on site at the Charles Darwin Research Station, Isla Santa Cruz, Galápagos Islands, Ecuador.
DOI: 10.6084/m9.figshare.3552222
title: Appendix B. Statistical tables describing relationships among species from 20 field sites in the Galápagos.

description: Statistical tables describing relationships among species from 20 field sites in the Galápagos.
DOI: 10.6084/m9.figshare.3552219
title: Appendix A. Description of techniques used to map and monitor barnacles and tables of statistical results.

description: Description of techniques used to map and monitor barnacles and tables of statistical results.
DOI: 10.6084/m9.figshare.3552219.v1
title: Appendix A. Description of techniques used to map and monitor barnacles and tables of statistical results.

description: Description of techniques used to map and monitor barnacles and tables of statistical results.
DOI: 10.6084/m9.figshare.3552216
title: Appendix A. Maps showing the distribution of Microstegium and the collection sites in the native and introduced ranges.

description: Maps showing the distribution of Microstegium and the collection sites in the native and introduced ranges.
DOI: 10.6084/m9.figshare.3552216.v1
title: Appendix A. Maps showing the distribution of Microstegium and the collection sites in the native and introduced ranges.

description: Maps showing the distribution of Microstegium and the collection sites in the native and introduced ranges.
DOI: 10.6084/m9.figshare.3552213
title: Appendix B. Location and habitat information for the native and introduced Microstegium populations.

description: Location and habitat information for the native and introduced Microstegium populations.
DOI: 10.6084/m9.figshare.3552213.v1
title: Appendix B. Location and habitat information for the native and introduced Microstegium populations.

description: Location and habitat information for the native and introduced Microstegium populations.
DOI: 10.6084/m9.figshare.3552210
title: Appendix C. Habitat descriptions and environmental characteristics that were significantly correlated with Microstegium performance across the 22 common garden sites.

description: Habitat descriptions and environmental characteristics that were significantly correlated with Microstegium performance across the 22 common garden sites.
DOI: 10.6084/m9.figshare.3552210.v1
title: Appendix C. Habitat descriptions and environmental characteristics that were significantly correlated with Microstegium performance across the 22 common garden sites.

description: Habitat descriptions and environmental characteristics that were significantly correlated with Microstegium performance across the 22 common garden sites.
DOI: 10.6084/m9.figshare.3552207
title: Appendix D. Information on the materials and methods used for collecting data on environmental characteristics at the common garden sites.

description: Information on the materials and methods used for collecting data on environmental characteristics at the common garden sites.
DOI: 10.6084/m9.figshare.3552207.v1
title: Appendix D. Information on the materials and methods used for collecting data on environmental characteristics at the common garden sites.

description: Information on the materials and methods used for collecting data on environmental characteristics at the common garden sites.
DOI: 10.6084/m9.figshare.3552204
title: Appendix A. Two figures presenting additional demographic responses to the experimental manipulation of the first major rains for the three focal species of the study.

description: Two figures presenting additional demographic responses to the experimental manipulation of the first major rains for the three focal species of the study.
DOI: 10.6084/m9.figshare.3552204.v1
title: Appendix A. Two figures presenting additional demographic responses to the experimental manipulation of the first major rains for the three focal species of the study.

description: Two figures presenting additional demographic responses to the experimental manipulation of the first major rains for the three focal species of the study.
DOI: 10.6084/m9.figshare.3552201
title: Appendix A. Species-specific values for natural-history categories and other variables used in analyses at our three focal sites.

description: Species-specific values for natural-history categories and other variables used in analyses at our three focal sites.
DOI: 10.6084/m9.figshare.3552201.v1
title: Appendix A. Species-specific values for natural-history categories and other variables used in analyses at our three focal sites.

description: Species-specific values for natural-history categories and other variables used in analyses at our three focal sites.
DOI: 10.6084/m9.figshare.3552198
title: Appendix B. Details associated with mitochondrial data and analyses involving sequence data.

description: Details associated with mitochondrial data and analyses involving sequence data.
DOI: 10.6084/m9.figshare.3552198.v1
title: Appendix B. Details associated with mitochondrial data and analyses involving sequence data.

description: Details associated with mitochondrial data and analyses involving sequence data.
DOI: 10.6084/m9.figshare.3552195
title: Appendix C. Detailed results from logistic regressions and phenological analyses, by site and species.

description: Detailed results from logistic regressions and phenological analyses, by site and species.
DOI: 10.6084/m9.figshare.3552195.v1
title: Appendix C. Detailed results from logistic regressions and phenological analyses, by site and species.

description: Detailed results from logistic regressions and phenological analyses, by site and species.
DOI: 10.6084/m9.figshare.3552192
title: Appendix D. Results of Bayesian model averaging involving continuous and categorical predictor variables.

description: Results of Bayesian model averaging involving continuous and categorical predictor variables.
DOI: 10.6084/m9.figshare.3552192.v1
title: Appendix D. Results of Bayesian model averaging involving continuous and categorical predictor variables.

description: Results of Bayesian model averaging involving continuous and categorical predictor variables.
DOI: 10.6084/m9.figshare.3552189
title: Appendix A. Supporting tables including lower development temperature and development times, and supporting figures depicting degree days, available generations, model predictions, and model performance.

description: Supporting tables including lower development temperature and development times, and supporting figures depicting degree days, available generations, model predictions, and model performance.
DOI: 10.6084/m9.figshare.3552186
title: Appendix A. Sites at which neighbor-removal competition experiments were conducted with Centaurea stoebe as the target.

description: Sites at which neighbor-removal competition experiments were conducted with Centaurea stoebe as the target.
DOI: 10.6084/m9.figshare.3552189.v1
title: Appendix A. Supporting tables including lower development temperature and development times, and supporting figures depicting degree days, available generations, model predictions, and model performance.

description: Supporting tables including lower development temperature and development times, and supporting figures depicting degree days, available generations, model predictions, and model performance.
DOI: 10.6084/m9.figshare.3552186.v1
title: Appendix A. Sites at which neighbor-removal competition experiments were conducted with Centaurea stoebe as the target.

description: Sites at which neighbor-removal competition experiments were conducted with Centaurea stoebe as the target.
DOI: 10.6084/m9.figshare.3552183
title: Appendix A. Likelihood-based spatially explicit capture–recapture models for polygon searches.

description: Likelihood-based spatially explicit capture–recapture models for polygon searches.
DOI: 10.6084/m9.figshare.3552183.v1
title: Appendix A. Likelihood-based spatially explicit capture–recapture models for polygon searches.

description: Likelihood-based spatially explicit capture–recapture models for polygon searches.
DOI: 10.6084/m9.figshare.3552180
title: Appendix B. Revised analysis of a horned lizard data set (Royle and Young 2008).

description: Revised analysis of a horned lizard data set (Royle and Young 2008).
DOI: 10.6084/m9.figshare.3552180.v1
title: Appendix B. Revised analysis of a horned lizard data set (Royle and Young 2008).

description: Revised analysis of a horned lizard data set (Royle and Young 2008).
DOI: 10.6084/m9.figshare.3552177
title: Appendix C. R code for likelihood-based analyses of horned lizard data and simulations.

description: R code for likelihood-based analyses of horned lizard data and simulations.
DOI: 10.6084/m9.figshare.3552174
title: Appendix D. Likelihood-based spatially explicit capture–recapture models for linear searches.

description: Likelihood-based spatially explicit capture–recapture models for linear searches.
DOI: 10.6084/m9.figshare.3552174.v1
title: Appendix D. Likelihood-based spatially explicit capture–recapture models for linear searches.

description: Likelihood-based spatially explicit capture–recapture models for linear searches.
DOI: 10.6084/m9.figshare.3552171
title: Appendix A. Estimates in the case where jumps are set to zero of drift rate μ, diffusion standard deviation σD, total standard deviation σT and jump intensity λ vs. P mass in the lake.

description: Estimates in the case where jumps are set to zero of drift rate μ, diffusion standard deviation σD, total standard deviation σT and jump intensity λ vs. P mass in the lake.
DOI: 10.6084/m9.figshare.3552171.v1
title: Appendix A. Estimates in the case where jumps are set to zero of drift rate μ, diffusion standard deviation σD, total standard deviation σT and jump intensity λ vs. P mass in the lake.

description: Estimates in the case where jumps are set to zero of drift rate μ, diffusion standard deviation σD, total standard deviation σT and jump intensity λ vs. P mass in the lake.
DOI: 10.6084/m9.figshare.3552168
title: Supplement 1. R code to compute nonparametric estimates of drift, total sigma, diffusion, jump intensity, and jump magnitude for a univariate time series supplied by the user.

description: File List Bandi4d.r Description Bandi4d.r contains R code to compute nonparametric estimates of drift, total sigma, diffusion, jump intensity and jump magnitude for a univariate time series supplied by the user. Comment lines specify the inputs to the function and the outputs from the function. The code may be called from an R program as an external function, or it may be placed in-line within a R program.