cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3554694
title: Appendix D. Figure showing establishment success of Tetrix subulata founder groups as a function of reproductive capacity in the source population.

description: Figure showing establishment success of Tetrix subulata founder groups as a function of reproductive capacity in the source population.
DOI: 10.6084/m9.figshare.3554694.v1
title: Appendix D. Figure showing establishment success of Tetrix subulata founder groups as a function of reproductive capacity in the source population.

description: Figure showing establishment success of Tetrix subulata founder groups as a function of reproductive capacity in the source population.
DOI: 10.6084/m9.figshare.3554691
title: Appendix E. Figure showing color morph diversity in established populations as a function of the number of morphs included in the founder group.

description: Figure showing color morph diversity in established populations as a function of the number of morphs included in the founder group.
DOI: 10.6084/m9.figshare.3554691.v1
title: Appendix E. Figure showing color morph diversity in established populations as a function of the number of morphs included in the founder group.

description: Figure showing color morph diversity in established populations as a function of the number of morphs included in the founder group.
DOI: 10.6084/m9.figshare.3554688
title: Appendix F. Figure showing the relationship between the relative frequencies of different color morphs among individuals in established populations and in experimental founder groups.

description: Figure showing the relationship between the relative frequencies of different color morphs among individuals in established populations and in experimental founder groups.
DOI: 10.6084/m9.figshare.3554688.v1
title: Appendix F. Figure showing the relationship between the relative frequencies of different color morphs among individuals in established populations and in experimental founder groups.

description: Figure showing the relationship between the relative frequencies of different color morphs among individuals in established populations and in experimental founder groups.
DOI: 10.6084/m9.figshare.3554685
title: Appendix A. Additional methodology on data restriction.

description: Additional methodology on data restriction.
DOI: 10.6084/m9.figshare.3554685.v1
title: Appendix A. Additional methodology on data restriction.

description: Additional methodology on data restriction.
DOI: 10.6084/m9.figshare.3554682
title: Appendix B. Figures for all the data and the functions used to characterize the macroecological pattern parameters.

description: Figures for all the data and the functions used to characterize the macroecological pattern parameters.
DOI: 10.6084/m9.figshare.3554682.v1
title: Appendix B. Figures for all the data and the functions used to characterize the macroecological pattern parameters.

description: Figures for all the data and the functions used to characterize the macroecological pattern parameters.
DOI: 10.6084/m9.figshare.3554679
title: Appendix C. Details on the methods and results of equivalence testing.

description: Details on the methods and results of equivalence testing.
DOI: 10.6084/m9.figshare.3554679.v1
title: Appendix C. Details on the methods and results of equivalence testing.

description: Details on the methods and results of equivalence testing.
DOI: 10.6084/m9.figshare.3554676
title: Appendix D. Tables showing the transformations applied to each variable and the P values for the conventional and equivalence statistical tests comparing parameters between the control plots and each of the experimental treatment plots.

description: Tables showing the transformations applied to each variable and the P values for the conventional and equivalence statistical tests comparing parameters between the control plots and each of the experimental treatment plots.
DOI: 10.6084/m9.figshare.3554676.v1
title: Appendix D. Tables showing the transformations applied to each variable and the P values for the conventional and equivalence statistical tests comparing parameters between the control plots and each of the experimental treatment plots.

description: Tables showing the transformations applied to each variable and the P values for the conventional and equivalence statistical tests comparing parameters between the control plots and each of the experimental treatment plots.
DOI: 10.6084/m9.figshare.3554673
title: Supplement 1. Code for conducting the analyses and generating the figures in this paper.

description: File List PortalPlants_ms12-0370R2.R <br> R script that cleans the data of errors, constructs the macroecological patterns, pulls out descriptive parameters of these patterns, runs the statistical analyses, and outputs figures. PortalPlants_fxns.R<br> R script that holds the relevant functions for executing the PortalPlants_ms12-0370R2.R script. PortalSummerAnnuals_1995_2009.csv <br> Data file containing raw summer annual plant community abundance data for years 1995–2009. PortalWinterAnnuals_1995_2009.csv <br> Data file containing raw winter annual plant community abundance data for years 1995–2009. Description The code and data in this supplement allow for the analyses and figures in the paper to be fully replicated using a subset of the published Portal data set which includes annual plant data from 1995–2009. Requirements: R 2.x and the following packages: Biodiversity R, car, CCA, equivalence, gplots, graphics, languageR, lme4, nlme, plotrix, poilog, vegan, VGAM and the file containing functions specific to this code, PortalPlants_fxns.R. The analyses can then be replicated by changing the working directory at the top of the file PortalPlants_ms12-0370R2.R to the location on your computer where you have stored the .R and .csv files and running the code. Please note that the <i>p</i> values generated for Appendix D in the published paper were generated using R 2.12.2. Because of approximations, the values for SAD sigma and mu may differ slightly (around the 10th decimal place) from Appendix D, Tables D2 and D3. Because the equivalence testing also uses approximations, there may be very small differences in the exact values generated compared to Appendix D, Tables D4 and D5. It should take approximately 30 minutes to run all the code from start to finish. Figures should output as pdfs in your working directory. Version Control Repository: The full version control repository for this project (including post-publication improvements) is publicly available at https://github.com/weecology/portal-experimental-macroeco. If you would like to use the code in this Supplement for your own analyses it is strongly suggested that you use the equivalent code in the repositories as this is the code that is being actively maintained. Data use: Data is provided in this supplement for the purposes of replication. If you wish to use the data for additional research, they should be obtained from the published source (Ecological Archives E090-118-D1; S. K. Morgan Ernest, Thomas J. Valone, and James H. Brown. 2009. Long-term monitoring and experimental manipulation of a Chihuahuan Desert ecosystem near Portal, Arizona, USA. Ecology 90:1708. doi:10.1890/08-1222.1)
DOI: 10.6084/m9.figshare.3554673.v1
title: Supplement 1. Code for conducting the analyses and generating the figures in this paper.

description: File List PortalPlants_ms12-0370R2.R <br> R script that cleans the data of errors, constructs the macroecological patterns, pulls out descriptive parameters of these patterns, runs the statistical analyses, and outputs figures. PortalPlants_fxns.R<br> R script that holds the relevant functions for executing the PortalPlants_ms12-0370R2.R script. PortalSummerAnnuals_1995_2009.csv <br> Data file containing raw summer annual plant community abundance data for years 1995–2009. PortalWinterAnnuals_1995_2009.csv <br> Data file containing raw winter annual plant community abundance data for years 1995–2009. Description The code and data in this supplement allow for the analyses and figures in the paper to be fully replicated using a subset of the published Portal data set which includes annual plant data from 1995–2009. Requirements: R 2.x and the following packages: Biodiversity R, car, CCA, equivalence, gplots, graphics, languageR, lme4, nlme, plotrix, poilog, vegan, VGAM and the file containing functions specific to this code, PortalPlants_fxns.R. The analyses can then be replicated by changing the working directory at the top of the file PortalPlants_ms12-0370R2.R to the location on your computer where you have stored the .R and .csv files and running the code. Please note that the <i>p</i> values generated for Appendix D in the published paper were generated using R 2.12.2. Because of approximations, the values for SAD sigma and mu may differ slightly (around the 10th decimal place) from Appendix D, Tables D2 and D3. Because the equivalence testing also uses approximations, there may be very small differences in the exact values generated compared to Appendix D, Tables D4 and D5. It should take approximately 30 minutes to run all the code from start to finish. Figures should output as pdfs in your working directory. Version Control Repository: The full version control repository for this project (including post-publication improvements) is publicly available at https://github.com/weecology/portal-experimental-macroeco. If you would like to use the code in this Supplement for your own analyses it is strongly suggested that you use the equivalent code in the repositories as this is the code that is being actively maintained. Data use: Data is provided in this supplement for the purposes of replication. If you wish to use the data for additional research, they should be obtained from the published source (Ecological Archives E090-118-D1; S. K. Morgan Ernest, Thomas J. Valone, and James H. Brown. 2009. Long-term monitoring and experimental manipulation of a Chihuahuan Desert ecosystem near Portal, Arizona, USA. Ecology 90:1708. doi:10.1890/08-1222.1)
DOI: 10.6084/m9.figshare.3554670
title: Data Paper. Data Paper

description: File List WE_summary_V2_May2012.csv -- 3444 records (1722 pairs), ASCII text, comma separated. Description The encroachment of woody plants into grasslands, and the conversion of savannas and open woodlands into shrublands, has been widely reported during the past decade. Encroachment has generated considerable interest among ecologists worldwide, but there have been few quantitative syntheses of the effects of encroachment on ecosystem processes across large areas of the globe. Here we summarize the results of observations of the effects of encroachment by woody plants on 111 ecosystem response variables using data obtained from 1722 encroached–unencroached pairs, reported in 160 studies from North and South America, Africa, Europe, Australia, and Asia. We used an extensive review of the literature, including both published and unpublished data, to summarize available data on the effects of a change from open woodland or grassland to shrubland or closed woodland, on richness of plant and animal taxa, soil chemistry, and the status of the soil surface. Our database is restricted to arid, semi-arid, and dry sub-humid environments (drylands) receiving average annual rainfall between 850 and 200 mm. An analysis of the impacts of shrub encroachment on ecosystem structure and function has already been reported using a large subset of these data. This updated data set can provide an opportunity to test further hypotheses about the effects of encroachment on plant and animal communities and on soil processes related to ecosystem functioning. <i>Key words: degradation; desertification; ecosystem processes; encroachment; invasion; shrub; shrubland; thickening; woody.</i>
DOI: 10.6084/m9.figshare.3554667
title: Appendix A. Parameter and AIC estimates for all analyzed models and all supplementary figures.

description: Parameter and AIC estimates for all analyzed models and all supplementary figures.
DOI: 10.6084/m9.figshare.3554667.v1
title: Appendix A. Parameter and AIC estimates for all analyzed models and all supplementary figures.

description: Parameter and AIC estimates for all analyzed models and all supplementary figures.
DOI: 10.6084/m9.figshare.3554664
title: Appendix B. Respiration methods and conversion from oxygen consumption to carbon respired.

description: Respiration methods and conversion from oxygen consumption to carbon respired.
DOI: 10.6084/m9.figshare.3554664.v1
title: Appendix B. Respiration methods and conversion from oxygen consumption to carbon respired.

description: Respiration methods and conversion from oxygen consumption to carbon respired.
DOI: 10.6084/m9.figshare.3554661
title: Appendix C. List of sources used in the meta-analysis.

description: List of sources used in the meta-analysis.
DOI: 10.6084/m9.figshare.3554661.v1
title: Appendix C. List of sources used in the meta-analysis.

description: List of sources used in the meta-analysis.
DOI: 10.6084/m9.figshare.3554658
title: Appendix A. Supplemental descriptions of sampling and analytical methods.

description: Supplemental descriptions of sampling and analytical methods.
DOI: 10.6084/m9.figshare.3554658.v1
title: Appendix A. Supplemental descriptions of sampling and analytical methods.

description: Supplemental descriptions of sampling and analytical methods.
DOI: 10.6084/m9.figshare.3554655
title: Appendix B. Late-winter elk classification data from the Northern Yellowstone Cooperative Wildlife Working Group (1988–2007).

description: Late-winter elk classification data from the Northern Yellowstone Cooperative Wildlife Working Group (1988–2007).
DOI: 10.6084/m9.figshare.3554655.v1
title: Appendix B. Late-winter elk classification data from the Northern Yellowstone Cooperative Wildlife Working Group (1988–2007).

description: Late-winter elk classification data from the Northern Yellowstone Cooperative Wildlife Working Group (1988–2007).
DOI: 10.6084/m9.figshare.3554652
title: Appendix C. Map of Elk Count Units and bone survey locations on the Northern Range of Yellowstone National Park.

description: Map of Elk Count Units and bone survey locations on the Northern Range of Yellowstone National Park.
DOI: 10.6084/m9.figshare.3554652.v1
title: Appendix C. Map of Elk Count Units and bone survey locations on the Northern Range of Yellowstone National Park.

description: Map of Elk Count Units and bone survey locations on the Northern Range of Yellowstone National Park.
DOI: 10.6084/m9.figshare.3554649
title: Appendix D. Shed antler results from Yellowstone bone surveys.

description: Shed antler results from Yellowstone bone surveys.
DOI: 10.6084/m9.figshare.3554649.v1
title: Appendix D. Shed antler results from Yellowstone bone surveys.

description: Shed antler results from Yellowstone bone surveys.
DOI: 10.6084/m9.figshare.3554646
title: Appendix E. Shed antler results, expected antler concentrations, and error intervals for Validation Sample Plots.

description: Shed antler results, expected antler concentrations, and error intervals for Validation Sample Plots.
DOI: 10.6084/m9.figshare.3554646.v1
title: Appendix E. Shed antler results, expected antler concentrations, and error intervals for Validation Sample Plots.

description: Shed antler results, expected antler concentrations, and error intervals for Validation Sample Plots.
DOI: 10.6084/m9.figshare.3554643
title: Appendix F. Neonatal results from Yellowstone bone surveys.

description: Neonatal results from Yellowstone bone surveys.
DOI: 10.6084/m9.figshare.3554643.v1
title: Appendix F. Neonatal results from Yellowstone bone surveys.

description: Neonatal results from Yellowstone bone surveys.
DOI: 10.6084/m9.figshare.3554640
title: Appendix A. Details of the closed-capture model that was used to estimate the probability of trapping an individual at least once.

description: Details of the closed-capture model that was used to estimate the probability of trapping an individual at least once.
DOI: 10.6084/m9.figshare.3554640.v1
title: Appendix A. Details of the closed-capture model that was used to estimate the probability of trapping an individual at least once.

description: Details of the closed-capture model that was used to estimate the probability of trapping an individual at least once.
DOI: 10.6084/m9.figshare.3554637
title: Appendix B. Photographs of the study system at different scales illustrating the extent of the study system and habitat patches.

description: Photographs of the study system at different scales illustrating the extent of the study system and habitat patches.
DOI: 10.6084/m9.figshare.3554637.v1
title: Appendix B. Photographs of the study system at different scales illustrating the extent of the study system and habitat patches.

description: Photographs of the study system at different scales illustrating the extent of the study system and habitat patches.
DOI: 10.6084/m9.figshare.3554634
title: Supplement 1. British national grid XY coordinates of habitat patches, colony size data which give the number of individuals in a patch per year, and the OpenBUGS code for implementing the SPOM.

description: File List XY_data.txt (MD5: 9174c10342b9d0d1d94397fa6ce5d4be)<br> local_pop_data.txt (MD5: 513ef66f95dbfc8629a07bccc97d9f9a)<br> SPOM_bugs.txt(MD5: b4156301e75a180d6138e43eb352daa9)Description XY_data.txt: Site coordinates (x and y) on the British National Grid (BNG)<br> local_pop_data.txt: Total number of individuals trapped per site, per year.<br> SPOM_bugs: OpenBUGS code for the Stochastic Patch Occupancy Model that includes demographic stage structure and spatially correlated extinctions. The code provided includes a rescue effect.
DOI: 10.6084/m9.figshare.3554634.v1
title: Supplement 1. British national grid XY coordinates of habitat patches, colony size data which give the number of individuals in a patch per year, and the OpenBUGS code for implementing the SPOM.

description: File List XY_data.txt (MD5: 9174c10342b9d0d1d94397fa6ce5d4be)<br> local_pop_data.txt (MD5: 513ef66f95dbfc8629a07bccc97d9f9a)<br> SPOM_bugs.txt(MD5: b4156301e75a180d6138e43eb352daa9)Description XY_data.txt: Site coordinates (x and y) on the British National Grid (BNG)<br> local_pop_data.txt: Total number of individuals trapped per site, per year.<br> SPOM_bugs: OpenBUGS code for the Stochastic Patch Occupancy Model that includes demographic stage structure and spatially correlated extinctions. The code provided includes a rescue effect.
DOI: 10.6084/m9.figshare.3554631
title: Appendix A. Matrix model used in the state-space formulation, full parameterization of the variance–covariance matrix between model parameters, and regression between the population counts time series.

description: Matrix model used in the state-space formulation, full parameterization of the variance–covariance matrix between model parameters, and regression between the population counts time series.
DOI: 10.6084/m9.figshare.3554631.v1
title: Appendix A. Matrix model used in the state-space formulation, full parameterization of the variance–covariance matrix between model parameters, and regression between the population counts time series.

description: Matrix model used in the state-space formulation, full parameterization of the variance–covariance matrix between model parameters, and regression between the population counts time series.
DOI: 10.6084/m9.figshare.3554628
title: Supplement 1. WinBUGS code for the two-species integrated model.

description: File List Peron and Koons 2012 - WinBUGS code.txt (md5: 0972cd2cbe2bb7ce64ff01a1269cbe8e) Description WinBUGS code for the two-species integrated model (CANV= canvasback, REDH=Redhead).
DOI: 10.6084/m9.figshare.3554628.v1
title: Supplement 1. WinBUGS code for the two-species integrated model.

description: File List Peron and Koons 2012 - WinBUGS code.txt (md5: 0972cd2cbe2bb7ce64ff01a1269cbe8e) Description WinBUGS code for the two-species integrated model (CANV= canvasback, REDH=Redhead).
DOI: 10.6084/m9.figshare.3554625
title: Appendix A. Relationship between interannual turnover and monthly richness.

description: Relationship between interannual turnover and monthly richness.
DOI: 10.6084/m9.figshare.3554625.v1
title: Appendix A. Relationship between interannual turnover and monthly richness.

description: Relationship between interannual turnover and monthly richness.
DOI: 10.6084/m9.figshare.3554622
title: Appendix B. Analysis of the deviation between the observed annual species time relationships and a null model (SIM-8).

description: Analysis of the deviation between the observed annual species time relationships and a null model (SIM-8).
DOI: 10.6084/m9.figshare.3554622.v1
title: Appendix B. Analysis of the deviation between the observed annual species time relationships and a null model (SIM-8).

description: Analysis of the deviation between the observed annual species time relationships and a null model (SIM-8).
DOI: 10.6084/m9.figshare.3554619
title: Appendix C. Relationship between annual turnover and autocorrelation of species.

description: Relationship between annual turnover and autocorrelation of species.
DOI: 10.6084/m9.figshare.3554619.v1
title: Appendix C. Relationship between annual turnover and autocorrelation of species.

description: Relationship between annual turnover and autocorrelation of species.
DOI: 10.6084/m9.figshare.3554613
title: Appendix A. Descriptions of the process model explanatory variables used in the analyses.

description: Descriptions of the process model explanatory variables used in the analyses.
DOI: 10.6084/m9.figshare.3554610
title: Appendix B. Detail about the multinomial model and calculation of Jackknife standard errors, and goodness-of-fit analysis.

description: Detail about the multinomial model and calculation of Jackknife standard errors, and goodness-of-fit analysis.
DOI: 10.6084/m9.figshare.3554607
title: Appendix C. Supplemental tables with AIC values evaluated for selection of variables in the various models.

description: Supplemental tables with AIC values evaluated for selection of variables in the various models.
DOI: 10.6084/m9.figshare.3554607.v1
title: Appendix C. Supplemental tables with AIC values evaluated for selection of variables in the various models.

description: Supplemental tables with AIC values evaluated for selection of variables in the various models.
DOI: 10.6084/m9.figshare.3554604
title: Appendix D. Figures showing observed yearly total areas attacked and mean values for the weather drivers with significant influence on the probability of outbreaks, spatial correlation of data, and for model residuals, estimated log-odds for the probability of new attacks, estimated log-odds for the conditional probability of at least 1000 trees killed, and estimated influence of the selected climatological temperature and drought variables.

description: Figures showing observed yearly total areas attacked and mean values for the weather drivers with significant influence on the probability of outbreaks, spatial correlation of data, and for model residuals, estimated log-odds for the probability of new attacks, estimated log-odds for the conditional probability of at least 1000 trees killed, and estimated influence of the selected climatological temperature and drought variables.
DOI: 10.6084/m9.figshare.3554604.v1
title: Appendix D. Figures showing observed yearly total areas attacked and mean values for the weather drivers with significant influence on the probability of outbreaks, spatial correlation of data, and for model residuals, estimated log-odds for the probability of new attacks, estimated log-odds for the conditional probability of at least 1000 trees killed, and estimated influence of the selected climatological temperature and drought variables.

description: Figures showing observed yearly total areas attacked and mean values for the weather drivers with significant influence on the probability of outbreaks, spatial correlation of data, and for model residuals, estimated log-odds for the probability of new attacks, estimated log-odds for the conditional probability of at least 1000 trees killed, and estimated influence of the selected climatological temperature and drought variables.