cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3555243
title: Supplement 1. Software implementation of Streambugs 1.0 in R.

description: File List streambugs.rar - Archive containing all files and folders<br> (md5: <i>3f68495fd06dc17a8b046fd80f5abaf6</i>) Main folder: define_and_draw_parametersample.r<br> (md5: <i>d9189de074fb0d296cafb50edab1a328</i>)<br> envpar_MA.r<br> (md5: <i>a77014966cbfefc81dde4f4c6af8eff6</i>)<br> inverts_MA_allsitesanddates.r<br> (md5: <i>a907086552b6e650d713b5620afb7487</i>)<br> model_inputs_catchment.r<br> (md5: <i>9d06d4b0a9c6d74cc58db99833daa2d3</i>)<br> sourcepool_taxa.r<br> (md5: <i>d5ca104637672604c0b0016acb22df43</i>) /databases/ read_currentpref.r<br> (md5: <i>159ee84eb1b37fff1c7d7a513cdcf96d</i>)<br> read_microhabitatpref.r<br> (md5: <i>6251987fcd4c02441484efeab9f1d02a</i>) /libraries/ check_survival.r<br> (md5: <i>ed164799933dea3c05cbaa82a42407c5</i>)<br> generate_pars_samp.r<br> (md5: <i>3491492da3b99ad067c097e7e7128497</i>)<br> get_parameters_environmental_traits.r<br> (md5: <i>72aa8bef16fc1de944e88b8233e0eb25</i>)<br> randsamp.r<br> (md5: <i>05f154b95d77724cb1dea022a5e39d76</i>)<br> rhs_benthos.r<br> (md5: <i>eee511d81128fc63d16cae39aebff9f6</i>)<br> stoichcalc_function.r<br> (md5: <i>feea27796c0794fa1dc8b06af3f51a15</i>) /MA167/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>420da60cabf341de99fc6a85ab13d663</i>) /MA168/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>387270564369c11b0ba9c071ba7852b8</i>) /MA437/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>4902b0b6d7a5cc48adf34f9b7b87a441</i>) /MA438/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>9b9fe02be321030280814799d7eb5d9e</i>) Description The model Streambugs 1.0 was implemented with the statistics and graphics software R (r-project.org). To run the model, the following steps have to be carried out: Generate sample with universal parameters<br> Execute define_and_draw_parametersample.r from the main folder. Run the model for the four sites:<br> Execute execute_model.r from /MA167, /MA168, /MA437, and /MA438.<br> Results will be written to /results. Access to the databases used in the model: freshwaterecology.info: freshwaterecology.info/conditions.php Schmidt-Kloiber, A. and D. Hering, Editors. 2012. freshwaterecology.info - the taxa and autecology database for freshwater organisms, version 5.0 (accessed on 02/2011: version 4.0/2009). CASiMiR: Contact Ianina Kopecki, Institute of Hydraulic Engineering, University of Stuttgart IWS (2002): Strömungspräferenzen für Benthosorganismen auf der Basis von FST-Halbkugeln, Microsoft Access-Datenbank. Universität Stuttgart, Institut für Wasserbau) SPEAR: systemecology.eu/SPEAR, Contact Matthias Liess, Department System Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research.
DOI: 10.6084/m9.figshare.3555243.v1
title: Supplement 1. Software implementation of Streambugs 1.0 in R.

description: File List streambugs.rar - Archive containing all files and folders<br> (md5: <i>3f68495fd06dc17a8b046fd80f5abaf6</i>) Main folder: define_and_draw_parametersample.r<br> (md5: <i>d9189de074fb0d296cafb50edab1a328</i>)<br> envpar_MA.r<br> (md5: <i>a77014966cbfefc81dde4f4c6af8eff6</i>)<br> inverts_MA_allsitesanddates.r<br> (md5: <i>a907086552b6e650d713b5620afb7487</i>)<br> model_inputs_catchment.r<br> (md5: <i>9d06d4b0a9c6d74cc58db99833daa2d3</i>)<br> sourcepool_taxa.r<br> (md5: <i>d5ca104637672604c0b0016acb22df43</i>) /databases/ read_currentpref.r<br> (md5: <i>159ee84eb1b37fff1c7d7a513cdcf96d</i>)<br> read_microhabitatpref.r<br> (md5: <i>6251987fcd4c02441484efeab9f1d02a</i>) /libraries/ check_survival.r<br> (md5: <i>ed164799933dea3c05cbaa82a42407c5</i>)<br> generate_pars_samp.r<br> (md5: <i>3491492da3b99ad067c097e7e7128497</i>)<br> get_parameters_environmental_traits.r<br> (md5: <i>72aa8bef16fc1de944e88b8233e0eb25</i>)<br> randsamp.r<br> (md5: <i>05f154b95d77724cb1dea022a5e39d76</i>)<br> rhs_benthos.r<br> (md5: <i>eee511d81128fc63d16cae39aebff9f6</i>)<br> stoichcalc_function.r<br> (md5: <i>feea27796c0794fa1dc8b06af3f51a15</i>) /MA167/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>420da60cabf341de99fc6a85ab13d663</i>) /MA168/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>387270564369c11b0ba9c071ba7852b8</i>) /MA437/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>4902b0b6d7a5cc48adf34f9b7b87a441</i>) /MA438/ execute_model.r<br> (md5: <i>469da77a9aca1d696df63c2ce2b538bc</i>)<br> model_inputs_site.r<br> (md5: <i>9b9fe02be321030280814799d7eb5d9e</i>) Description The model Streambugs 1.0 was implemented with the statistics and graphics software R (r-project.org). To run the model, the following steps have to be carried out: Generate sample with universal parameters<br> Execute define_and_draw_parametersample.r from the main folder. Run the model for the four sites:<br> Execute execute_model.r from /MA167, /MA168, /MA437, and /MA438.<br> Results will be written to /results. Access to the databases used in the model: freshwaterecology.info: freshwaterecology.info/conditions.php Schmidt-Kloiber, A. and D. Hering, Editors. 2012. freshwaterecology.info - the taxa and autecology database for freshwater organisms, version 5.0 (accessed on 02/2011: version 4.0/2009). CASiMiR: Contact Ianina Kopecki, Institute of Hydraulic Engineering, University of Stuttgart IWS (2002): Strömungspräferenzen für Benthosorganismen auf der Basis von FST-Halbkugeln, Microsoft Access-Datenbank. Universität Stuttgart, Institut für Wasserbau) SPEAR: systemecology.eu/SPEAR, Contact Matthias Liess, Department System Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research.
DOI: 10.6084/m9.figshare.3555240
title: Appendix A. A table describing the countries, major geographic areas (MGA), streams, age classes, and time series of data for which we modeled brown trout bioenergetics, along with the range of densities and the number of individual model simulations for each MGA and the details of bioenergetic simulations.

description: A table describing the countries, major geographic areas (MGA), streams, age classes, and time series of data for which we modeled brown trout bioenergetics, along with the range of densities and the number of individual model simulations for each MGA and the details of bioenergetic simulations.
DOI: 10.6084/m9.figshare.3555240.v1
title: Appendix A. A table describing the countries, major geographic areas (MGA), streams, age classes, and time series of data for which we modeled brown trout bioenergetics, along with the range of densities and the number of individual model simulations for each MGA and the details of bioenergetic simulations.

description: A table describing the countries, major geographic areas (MGA), streams, age classes, and time series of data for which we modeled brown trout bioenergetics, along with the range of densities and the number of individual model simulations for each MGA and the details of bioenergetic simulations.
DOI: 10.6084/m9.figshare.3555237
title: Appendix B. World map along with native and introduced ranges of brown trout (Salmo trutta) identifying major geographic areas (MGAs).

description: World map along with native and introduced ranges of brown trout (Salmo trutta) identifying major geographic areas (MGAs).
DOI: 10.6084/m9.figshare.3555237.v1
title: Appendix B. World map along with native and introduced ranges of brown trout (Salmo trutta) identifying major geographic areas (MGAs).

description: World map along with native and introduced ranges of brown trout (Salmo trutta) identifying major geographic areas (MGAs).
DOI: 10.6084/m9.figshare.3555234
title: Appendix A. Tables showing alphabetical lists of bat species (with varying feeding habits) captured at La Selva Biological Station, Costa Rica, with corresponding ratios of non-exchangeable hydrogen stable isotopes in fur keratin and of hydrogen stable isotopes in body water from field season A, and corresponding ratios of non-exchangeable hydrogen stable isotopes and nitrogen isotopes in hair keratin from field season B.

description: Tables showing alphabetical lists of bat species (with varying feeding habits) captured at La Selva Biological Station, Costa Rica, with corresponding ratios of non-exchangeable hydrogen stable isotopes in fur keratin and of hydrogen stable isotopes in body water from field season A, and corresponding ratios of non-exchangeable hydrogen stable isotopes and nitrogen isotopes in hair keratin from field season B.
DOI: 10.6084/m9.figshare.3555231
title: Appendix A. Model selection, sources of variation, effects of natal status, and summary statistics.

description: Model selection, sources of variation, effects of natal status, and summary statistics.
DOI: 10.6084/m9.figshare.3555231.v1
title: Appendix A. Model selection, sources of variation, effects of natal status, and summary statistics.

description: Model selection, sources of variation, effects of natal status, and summary statistics.
DOI: 10.6084/m9.figshare.3555228
title: Appendix A. Figure of settlement patterns and nest box availability at different densities throughout the breeding season.

description: Figure of settlement patterns and nest box availability at different densities throughout the breeding season.
DOI: 10.6084/m9.figshare.3555228.v1
title: Appendix A. Figure of settlement patterns and nest box availability at different densities throughout the breeding season.

description: Figure of settlement patterns and nest box availability at different densities throughout the breeding season.
DOI: 10.6084/m9.figshare.3555225
title: Appendix A. A description of the Hill model.

description: A description of the Hill model.
DOI: 10.6084/m9.figshare.3555225.v1
title: Appendix A. A description of the Hill model.

description: A description of the Hill model.
DOI: 10.6084/m9.figshare.3555222
title: Appendix B. Extended simulation methodology.

description: Extended simulation methodology.
DOI: 10.6084/m9.figshare.3555222.v1
title: Appendix B. Extended simulation methodology.

description: Extended simulation methodology.
DOI: 10.6084/m9.figshare.3555219
title: Appendix C. Extended simulation results.

description: Extended simulation results.
DOI: 10.6084/m9.figshare.3555219.v1
title: Appendix C. Extended simulation results.

description: Extended simulation results.
DOI: 10.6084/m9.figshare.3555216
title: Appendix D. Case study: estimating offspring size–fitness relationships using binary logistic regression.

description: Case study: estimating offspring size–fitness relationships using binary logistic regression.
DOI: 10.6084/m9.figshare.3555216.v1
title: Appendix D. Case study: estimating offspring size–fitness relationships using binary logistic regression.

description: Case study: estimating offspring size–fitness relationships using binary logistic regression.
DOI: 10.6084/m9.figshare.3555213
title: Supplement 1. R code used for simulations.

description: File List Ecology_Supplement.txt (MD5: 4a837168f51940092cfdbb2e1f559c07)Description This template, in conjunction with Appendix B, allows all simulations performed in the main text to be recreated in R.
DOI: 10.6084/m9.figshare.3555213.v1
title: Supplement 1. R code used for simulations.

description: File List Ecology_Supplement.txt (MD5: 4a837168f51940092cfdbb2e1f559c07)Description This template, in conjunction with Appendix B, allows all simulations performed in the main text to be recreated in R.
DOI: 10.6084/m9.figshare.3555210
title: Appendix A. A photograph of diagnostic bite marks left by Greater Sage-Grouse (Centrocercus urophasianus) on sagebrush (Artemisia spp.).

description: A photograph of diagnostic bite marks left by Greater Sage-Grouse (Centrocercus urophasianus) on sagebrush (Artemisia spp.).
DOI: 10.6084/m9.figshare.3555210.v1
title: Appendix A. A photograph of diagnostic bite marks left by Greater Sage-Grouse (Centrocercus urophasianus) on sagebrush (Artemisia spp.).

description: A photograph of diagnostic bite marks left by Greater Sage-Grouse (Centrocercus urophasianus) on sagebrush (Artemisia spp.).
DOI: 10.6084/m9.figshare.3555207
title: Appendix B. Supplementary information on the quantification of monoterpene concentrations in sagebrush (Artemisia spp.) samples, including methods, materials, and a table of gas chromatograph retention times.

description: Supplementary information on the quantification of monoterpene concentrations in sagebrush (Artemisia spp.) samples, including methods, materials, and a table of gas chromatograph retention times.
DOI: 10.6084/m9.figshare.3555207.v1
title: Appendix B. Supplementary information on the quantification of monoterpene concentrations in sagebrush (Artemisia spp.) samples, including methods, materials, and a table of gas chromatograph retention times.

description: Supplementary information on the quantification of monoterpene concentrations in sagebrush (Artemisia spp.) samples, including methods, materials, and a table of gas chromatograph retention times.
DOI: 10.6084/m9.figshare.3555204
title: Appendix C. Methods and materials used to quantify total phenolic concentrations in sagebrush (Artemisia spp.) samples.

description: Methods and materials used to quantify total phenolic concentrations in sagebrush (Artemisia spp.) samples.
DOI: 10.6084/m9.figshare.3555204.v1
title: Appendix C. Methods and materials used to quantify total phenolic concentrations in sagebrush (Artemisia spp.) samples.

description: Methods and materials used to quantify total phenolic concentrations in sagebrush (Artemisia spp.) samples.
DOI: 10.6084/m9.figshare.3555201
title: Appendix D. Model-selection tables for hierarchical analysis of Greater Sage-Grouse (Centrocercus urophasianus) habitat selection at each of three spatial scales.

description: Model-selection tables for hierarchical analysis of Greater Sage-Grouse (Centrocercus urophasianus) habitat selection at each of three spatial scales.
DOI: 10.6084/m9.figshare.3555201.v1
title: Appendix D. Model-selection tables for hierarchical analysis of Greater Sage-Grouse (Centrocercus urophasianus) habitat selection at each of three spatial scales.

description: Model-selection tables for hierarchical analysis of Greater Sage-Grouse (Centrocercus urophasianus) habitat selection at each of three spatial scales.
DOI: 10.6084/m9.figshare.3555198
title: Appendix E. A cross-tabulation of patch type by habitat type for analyzing the selection of sagebrush (Artemisia spp.) habitat type by Greater Sage-Grouse (Centrocercus urophasianus).

description: A cross-tabulation of patch type by habitat type for analyzing the selection of sagebrush (Artemisia spp.) habitat type by Greater Sage-Grouse (Centrocercus urophasianus).
DOI: 10.6084/m9.figshare.3555198.v1
title: Appendix E. A cross-tabulation of patch type by habitat type for analyzing the selection of sagebrush (Artemisia spp.) habitat type by Greater Sage-Grouse (Centrocercus urophasianus).

description: A cross-tabulation of patch type by habitat type for analyzing the selection of sagebrush (Artemisia spp.) habitat type by Greater Sage-Grouse (Centrocercus urophasianus).
DOI: 10.6084/m9.figshare.3555195
title: Appendix A. View of study sites and seed sampling locations in northern Spain.

description: View of study sites and seed sampling locations in northern Spain.
DOI: 10.6084/m9.figshare.3555192
title: Appendix B. Additional methods and results related to the marking of seeds with 15N stable isotope in the field.

description: Additional methods and results related to the marking of seeds with 15N stable isotope in the field.
DOI: 10.6084/m9.figshare.3555192.v1
title: Appendix B. Additional methods and results related to the marking of seeds with 15N stable isotope in the field.

description: Additional methods and results related to the marking of seeds with 15N stable isotope in the field.
DOI: 10.6084/m9.figshare.3555189
title: Appendix C. Details of a two-source simulation mixing-model used to detect presence of marked 15N seeds in batches of seeds found in seed traps, and methods for fitting 2Dt kernels to seed dispersal data.

description: Details of a two-source simulation mixing-model used to detect presence of marked 15N seeds in batches of seeds found in seed traps, and methods for fitting 2Dt kernels to seed dispersal data.
DOI: 10.6084/m9.figshare.3555189.v1
title: Appendix C. Details of a two-source simulation mixing-model used to detect presence of marked 15N seeds in batches of seeds found in seed traps, and methods for fitting 2Dt kernels to seed dispersal data.

description: Details of a two-source simulation mixing-model used to detect presence of marked 15N seeds in batches of seeds found in seed traps, and methods for fitting 2Dt kernels to seed dispersal data.
DOI: 10.6084/m9.figshare.3555186
title: Appendix D. Linear models (ANCOVA tables and parameter estimate tables) testing the effects of independent variables on seed dispersal rates of holly and hawthorn.

description: Linear models (ANCOVA tables and parameter estimate tables) testing the effects of independent variables on seed dispersal rates of holly and hawthorn.
DOI: 10.6084/m9.figshare.3555186.v1
title: Appendix D. Linear models (ANCOVA tables and parameter estimate tables) testing the effects of independent variables on seed dispersal rates of holly and hawthorn.

description: Linear models (ANCOVA tables and parameter estimate tables) testing the effects of independent variables on seed dispersal rates of holly and hawthorn.
DOI: 10.6084/m9.figshare.3555183
title: Supplement 1. R source code for a two-source simulation mixing model that detects 15N-enriched seed in seed batches composed of unknown quantities of 15N-enriched (marked) and normal (unmarked) seeds.

description: File List Isotope_mix.R (md5: 1ad414fab0125136b63280ca539c8e3e) – R source code for two-source mixing model<br> datos.csv (md5: 9c6bd3134e2b86bb3b2db0b129ceb1a5) – data file containing of <sup>15</sup>N atom % values and number of seeds per batch Description File contains the R source code Isotope_mix.R, a program to estimate the number of marked (<sup>15</sup>N- enriched) and unmarked (i.e., normal) seeds in a batch of n seeds. The program looks for the combination of marked and unmarked seeds that maximized the likelihood of observing a value of <sup>15</sup>N atom % similar to the observed one. The empirical distributions of <sup>15</sup>N from a particular combination of marked and unmarked seeds were estimated by simulating 10<sup>6</sup> (a million) such seed mixtures by sampling from the combinations of Gaussian distribution fitted to the positive and negative controls (with truncation for the marked ones). Confidence intervals were found by looking at those combinations of marked and un-marked seeds that where 2 likelihood units from the maximum.
DOI: 10.6084/m9.figshare.3555183.v1
title: Supplement 1. R source code for a two-source simulation mixing model that detects 15N-enriched seed in seed batches composed of unknown quantities of 15N-enriched (marked) and normal (unmarked) seeds.

description: File List Isotope_mix.R (md5: 1ad414fab0125136b63280ca539c8e3e) – R source code for two-source mixing model<br> datos.csv (md5: 9c6bd3134e2b86bb3b2db0b129ceb1a5) – data file containing of <sup>15</sup>N atom % values and number of seeds per batch Description File contains the R source code Isotope_mix.R, a program to estimate the number of marked (<sup>15</sup>N- enriched) and unmarked (i.e., normal) seeds in a batch of n seeds. The program looks for the combination of marked and unmarked seeds that maximized the likelihood of observing a value of <sup>15</sup>N atom % similar to the observed one. The empirical distributions of <sup>15</sup>N from a particular combination of marked and unmarked seeds were estimated by simulating 10<sup>6</sup> (a million) such seed mixtures by sampling from the combinations of Gaussian distribution fitted to the positive and negative controls (with truncation for the marked ones). Confidence intervals were found by looking at those combinations of marked and un-marked seeds that where 2 likelihood units from the maximum.
DOI: 10.6084/m9.figshare.3555180
title: Appendix A. Bird–fruit interaction web from the North Island of New Zealand.

description: Bird–fruit interaction web from the North Island of New Zealand.
DOI: 10.6084/m9.figshare.3555177
title: Appendix A. Details for computing the marginal likelihood and obtaining the maximum likelihood estimators.

description: Details for computing the marginal likelihood and obtaining the maximum likelihood estimators.
DOI: 10.6084/m9.figshare.3555177.v1
title: Appendix A. Details for computing the marginal likelihood and obtaining the maximum likelihood estimators.

description: Details for computing the marginal likelihood and obtaining the maximum likelihood estimators.
DOI: 10.6084/m9.figshare.3555174
title: Appendix B. MLE summary statistics for reanalysis of the systematic landscape.

description: MLE summary statistics for reanalysis of the systematic landscape.
DOI: 10.6084/m9.figshare.3555174.v1
title: Appendix B. MLE summary statistics for reanalysis of the systematic landscape.

description: MLE summary statistics for reanalysis of the systematic landscape.
DOI: 10.6084/m9.figshare.3555171
title: Supplement 1. R code for computing least-cost path distance and likelihood analysis of the spatial capture–recapture (SCR) model, for computing the marginal likelihood and obtaining the MLEs, and for simulation study, and a narrative walk-through in PDF format.

description: File List EDmanuscript-supplements.pdf (md5: 44eb27bf3d2ab768941365c6a9dc1d43) – R code in pdf form and extra explanation for supplement 1<br> leastcostpath.R (md5: f8d1a9c67e4ee10ed633937d82b68f3f) - R code for computing least-cost path distance and likelihood analysis of the SCR model<br> MLE.R (md5: 4a4f93a6aa444cb52f458e0dbdc80db5)- R code for computing the marginal likelihood and obtaining the MLEs<br> simstudy.R (md5: 1b05540b8556e498242191382ba37c1b) - R code for simulation study Description The supplement demonstrates the computation of least-cost path and its use in obtaining maximum likelihood estimates of model parameters. The file Leastcostpath.R is an R script which can be executed directly (narrative walk-through is provided by the PDF file EDmanuscript-supplements.pdf). The likelihood function (in the form of an R function) is provided in the R script MLE.R. Finally, the various pieces are put together to carry-out a simulation study in the R script simstudy.R.
DOI: 10.6084/m9.figshare.3555168
title: Appendix A. Scatterplots of the five "species", A, B, C, D, and E against the two "gradients" X and Y, for the artificial data set.

description: Scatterplots of the five "species", A, B, C, D, and E against the two "gradients" X and Y, for the artificial data set.
DOI: 10.6084/m9.figshare.3555168.v1
title: Appendix A. Scatterplots of the five "species", A, B, C, D, and E against the two "gradients" X and Y, for the artificial data set.

description: Scatterplots of the five "species", A, B, C, D, and E against the two "gradients" X and Y, for the artificial data set.
DOI: 10.6084/m9.figshare.3555165
title: Appendix B. The CCAs of the artificial data set, with explanatory variables coded into 3, 4, 5, 6, and 7 fuzzy categories, showing adjusted percentages of variance explained in each case.

description: The CCAs of the artificial data set, with explanatory variables coded into 3, 4, 5, 6, and 7 fuzzy categories, showing adjusted percentages of variance explained in each case.