cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3553263
title: Supplement 1. R code with general functions for calculating sensitivities and code used to conduct analyses in the paper.

description: File List functions.R (md5: cddb3d724691a2c5c7c6ded2a0f21bdc)<br> toads.R (md5: d23838869810c495ea1f0b86b7f5a5f5)<br> butterflies.R (md5: e76685d0f1eea2e4c525d9461e034be8)<br> eagles.R (md5: f22babc1ea9402d3e1793bafd6bf8318)<br> TransProbs.csv (md5: fb71eb184a4507d32d5c08473f6ec59c) Description Four scripts are included to create functions and run analyses described in the paper. Appendix A includes detailed background descriptions of how to conduct analyses including a large number of annotated examples of how the code is used. The first script, functions.R, includes a series of functions that can be called to conduct analyses. Prior to using the other scripts, this script must be run in R to load the functions. The included functions are: sens(R) - This function calculates sensitivities of the elements of the stationary state distribution to changes in each of the transition elements of R. No compensation method is used. Two outputs are given: sensitivities is the 3-dimensional array of sensitivities and ssd is the stationary state distribution. markov.sens(R) - This function calculates sensitivities of the elements of the stationary state distribution to changes in each of the transition elements of R with a compensation method imposed. Outputs are the sensitivities under uniform compensation - unif, under proportional compensation - prop, and the stationary state distribution - ssd. ssd.T(R,burn,iter) - This function calculates the stationary state distribution when R varies among time periods. Output is the stationary state distribution - e.T. unif.Tsens(R,q,burn,iter) - This function calculates the sensitivities of elements of the stationary state distribution to changes in elements of the transition matrix using uniform compensation. Outputs are the stationary state distribution - ssd, and the sensitivities - sens. prop.Tsens(R,q,burn,iter) - This function calculates the sensitivities of elements of the stationary state distribution to changes in elements of the transition matrix using proportional compensation. Outputs are the stationary state distribution - ssd, and the sensitivities - sens. lower.Tsens(R,R2,q,burn,iter) - This function can be generalized to calculate a wide variety of sensitivities when temporal variation in transitions occur. Outputs include the sensitivities - sens, as well as the stationary state distribution for the original and perturbed matrices - e.T and p.T, respectively. The additional scripts, toads.R, butterflies.R, and eagles.R, were used to conduct all the calculations presented in the paper and Appendix B. The data set for the arroyo toad example, which is read by the toads.R script, is in the file TransProbs.csv.
DOI: 10.6084/m9.figshare.3553263.v1
title: Supplement 1. R code with general functions for calculating sensitivities and code used to conduct analyses in the paper.

description: File List functions.R (md5: cddb3d724691a2c5c7c6ded2a0f21bdc)<br> toads.R (md5: d23838869810c495ea1f0b86b7f5a5f5)<br> butterflies.R (md5: e76685d0f1eea2e4c525d9461e034be8)<br> eagles.R (md5: f22babc1ea9402d3e1793bafd6bf8318)<br> TransProbs.csv (md5: fb71eb184a4507d32d5c08473f6ec59c) Description Four scripts are included to create functions and run analyses described in the paper. Appendix A includes detailed background descriptions of how to conduct analyses including a large number of annotated examples of how the code is used. The first script, functions.R, includes a series of functions that can be called to conduct analyses. Prior to using the other scripts, this script must be run in R to load the functions. The included functions are: sens(R) - This function calculates sensitivities of the elements of the stationary state distribution to changes in each of the transition elements of R. No compensation method is used. Two outputs are given: sensitivities is the 3-dimensional array of sensitivities and ssd is the stationary state distribution. markov.sens(R) - This function calculates sensitivities of the elements of the stationary state distribution to changes in each of the transition elements of R with a compensation method imposed. Outputs are the sensitivities under uniform compensation - unif, under proportional compensation - prop, and the stationary state distribution - ssd. ssd.T(R,burn,iter) - This function calculates the stationary state distribution when R varies among time periods. Output is the stationary state distribution - e.T. unif.Tsens(R,q,burn,iter) - This function calculates the sensitivities of elements of the stationary state distribution to changes in elements of the transition matrix using uniform compensation. Outputs are the stationary state distribution - ssd, and the sensitivities - sens. prop.Tsens(R,q,burn,iter) - This function calculates the sensitivities of elements of the stationary state distribution to changes in elements of the transition matrix using proportional compensation. Outputs are the stationary state distribution - ssd, and the sensitivities - sens. lower.Tsens(R,R2,q,burn,iter) - This function can be generalized to calculate a wide variety of sensitivities when temporal variation in transitions occur. Outputs include the sensitivities - sens, as well as the stationary state distribution for the original and perturbed matrices - e.T and p.T, respectively. The additional scripts, toads.R, butterflies.R, and eagles.R, were used to conduct all the calculations presented in the paper and Appendix B. The data set for the arroyo toad example, which is read by the toads.R script, is in the file TransProbs.csv.
DOI: 10.6084/m9.figshare.3553260
title: Appendix A. Arrangement of the 1-ha treatment (snake-exclosure) and control (snake-present) plots with sampling transects on Guam.

description: Arrangement of the 1-ha treatment (snake-exclosure) and control (snake-present) plots with sampling transects on Guam.
DOI: 10.6084/m9.figshare.3553260.v1
title: Appendix A. Arrangement of the 1-ha treatment (snake-exclosure) and control (snake-present) plots with sampling transects on Guam.

description: Arrangement of the 1-ha treatment (snake-exclosure) and control (snake-present) plots with sampling transects on Guam.
DOI: 10.6084/m9.figshare.3553257
title: Appendix B. Bayesian model selection procedure used to analyze evidence in favor of each of the different treatment models (trend treatment and constant treatment) versus a no-treatment model.

description: Bayesian model selection procedure used to analyze evidence in favor of each of the different treatment models (trend treatment and constant treatment) versus a no-treatment model.
DOI: 10.6084/m9.figshare.3553257.v1
title: Appendix B. Bayesian model selection procedure used to analyze evidence in favor of each of the different treatment models (trend treatment and constant treatment) versus a no-treatment model.

description: Bayesian model selection procedure used to analyze evidence in favor of each of the different treatment models (trend treatment and constant treatment) versus a no-treatment model.
DOI: 10.6084/m9.figshare.3553254
title: Appendix C. Brown treesnake (Boiga irregularis) population estimates for 1-ha plots during monitoring period 2 (post-construction of barrier but prior to its electrification) and number of snakes removed from treatment exclosures.

description: Brown treesnake (Boiga irregularis) population estimates for 1-ha plots during monitoring period 2 (post-construction of barrier but prior to its electrification) and number of snakes removed from treatment exclosures.
DOI: 10.6084/m9.figshare.3553254.v1
title: Appendix C. Brown treesnake (Boiga irregularis) population estimates for 1-ha plots during monitoring period 2 (post-construction of barrier but prior to its electrification) and number of snakes removed from treatment exclosures.

description: Brown treesnake (Boiga irregularis) population estimates for 1-ha plots during monitoring period 2 (post-construction of barrier but prior to its electrification) and number of snakes removed from treatment exclosures.
DOI: 10.6084/m9.figshare.3553251
title: Appendix D. Mean snout-vent length (SVL), measured in millimeters, of four species of lizards captured during removal sampling (100-m² subplot) conducted on treatment and control plots following the final post-treatment monitoring period (period 6).

description: Mean snout-vent length (SVL), measured in millimeters, of four species of lizards captured during removal sampling (100-m² subplot) conducted on treatment and control plots following the final post-treatment monitoring period (period 6).
DOI: 10.6084/m9.figshare.3553251.v1
title: Appendix D. Mean snout-vent length (SVL), measured in millimeters, of four species of lizards captured during removal sampling (100-m² subplot) conducted on treatment and control plots following the final post-treatment monitoring period (period 6).

description: Mean snout-vent length (SVL), measured in millimeters, of four species of lizards captured during removal sampling (100-m² subplot) conducted on treatment and control plots following the final post-treatment monitoring period (period 6).
DOI: 10.6084/m9.figshare.3553248
title: Appendix A. Detailed methods for sound recordings, sound analysis, and parameters for identification of difficult species.

description: Detailed methods for sound recordings, sound analysis, and parameters for identification of difficult species.
DOI: 10.6084/m9.figshare.3553248.v1
title: Appendix A. Detailed methods for sound recordings, sound analysis, and parameters for identification of difficult species.

description: Detailed methods for sound recordings, sound analysis, and parameters for identification of difficult species.
DOI: 10.6084/m9.figshare.3553245
title: Appendix B. Abundance index and feeding attempts per species and for all sites across the Isthmus of Panama compared with LMMs and Tukey multiple comparisons test.

description: Abundance index and feeding attempts per species and for all sites across the Isthmus of Panama compared with LMMs and Tukey multiple comparisons test.
DOI: 10.6084/m9.figshare.3553242
title: Appendix C. Total abundance index per transect at three sites across the Isthmus of Panama.

description: Total abundance index per transect at three sites across the Isthmus of Panama.
DOI: 10.6084/m9.figshare.3553245.v1
title: Appendix B. Abundance index and feeding attempts per species and for all sites across the Isthmus of Panama compared with LMMs and Tukey multiple comparisons test.

description: Abundance index and feeding attempts per species and for all sites across the Isthmus of Panama compared with LMMs and Tukey multiple comparisons test.
DOI: 10.6084/m9.figshare.3553242.v1
title: Appendix C. Total abundance index per transect at three sites across the Isthmus of Panama.

description: Total abundance index per transect at three sites across the Isthmus of Panama.
DOI: 10.6084/m9.figshare.3553239
title: Appendix A. Search strategy.

description: Search strategy.
DOI: 10.6084/m9.figshare.3553239.v1
title: Appendix A. Search strategy.

description: Search strategy.
DOI: 10.6084/m9.figshare.3553236
title: Appendix B. Tables listing studies that observationally quantified or manipulated subsidies for testing our hypotheses.

description: Tables listing studies that observationally quantified or manipulated subsidies for testing our hypotheses.
DOI: 10.6084/m9.figshare.3553236.v1
title: Appendix B. Tables listing studies that observationally quantified or manipulated subsidies for testing our hypotheses.

description: Tables listing studies that observationally quantified or manipulated subsidies for testing our hypotheses.
DOI: 10.6084/m9.figshare.3553233
title: Appendix C. Results for lentic ecosystems.

description: Results for lentic ecosystems.
DOI: 10.6084/m9.figshare.3553233.v1
title: Appendix C. Results for lentic ecosystems.

description: Results for lentic ecosystems.
DOI: 10.6084/m9.figshare.3553230
title: Appendix A. A table of taxa found in experimental communities.

description: A table of taxa found in experimental communities.
DOI: 10.6084/m9.figshare.3553230.v1
title: Appendix A. A table of taxa found in experimental communities.

description: A table of taxa found in experimental communities.
DOI: 10.6084/m9.figshare.3553227
title: Appendix B. Details of study site, experimental setup, statistical methods, and supplementary results, including tables of statistical analysis and figures of common species.

description: Details of study site, experimental setup, statistical methods, and supplementary results, including tables of statistical analysis and figures of common species.
DOI: 10.6084/m9.figshare.3553227.v1
title: Appendix B. Details of study site, experimental setup, statistical methods, and supplementary results, including tables of statistical analysis and figures of common species.

description: Details of study site, experimental setup, statistical methods, and supplementary results, including tables of statistical analysis and figures of common species.
DOI: 10.6084/m9.figshare.3553224
title: Appendix C. Comparisons of community structure of experiments 1 and 2 Williamstown.

description: Comparisons of community structure of experiments 1 and 2 Williamstown.
DOI: 10.6084/m9.figshare.3553224.v1
title: Appendix C. Comparisons of community structure of experiments 1 and 2 Williamstown.

description: Comparisons of community structure of experiments 1 and 2 Williamstown.
DOI: 10.6084/m9.figshare.3553221
title: Appendix A. Laboratory test of resource consumption in monoculture and polyculture.

description: Laboratory test of resource consumption in monoculture and polyculture.
DOI: 10.6084/m9.figshare.3553221.v1
title: Appendix A. Laboratory test of resource consumption in monoculture and polyculture.

description: Laboratory test of resource consumption in monoculture and polyculture.
DOI: 10.6084/m9.figshare.3553218
title: Appendix A. Figures showing additional results and further diversity measures, especially for γ- and α-diversity.

description: Figures showing additional results and further diversity measures, especially for γ- and α-diversity.
DOI: 10.5066/p9ebord5
title: Compilation of wells sampled, physical characteristics of wells, links to water-quality data, and quality assurance and quality control data for domestic wells sampled by the U.S. Geological Survey in Potter County, Pennsylvania, April-September 2017

description: This dataset contains the lithologic class and topographic position index information and quality-assurance and quality-control data not available in the online National Water Information System for 47 domestic wells sampled by the U.S. Geological Survey in Potter County, Pennsylvania, April-September 2017. The topographic position index (TPI) for each well location was computed on the basis of a 25-meter digital elevation model (U.S. Geological Survey, 2009) using criteria reported by Llewellyn (2014) to indicate potential classes for topographic setting. The bedrock geologic unit and primary lithology were determined for each well location on the basis of the digital bedrock geologic map of Pennsylvania (Miles and Whitfield, 2001). The quality-assurance and quality-control data (such as blanks or replicates) were collected at a subset of sites to ensure that the data met specific data-quality objectives outlined for the study.
DOI: 10.6084/m9.figshare.3553218.v1
title: Appendix A. Figures showing additional results and further diversity measures, especially for γ- and α-diversity.

description: Figures showing additional results and further diversity measures, especially for γ- and α-diversity.
DOI: 10.6084/m9.figshare.3553215
title: Appendix A. A table reporting the estimate of neutral parameters and a figure using the Bray-Curtis Distance as index for quantifying community dissimilarity.

description: A table reporting the estimate of neutral parameters and a figure using the Bray-Curtis Distance as index for quantifying community dissimilarity.
DOI: 10.6084/m9.figshare.3553215.v1
title: Appendix A. A table reporting the estimate of neutral parameters and a figure using the Bray-Curtis Distance as index for quantifying community dissimilarity.

description: A table reporting the estimate of neutral parameters and a figure using the Bray-Curtis Distance as index for quantifying community dissimilarity.
DOI: 10.6084/m9.figshare.3553212
title: Appendix B. Results of meta-analysis with dataset s19 included in the analysis.

description: Results of meta-analysis with dataset s19 included in the analysis.
DOI: 10.6084/m9.figshare.3553212.v1
title: Appendix B. Results of meta-analysis with dataset s19 included in the analysis.

description: Results of meta-analysis with dataset s19 included in the analysis.
DOI: 10.6084/m9.figshare.3553209
title: Appendix A. The list of vascular plant, bryophyte, and mollusk species identified as calcareous-fen specialists.

description: The list of vascular plant, bryophyte, and mollusk species identified as calcareous-fen specialists.
DOI: 10.6084/m9.figshare.3553209.v1
title: Appendix A. The list of vascular plant, bryophyte, and mollusk species identified as calcareous-fen specialists.

description: The list of vascular plant, bryophyte, and mollusk species identified as calcareous-fen specialists.
DOI: 10.6084/m9.figshare.3553206
title: Appendix B. Descriptive statistics for variables used in the analysis.

description: Descriptive statistics for variables used in the analysis.
DOI: 10.6084/m9.figshare.3553203
title: Appendix C. Scatter plots between four predictors (habitat age, habitat area, altitude, and isolation) used in path analysis to explain variation of individual species richness categories.

description: Scatter plots between four predictors (habitat age, habitat area, altitude, and isolation) used in path analysis to explain variation of individual species richness categories.
DOI: 10.6084/m9.figshare.3553206.v1
title: Appendix B. Descriptive statistics for variables used in the analysis.

description: Descriptive statistics for variables used in the analysis.
DOI: 10.6084/m9.figshare.3553203.v1
title: Appendix C. Scatter plots between four predictors (habitat age, habitat area, altitude, and isolation) used in path analysis to explain variation of individual species richness categories.

description: Scatter plots between four predictors (habitat age, habitat area, altitude, and isolation) used in path analysis to explain variation of individual species richness categories.
DOI: 10.6084/m9.figshare.3553200
title: Appendix A. Additional figure of infection prevalence as a function of host abundance and tables detailing the results of model selection and variation partitioning.

description: Additional figure of infection prevalence as a function of host abundance and tables detailing the results of model selection and variation partitioning.
DOI: 10.6084/m9.figshare.3553197
title: Appendix A. Site description.

description: Site description.
DOI: 10.6084/m9.figshare.3553197.v1
title: Appendix A. Site description.

description: Site description.
DOI: 10.6084/m9.figshare.3553194
title: Appendix B. Age-height offset analysis.

description: Age-height offset analysis.
DOI: 10.6084/m9.figshare.3553191
title: Appendix C. Establishment-precipitation regressions.

description: Establishment-precipitation regressions.
DOI: 10.6084/m9.figshare.3553191.v1
title: Appendix C. Establishment-precipitation regressions.

description: Establishment-precipitation regressions.
DOI: 10.6084/m9.figshare.3553188
title: Appendix D. Among-population-growth comparison.

description: Among-population-growth comparison.
DOI: 10.6084/m9.figshare.3553188.v1
title: Appendix D. Among-population-growth comparison.

description: Among-population-growth comparison.
DOI: 10.6084/m9.figshare.3553185
title: Appendix E. Establishment and cumulative growth data.

description: Establishment and cumulative growth data.
DOI: 10.6084/m9.figshare.3553185.v1
title: Appendix E. Establishment and cumulative growth data.

description: Establishment and cumulative growth data.
DOI: 10.6084/m9.figshare.3553182
title: Appendix A. Herbivore damage and insect herbivore abundances in early- and late-successional fields.

description: Herbivore damage and insect herbivore abundances in early- and late-successional fields.
DOI: 10.6084/m9.figshare.3553182.v1
title: Appendix A. Herbivore damage and insect herbivore abundances in early- and late-successional fields.

description: Herbivore damage and insect herbivore abundances in early- and late-successional fields.
DOI: 10.6084/m9.figshare.3553179
title: Appendix B. Goldenrod resistance, biomass, and tolerance in response to the experimental treatments successional stage, goldenrod genotype, and insecticide application.

description: Goldenrod resistance, biomass, and tolerance in response to the experimental treatments successional stage, goldenrod genotype, and insecticide application.
DOI: 10.6084/m9.figshare.3553179.v1
title: Appendix B. Goldenrod resistance, biomass, and tolerance in response to the experimental treatments successional stage, goldenrod genotype, and insecticide application.

description: Goldenrod resistance, biomass, and tolerance in response to the experimental treatments successional stage, goldenrod genotype, and insecticide application.
DOI: 10.6084/m9.figshare.3553176
title: Appendix C. Results from separate nested ANCOVA tests to determine whether there was evidence of trade-offs, costs, and selection gradients associated with resistance and tolerance in goldenrod.

description: Results from separate nested ANCOVA tests to determine whether there was evidence of trade-offs, costs, and selection gradients associated with resistance and tolerance in goldenrod.
DOI: 10.6084/m9.figshare.3553176.v1
title: Appendix C. Results from separate nested ANCOVA tests to determine whether there was evidence of trade-offs, costs, and selection gradients associated with resistance and tolerance in goldenrod.

description: Results from separate nested ANCOVA tests to determine whether there was evidence of trade-offs, costs, and selection gradients associated with resistance and tolerance in goldenrod.
DOI: 10.6084/m9.figshare.3553173
title: Appendix A. Landcover types with floral densities averaged over the entire study season.

description: Landcover types with floral densities averaged over the entire study season.
DOI: 10.6084/m9.figshare.3553170
title: Appendix B. Photo of a field nest box containing a Bombus vosnesenskii study colony.

description: Photo of a field nest box containing a Bombus vosnesenskii study colony.
DOI: 10.6084/m9.figshare.3553167
title: Appendix C. Flower abundance in different regions of the landscape in spring and summer.

description: Flower abundance in different regions of the landscape in spring and summer.
DOI: 10.6084/m9.figshare.3553170.v1
title: Appendix B. Photo of a field nest box containing a Bombus vosnesenskii study colony.

description: Photo of a field nest box containing a Bombus vosnesenskii study colony.
DOI: 10.6084/m9.figshare.3553164
title: Appendix A. The names and attributes of Clarkia xantiana ssp. xantiana populations in this study.

description: The names and attributes of Clarkia xantiana ssp. xantiana populations in this study.
DOI: 10.6084/m9.figshare.3553164.v1
title: Appendix A. The names and attributes of Clarkia xantiana ssp. xantiana populations in this study.

description: The names and attributes of Clarkia xantiana ssp. xantiana populations in this study.
DOI: 10.6084/m9.figshare.3553161
title: Appendix B. The results of regression analyses of bee collection rate in relation to precipitation.

description: The results of regression analyses of bee collection rate in relation to precipitation.
DOI: 10.6084/m9.figshare.3553161.v1
title: Appendix B. The results of regression analyses of bee collection rate in relation to precipitation.

description: The results of regression analyses of bee collection rate in relation to precipitation.