cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3531014
title: Supplement 1. A spreadsheet to estimate extinction times based on a sighting record.

description: File List Inferring_Extinction_Timing.xls Inferring_Extinction_Timing.csv VBA_Macro_Inferring_Extinction_Timing.txt Description Inferring Extinction Timing.xls The file contains a visual basic macro that runs in MS Excel. This macro calculates the upper boundary of 95 % confidence interval of the estimated extinction times, based on observed sightings, and according the seven methods evaluated in the paper. The program has been built and tested in MS Excel 2007 using Windows XP. Macros must be enabled to run the program. Please note that macros are not supported in MS Office 2008 for Macintosh. Inferring Extinction Timing.csv is a comma-delimited version of the main worksheet in the xls file. VBA Macro Inferring Extinction Timing.txt is a text file of the source code for the visual basic macro used in the xls model.
DOI: 10.6084/m9.figshare.3531014.v1
title: Supplement 1. A spreadsheet to estimate extinction times based on a sighting record.

description: File List Inferring_Extinction_Timing.xls Inferring_Extinction_Timing.csv VBA_Macro_Inferring_Extinction_Timing.txt Description Inferring Extinction Timing.xls The file contains a visual basic macro that runs in MS Excel. This macro calculates the upper boundary of 95 % confidence interval of the estimated extinction times, based on observed sightings, and according the seven methods evaluated in the paper. The program has been built and tested in MS Excel 2007 using Windows XP. Macros must be enabled to run the program. Please note that macros are not supported in MS Office 2008 for Macintosh. Inferring Extinction Timing.csv is a comma-delimited version of the main worksheet in the xls file. VBA Macro Inferring Extinction Timing.txt is a text file of the source code for the visual basic macro used in the xls model.
DOI: 10.6084/m9.figshare.3531011
title: Supplement 1, Revision 1. A spreadsheet to estimate extinction times based on a sighting record, with corrected formulas for two methods.

description: File ListSupplement 1, original Inferring_Extinction_Timing.xls Inferring_Extinction_Timing.csv VBA_Macro_Inferring_Extinction_Timing.txt Supplement 1, Revision 1 VBA_Inferring_Extinction_Timing(version1.1).xlsm Inferring_Extinction_Timing(version1.1).csv VBA_Macro_Inferring_Extinction_Timing(version1.1).txt DescriptionSupplement 1, original Inferring Extinction Timing.xls The file contains a visual basic macro that runs in MS Excel. This macro calculates the upper boundary of 95 % confidence interval of the estimated extinction times, based on observed sightings, and according the seven methods evaluated in the paper. The program has been built and tested in MS Excel 2007 using Windows XP. Macros must be enabled to run the program. Please note that macros are not supported in MS Office 2008 for Macintosh. Inferring Extinction Timing.csv is a comma-delimited version of the main worksheet in the xls file. VBA Macro Inferring Extinction Timing.txt is a text file of the source code for the visual basic macro used in the xls model. Supplement 1, Revision 1 Inferring_Extinction_Timing (version 1.1).xlsm This file contains an amended version of the Visual Basic Macro for MS Excel presented by Rivadeneira et al. (2009, Ecology 90: 1291–1300 Ecological Archives E090-084-S1). The VBA macro is aimed to calculate the upper boundary of 95 % confidence interval of the estimated extinction times, based on observed sightings, and according the seven methods evaluated by Rivadeneira et al. (2009). The new version of the VBA macro provides corrected formulas for two sighting methods. The program has been built and tested in MS Excel 2011 for Mac OS X 10.7.5. Macros must be enabled to run the program. Note: ESA cannot guarantee the portability of Excel files. Inferring_Extinction_Timing (version 1.1).csv is a comma-delimited version of the main worksheet in the xls file. VBA_Macro_Inferring_Extinction_Timing (version 1.1).txt is a text file of the source code for the visual basic macro used in the xlsm model.
DOI: 10.6084/m9.figshare.3531008
title: Appendix A. A list of 90 butterfly species detected in 13 transects indicating the number of transects in which each species was detected and estimated detectability (with 95% credible intervals) per secondary sample under the constant p RD model {RD, ψ(species×season), p(species)}.

description: A list of 90 butterfly species detected in 13 transects indicating the number of transects in which each species was detected and estimated detectability (with 95% credible intervals) per secondary sample under the constant p RD model {RD, ψ(species×season), p(species)}.
DOI: 10.6084/m9.figshare.3531008.v1
title: Appendix A. A list of 90 butterfly species detected in 13 transects indicating the number of transects in which each species was detected and estimated detectability (with 95% credible intervals) per secondary sample under the constant p RD model {RD, ψ(species×season), p(species)}.

description: A list of 90 butterfly species detected in 13 transects indicating the number of transects in which each species was detected and estimated detectability (with 95% credible intervals) per secondary sample under the constant p RD model {RD, ψ(species×season), p(species)}.
DOI: 10.6084/m9.figshare.3531005
title: Supplement 1. WinBUGS model specifications for the models described in the paper.

description: File List model-pd.txt -- WinBUGS specification, model for the pooled data (PD) model-rdA.txt -- WinBUGS specification, model for the robust design data with constant, species-specific detection probabilities (constant <i>p</i> RD model) model-rdB(seas).txt -- WinBUGS specification, model for the robust design data with seasonal, species-specific detection probabilities (season <i>p</i> RD model) Description The files are standard WinBUGS model specifications.
DOI: 10.6084/m9.figshare.3531005.v1
title: Supplement 1. WinBUGS model specifications for the models described in the paper.

description: File List model-pd.txt -- WinBUGS specification, model for the pooled data (PD) model-rdA.txt -- WinBUGS specification, model for the robust design data with constant, species-specific detection probabilities (constant <i>p</i> RD model) model-rdB(seas).txt -- WinBUGS specification, model for the robust design data with seasonal, species-specific detection probabilities (season <i>p</i> RD model) Description The files are standard WinBUGS model specifications.
DOI: 10.6084/m9.figshare.3531002
title: Appendix A. Autoregressive (AR) and autoregressive moving average (ARMA) models fitted to 50 different data sets from diverse taxa.

description: Autoregressive (AR) and autoregressive moving average (ARMA) models fitted to 50 different data sets from diverse taxa.
DOI: 10.6084/m9.figshare.3530999
title: Appendix A. Variation in 13 extracted features of time series for each of 11 trace elemental ratios recorded in the otoliths of Forsterygion lapillum.

description: Variation in 13 extracted features of time series for each of 11 trace elemental ratios recorded in the otoliths of Forsterygion lapillum.
DOI: 10.6084/m9.figshare.3530996
title: Appendix A. Ordination of sampling sites using multidimensional scaling (MDS) based on distances between sites by sea and measurement of coastline fractal dimension.

description: Ordination of sampling sites using multidimensional scaling (MDS) based on distances between sites by sea and measurement of coastline fractal dimension.
DOI: 10.6084/m9.figshare.3530996.v1
title: Appendix A. Ordination of sampling sites using multidimensional scaling (MDS) based on distances between sites by sea and measurement of coastline fractal dimension.

description: Ordination of sampling sites using multidimensional scaling (MDS) based on distances between sites by sea and measurement of coastline fractal dimension.
DOI: 10.6084/m9.figshare.3530993
title: Appendix B. Recovering spectral exponents from simulated data using repeated hierarchical analysis of variance over a range of nested spatial scales.

description: Recovering spectral exponents from simulated data using repeated hierarchical analysis of variance over a range of nested spatial scales.
DOI: 10.6084/m9.figshare.3530993.v1
title: Appendix B. Recovering spectral exponents from simulated data using repeated hierarchical analysis of variance over a range of nested spatial scales.

description: Recovering spectral exponents from simulated data using repeated hierarchical analysis of variance over a range of nested spatial scales.
DOI: 10.6084/m9.figshare.3530990
title: Appendix C. Modes of reproduction in intertidal species used in the analysis of spatial scales of variation as described by β values.

description: Modes of reproduction in intertidal species used in the analysis of spatial scales of variation as described by β values.
DOI: 10.6084/m9.figshare.3530990.v1
title: Appendix C. Modes of reproduction in intertidal species used in the analysis of spatial scales of variation as described by β values.

description: Modes of reproduction in intertidal species used in the analysis of spatial scales of variation as described by β values.
DOI: 10.6084/m9.figshare.3530987
title: Supplement 1. The R code for simulating 2-D data with known spectral exponents, sampling, and ANOVA estimation of β.

description: File List SynthesiseSpectra2DBetaDetection1000.r -- r code for generating 2D data and determining variance spectra repeatedly from subsamples (<i>n</i> = 1000) Description The SynthesiseSpectra2DBetaDetection1000.r program uses r code to recover spectral exponents from 2D simulated data using repeated hierarchical analysis of variance over a range of nested spatial scales. The method for generating the simulated data using inverse Fourier transforms of 1/<i>f<sup> β</sup></i> weighted random phases and numbers, and the returned <i>β</i>-values are given in Appendix B.
DOI: 10.6084/m9.figshare.3530987.v1
title: Supplement 1. The R code for simulating 2-D data with known spectral exponents, sampling, and ANOVA estimation of β.

description: File List SynthesiseSpectra2DBetaDetection1000.r -- r code for generating 2D data and determining variance spectra repeatedly from subsamples (<i>n</i> = 1000) Description The SynthesiseSpectra2DBetaDetection1000.r program uses r code to recover spectral exponents from 2D simulated data using repeated hierarchical analysis of variance over a range of nested spatial scales. The method for generating the simulated data using inverse Fourier transforms of 1/<i>f<sup> β</sup></i> weighted random phases and numbers, and the returned <i>β</i>-values are given in Appendix B.
DOI: 10.6084/m9.figshare.3530984
title: Appendix A. Responses of individual periphyton species to nutrient enrichment.

description: Responses of individual periphyton species to nutrient enrichment.
DOI: 10.6084/m9.figshare.3530984.v1
title: Appendix A. Responses of individual periphyton species to nutrient enrichment.

description: Responses of individual periphyton species to nutrient enrichment.
DOI: 10.6084/m9.figshare.3530981
title: Supplement 1. Original data used for all analyses and figures in the main article.

description: File List Cardinale_et_al_2008dataset.txt Description Cardinale_et_al_2008dataset.txt is a tab-delimited file that contains all of the original data used for all analyses and figures in Cardinale, B. J., D. Bennett, C. Nelson, and K. Gross. Does productivity drive diversity or vice versa? Support for the multivariate productivity–diversity hypothesis in streams. <i>Ecology</i> 90:1227–1241. Column numbers, headings, descriptions, and column sums of numerical data for checking file upload are as follows: -- TABLE: Please see in attached file. --
DOI: 10.6084/m9.figshare.3530981.v1
title: Supplement 1. Original data used for all analyses and figures in the main article.

description: File List Cardinale_et_al_2008dataset.txt Description Cardinale_et_al_2008dataset.txt is a tab-delimited file that contains all of the original data used for all analyses and figures in Cardinale, B. J., D. Bennett, C. Nelson, and K. Gross. Does productivity drive diversity or vice versa? Support for the multivariate productivity–diversity hypothesis in streams. <i>Ecology</i> 90:1227–1241. Column numbers, headings, descriptions, and column sums of numerical data for checking file upload are as follows: -- TABLE: Please see in attached file. --
DOI: 10.6084/m9.figshare.3530978
title: Appendix A. The data correction method used to exclude the possible effect of selective predation on tadpoles having low bulginess induction.

description: The data correction method used to exclude the possible effect of selective predation on tadpoles having low bulginess induction.
DOI: 10.6084/m9.figshare.3530978.v1
title: Appendix A. The data correction method used to exclude the possible effect of selective predation on tadpoles having low bulginess induction.

description: The data correction method used to exclude the possible effect of selective predation on tadpoles having low bulginess induction.
DOI: 10.6084/m9.figshare.3530975
title: Appendix A. Presence of otters and polecats at the River Thames study site.

description: Presence of otters and polecats at the River Thames study site.
DOI: 10.6084/m9.figshare.3530975.v1
title: Appendix A. Presence of otters and polecats at the River Thames study site.

description: Presence of otters and polecats at the River Thames study site.
DOI: 10.6084/m9.figshare.3530972
title: Appendix B. Radio-tracking details for mink populations.

description: Radio-tracking details for mink populations.
DOI: 10.6084/m9.figshare.3530972.v1
title: Appendix B. Radio-tracking details for mink populations.

description: Radio-tracking details for mink populations.
DOI: 10.6084/m9.figshare.3530969
title: Appendix C. Spatial distribution of mink and otter signs along rivers in the upper Thames Valley.

description: Spatial distribution of mink and otter signs along rivers in the upper Thames Valley.
DOI: 10.6084/m9.figshare.3530969.v1
title: Appendix C. Spatial distribution of mink and otter signs along rivers in the upper Thames Valley.

description: Spatial distribution of mink and otter signs along rivers in the upper Thames Valley.
DOI: 10.6084/m9.figshare.3530966
title: Appendix A. Table of parameter estimates for the relationships between the distance a sampling point lay from the Pseudacteon curvatus release site (BFL) and the density of the Pseudacteon species present.

description: Table of parameter estimates for the relationships between the distance a sampling point lay from the Pseudacteon curvatus release site (BFL) and the density of the Pseudacteon species present.
DOI: 10.6084/m9.figshare.3530966.v1
title: Appendix A. Table of parameter estimates for the relationships between the distance a sampling point lay from the Pseudacteon curvatus release site (BFL) and the density of the Pseudacteon species present.

description: Table of parameter estimates for the relationships between the distance a sampling point lay from the Pseudacteon curvatus release site (BFL) and the density of the Pseudacteon species present.
DOI: 10.6084/m9.figshare.3530963
title: Appendix B. A figure showing the time course of the colony response to nest disturbance.

description: A figure showing the time course of the colony response to nest disturbance.
DOI: 10.6084/m9.figshare.3530963.v1
title: Appendix B. A figure showing the time course of the colony response to nest disturbance.

description: A figure showing the time course of the colony response to nest disturbance.
DOI: 10.6084/m9.figshare.3530960
title: Appendix A. Photographs of bills of Eulampis jugularis, flowers and inflorescences of Heliconia species on St. Lucia, West Indies, orientation of birds during feeding visits to heliconias, and measurements of bill and flower chords and angles.

description: Photographs of bills of Eulampis jugularis, flowers and inflorescences of Heliconia species on St. Lucia, West Indies, orientation of birds during feeding visits to heliconias, and measurements of bill and flower chords and angles.
DOI: 10.6084/m9.figshare.3530957
title: Appendix B. Artificial Heliconia inflorescences and flowers: instructions for their construction, dimension, and images.

description: Artificial Heliconia inflorescences and flowers: instructions for their construction, dimension, and images.
DOI: 10.6084/m9.figshare.3530954
title: Appendix C. Figures and regression statistics for relationships between total bill lengths and maximum extraction depths of male and female Eulampis jugularis at artificial flowers of increasing curvatures.

description: Figures and regression statistics for relationships between total bill lengths and maximum extraction depths of male and female Eulampis jugularis at artificial flowers of increasing curvatures.
DOI: 10.6084/m9.figshare.3530951
title: Appendix D. Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at artificial flowers of increasing curvature and long lengths.

description: Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at artificial flowers of increasing curvature and long lengths.
DOI: 10.6084/m9.figshare.3530951.v1
title: Appendix D. Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at artificial flowers of increasing curvature and long lengths.

description: Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at artificial flowers of increasing curvature and long lengths.
DOI: 10.6084/m9.figshare.3530948
title: Appendix E. Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at narrow artificial flowers.

description: Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at narrow artificial flowers.
DOI: 10.6084/m9.figshare.3530948.v1
title: Appendix E. Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at narrow artificial flowers.

description: Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at narrow artificial flowers.
DOI: 10.6084/m9.figshare.3530945
title: Appendix F. Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at straight artificial flowers.

description: Figures and regression statistics for relationships between handling times and total bill lengths of male and female Eulampis jugularis at straight artificial flowers.
DOI: 10.6084/m9.figshare.3530942
title: Appendix A. The SC model.

description: The SC model.
DOI: 10.6084/m9.figshare.3530942.v1
title: Appendix A. The SC model.

description: The SC model.
DOI: 10.6084/m9.figshare.3530939
title: Appendix B. Parameter estimates.

description: Parameter estimates.
DOI: 10.6084/m9.figshare.3530939.v1
title: Appendix B. Parameter estimates.

description: Parameter estimates.
DOI: 10.6084/m9.figshare.3530936
title: Supplement 1. The WinBUGS code.

description: File List Lessepsian_WinBUGS.txt -- WinBUGS code Description The file "Lessepsian_WinBUGS.txt" contains the code for fitting the Bayesian model. To execute the code, the text must be pasted into a document window in WinBugs. To insert one's own data, replace the original data with the new data, which must include the number of sampling intervals (<i>T</i>), two vectors containing the number of new endemic and introduced species recorded at time <i>t</i> (new_species and new_species_L, respectively) and two vectors containing the cumulative number of endemic and introduced species recorded at time <i>t</i> (SM1 and SR1, respectively). It will probably be necessary to change the values of the initials before the model can run on a different data set. To construct a full model that allows for a linear monotonic trend in <i>u</i> through time, simply remove the # sing from the parameter "<i>beta1</i>" and replace the # signs between the two versions of logit(u[1]) and logit(u[i]). Note, that under the full model it is invalid to estimate <i>z</i>. <em>Note</em>: WinBUGS parameterizes the normal distribution in terms of the precision parameter "<i>tau</i>" which is the reciprocal of the variance parameter.
DOI: 10.6084/m9.figshare.3530936.v1
title: Supplement 1. The WinBUGS code.

description: File List Lessepsian_WinBUGS.txt -- WinBUGS code Description The file "Lessepsian_WinBUGS.txt" contains the code for fitting the Bayesian model. To execute the code, the text must be pasted into a document window in WinBugs. To insert one's own data, replace the original data with the new data, which must include the number of sampling intervals (<i>T</i>), two vectors containing the number of new endemic and introduced species recorded at time <i>t</i> (new_species and new_species_L, respectively) and two vectors containing the cumulative number of endemic and introduced species recorded at time <i>t</i> (SM1 and SR1, respectively). It will probably be necessary to change the values of the initials before the model can run on a different data set. To construct a full model that allows for a linear monotonic trend in <i>u</i> through time, simply remove the # sing from the parameter "<i>beta1</i>" and replace the # signs between the two versions of logit(u[1]) and logit(u[i]). Note, that under the full model it is invalid to estimate <i>z</i>. <em>Note</em>: WinBUGS parameterizes the normal distribution in terms of the precision parameter "<i>tau</i>" which is the reciprocal of the variance parameter.
DOI: 10.6084/m9.figshare.3530933
title: Appendix A. Statistical derivations.

description: Statistical derivations.
DOI: 10.6084/m9.figshare.3530933.v1
title: Appendix A. Statistical derivations.

description: Statistical derivations.
DOI: 10.6084/m9.figshare.3530930
title: Supplement 1. Excel-sheet calculator and calculator instructions.

description: File List Supp1ExcelGuide.pdf Supp2ExcelCalculator.xls ExcelCalculatorAbundanceData.pdf ExcelCalculatorIncidenceData.pdf Description Supp1ExcelGuide.pdf contains a complete description of the variables and how to use the Excel Spreadsheet calculator. Supp2ExcelCalculator.xls is an Excel spreadsheet with formulas to calculate the statistics described in the paper.
DOI: 10.6084/m9.figshare.3530927
title: Appendix A. Survivorship data for the 58 mammal species considered in survivorship analysis.

description: Survivorship data for the 58 mammal species considered in survivorship analysis.
DOI: 10.6084/m9.figshare.3530924
title: Appendix B. Survivorship model comparison.

description: Survivorship model comparison.
DOI: 10.6084/m9.figshare.3530924.v1
title: Appendix B. Survivorship model comparison.

description: Survivorship model comparison.
DOI: 10.6084/m9.figshare.3530921
title: Appendix A. A list of species seen at 10 forest sites in interior British Columbia, 1997–2007.

description: A list of species seen at 10 forest sites in interior British Columbia, 1997–2007.
DOI: 10.6084/m9.figshare.3530921.v1
title: Appendix A. A list of species seen at 10 forest sites in interior British Columbia, 1997–2007.

description: A list of species seen at 10 forest sites in interior British Columbia, 1997–2007.