cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3559572
title: Supplement 1. Details on the computational analyses needed to replicate the results.

description: File List community_response.R (MD5: fb68bd4556d88efa258ef31df99bd9ba)<br> R script that imports the data, summarizes the species-level and community-level diversity measures, runs the statistical analyses, and outputs figures. ExpRADsFunctions.R (MD5: 33f248b2586218cdfd39d1bdab7d5078)<br> R script that holds the relevant functions for executing the community_response.R script. ref_analysis_data.csv (MD5: 9711e20465ed8f66a3093cf49b1ca477)<br> Data file containing the citations and details for the references where the studies were found. community_analysis_data.csv (MD5: 7bded51aa20016eefc079a079500eb96)<br> Data file containing the community-level data. orderedcomparisons.csv (MD5: 11cdc68441e8dd2011da2594f6a70dfe)<br> Data file containing the details on which sites should be compared. experiments_analysis_data.csv (MD5: 9052fc375916c1fa36be1316988a5c13)<br> Data file containing the details about the controls and experimental treatments. sites_analysis_data.csv (MD5: 93ee3e4c9c4f9cfa99bddbe473b9c5ef)<br> Data file containing site-specific information for the studies. Description The code and data in this supplement allow for the analyses and figures in the paper to be fully replicated using a data set of manipulated communities collected from the literature. <i>Requirements: </i>R 3.x, and the following packages: vegan, BiodiversityR, plotrix, graphics, CCA, VGAM, nlme, lme4, poilog, scatterplot3d, hydroGOF, and VennDiagram, knitr, ggplot2, ggmap, gridExtra, GGally, and the file containing functions specific to this code, expRADsFunctions.R. The analyses can then be replicated by changing the working directory at the top of the file community_response.R to the location on your computer where you have stored the .R and .csv files and running the code. It should take approximately 10 minutes to run all the code from start to finish. Figures should output as pdfs in your working directory. <i>Version Control Repository: </i>The full version control repository for this project (including post- publication improvements) is publicly available at https://github.com/weecology/experimental- rads. 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. <i>Data use: </i>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 S. R. Supp or from the original authors who are cited in ref_analysis_data.csv and Appendix Table A1. The data is also published in a public figshare repository (MACD: Manipulated Animal Community Database. S. R. Supp. figshare. http://dx.doi.org/10.6084/m9.figshare.96831).
DOI: 10.6084/m9.figshare.3559572.v1
title: Supplement 1. Details on the computational analyses needed to replicate the results.

description: File List community_response.R (MD5: fb68bd4556d88efa258ef31df99bd9ba)<br> R script that imports the data, summarizes the species-level and community-level diversity measures, runs the statistical analyses, and outputs figures. ExpRADsFunctions.R (MD5: 33f248b2586218cdfd39d1bdab7d5078)<br> R script that holds the relevant functions for executing the community_response.R script. ref_analysis_data.csv (MD5: 9711e20465ed8f66a3093cf49b1ca477)<br> Data file containing the citations and details for the references where the studies were found. community_analysis_data.csv (MD5: 7bded51aa20016eefc079a079500eb96)<br> Data file containing the community-level data. orderedcomparisons.csv (MD5: 11cdc68441e8dd2011da2594f6a70dfe)<br> Data file containing the details on which sites should be compared. experiments_analysis_data.csv (MD5: 9052fc375916c1fa36be1316988a5c13)<br> Data file containing the details about the controls and experimental treatments. sites_analysis_data.csv (MD5: 93ee3e4c9c4f9cfa99bddbe473b9c5ef)<br> Data file containing site-specific information for the studies. Description The code and data in this supplement allow for the analyses and figures in the paper to be fully replicated using a data set of manipulated communities collected from the literature. <i>Requirements: </i>R 3.x, and the following packages: vegan, BiodiversityR, plotrix, graphics, CCA, VGAM, nlme, lme4, poilog, scatterplot3d, hydroGOF, and VennDiagram, knitr, ggplot2, ggmap, gridExtra, GGally, and the file containing functions specific to this code, expRADsFunctions.R. The analyses can then be replicated by changing the working directory at the top of the file community_response.R to the location on your computer where you have stored the .R and .csv files and running the code. It should take approximately 10 minutes to run all the code from start to finish. Figures should output as pdfs in your working directory. <i>Version Control Repository: </i>The full version control repository for this project (including post- publication improvements) is publicly available at https://github.com/weecology/experimental- rads. 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. <i>Data use: </i>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 S. R. Supp or from the original authors who are cited in ref_analysis_data.csv and Appendix Table A1. The data is also published in a public figshare repository (MACD: Manipulated Animal Community Database. S. R. Supp. figshare. http://dx.doi.org/10.6084/m9.figshare.96831).
DOI: 10.6084/m9.figshare.3559569
title: Data Paper. Data Paper

description: File List KMD13_occur.csv (MD5: 817da6ade01a91e557f2211b82831361) KMD13_sources.csv (MD5: a8be2715bc59257dcf43c610738db988) KMD13_traits.csv (MD5: 4a9dceb8a8bb8299a1f61d073bfb2b56) KMD13_Lformat.csv (MD5: 1ddaa3b060053b9584a9eb90f6a36573) Site_Chars.csv (MD5: 3d75cda6f57e4af118b372a0885909d4) Description Kenya is a world leader in conservation and host to one of the most diverse array of mammals on the planet. As a focus of scientific attention, it is important to be able to assess not only the current state of Kenya's mammal communities, but also how they have changed over anthropogenic timescales. Comprehensive lists of mammal species from known areas are essential for this goal, and these also provide comparative baselines for assessing changes in mammalian diversity in the future and in the fossil record. Though there is considerable literature available for mammals inhabiting Kenyan protected areas (National Parks and Reserves), species compilation projects vary greatly in scope, completeness, agreement, and accuracy. We combine the information in these databases for Kenya and supplement them with the most up-to-date knowledge available up to November 2013. Comprehensive historical species lists were compiled from specimen lists collected during 1888–1950 in ecosystems that today correspond to 13 different protected areas. We also provide analogous modern species lists based on data collected during 1950–2012. The data sets include both large and small mammals. A master list of a total of 413 species provides ecological information including body mass, diet, feeding and shelter habitat, and activity time. Historical data are based on museum specimens and sighting records, and modern data are based on museum data as well as literature, books, field guides, written accounts, photos, and videos. We used this compilation for an analysis comparing the two data sets (excluding volant and domestic species) for six protected areas with the most complete historical records and have shown in a separate publication that species richness is preserved, but beta diversity, based on pairwise comparisons of sites in this database, is being lost over the entire study area. <i>Key words</i>: <i>biodiversity; community ecology; East Africa; ecology; large mammals; mammals; protected areas; small mammals; species lists. </i>
DOI: 10.6084/m9.figshare.3559569.v1
title: Data Paper. Data Paper

description: File List KMD13_occur.csv (MD5: 817da6ade01a91e557f2211b82831361) KMD13_sources.csv (MD5: a8be2715bc59257dcf43c610738db988) KMD13_traits.csv (MD5: 4a9dceb8a8bb8299a1f61d073bfb2b56) KMD13_Lformat.csv (MD5: 1ddaa3b060053b9584a9eb90f6a36573) Site_Chars.csv (MD5: 3d75cda6f57e4af118b372a0885909d4) Description Kenya is a world leader in conservation and host to one of the most diverse array of mammals on the planet. As a focus of scientific attention, it is important to be able to assess not only the current state of Kenya's mammal communities, but also how they have changed over anthropogenic timescales. Comprehensive lists of mammal species from known areas are essential for this goal, and these also provide comparative baselines for assessing changes in mammalian diversity in the future and in the fossil record. Though there is considerable literature available for mammals inhabiting Kenyan protected areas (National Parks and Reserves), species compilation projects vary greatly in scope, completeness, agreement, and accuracy. We combine the information in these databases for Kenya and supplement them with the most up-to-date knowledge available up to November 2013. Comprehensive historical species lists were compiled from specimen lists collected during 1888–1950 in ecosystems that today correspond to 13 different protected areas. We also provide analogous modern species lists based on data collected during 1950–2012. The data sets include both large and small mammals. A master list of a total of 413 species provides ecological information including body mass, diet, feeding and shelter habitat, and activity time. Historical data are based on museum specimens and sighting records, and modern data are based on museum data as well as literature, books, field guides, written accounts, photos, and videos. We used this compilation for an analysis comparing the two data sets (excluding volant and domestic species) for six protected areas with the most complete historical records and have shown in a separate publication that species richness is preserved, but beta diversity, based on pairwise comparisons of sites in this database, is being lost over the entire study area. <i>Key words</i>: <i>biodiversity; community ecology; East Africa; ecology; large mammals; mammals; protected areas; small mammals; species lists. </i>
DOI: 10.6084/m9.figshare.3559563
title: Appendix A. The dependence of the exponent z on the width of the time window.

description: The dependence of the exponent z on the width of the time window.
DOI: 10.6084/m9.figshare.3559563.v1
title: Appendix A. The dependence of the exponent z on the width of the time window.

description: The dependence of the exponent z on the width of the time window.
DOI: 10.6084/m9.figshare.3559560
title: Appendix B. Artifacts of sampling errors and the double logarithmic scale.

description: Artifacts of sampling errors and the double logarithmic scale.
DOI: 10.6084/m9.figshare.3559560.v1
title: Appendix B. Artifacts of sampling errors and the double logarithmic scale.

description: Artifacts of sampling errors and the double logarithmic scale.
DOI: 10.6084/m9.figshare.3559557
title: Appendix C. The alpha-beta-gamma model (see Fig. 2).

description: The alpha-beta-gamma model (see Fig. 2).
DOI: 10.6084/m9.figshare.3559557.v1
title: Appendix C. The alpha-beta-gamma model (see Fig. 2).

description: The alpha-beta-gamma model (see Fig. 2).
DOI: 10.6084/m9.figshare.3559554
title: Appendix D. Cleaning the Breeding Bird Survey (BBS) data from sampling errors.

description: Cleaning the Breeding Bird Survey (BBS) data from sampling errors.
DOI: 10.6084/m9.figshare.3559554.v1
title: Appendix D. Cleaning the Breeding Bird Survey (BBS) data from sampling errors.

description: Cleaning the Breeding Bird Survey (BBS) data from sampling errors.
DOI: 10.6084/m9.figshare.3559551
title: Appendix E. Fluctuation scaling in the tropical forest—a supplement to Fig. 3.

description: Fluctuation scaling in the tropical forest—a supplement to Fig. 3.
DOI: 10.6084/m9.figshare.3559551.v1
title: Appendix E. Fluctuation scaling in the tropical forest—a supplement to Fig. 3.

description: Fluctuation scaling in the tropical forest—a supplement to Fig. 3.
DOI: 10.6084/m9.figshare.3559548
title: Supplement 1. Fortran code simulating a neutral community with demographic noise, used to generate Fig. 5.

description: File List Neutral_fortran.txt (MD5: 7d5175db22c1bf3d1724b608611568de) Description Neutral_Fortran is a program that simulates neutral dynamics (the selection strength is alpha, so alpha = 0 is neutral) for a panmictic population of n individuals. The initial conditions are 50 species, mutation rate is dmu. The output is the file st1.dat, which is a list of abundance of species (of families) - the list is not sorted so if st1.dat contains the numbers 13,25,11 it implies that one species has abundance 13, another has 25, another has 11 and so on.
DOI: 10.6084/m9.figshare.3559548.v1
title: Supplement 1. Fortran code simulating a neutral community with demographic noise, used to generate Fig. 5.

description: File List Neutral_fortran.txt (MD5: 7d5175db22c1bf3d1724b608611568de) Description Neutral_Fortran is a program that simulates neutral dynamics (the selection strength is alpha, so alpha = 0 is neutral) for a panmictic population of n individuals. The initial conditions are 50 species, mutation rate is dmu. The output is the file st1.dat, which is a list of abundance of species (of families) - the list is not sorted so if st1.dat contains the numbers 13,25,11 it implies that one species has abundance 13, another has 25, another has 11 and so on.
DOI: 10.6084/m9.figshare.3559545
title: Supplement 2. Matlab code simulating the alpha-beta-gamma model to check Eq. 3.

description: File List abc.m (MD5: 00196d8d3afef5257cb3d380ef8e0f1d) Description abc.m is a matlab script that simulates the alpha-beta-gamma model we introduced in thearticle. It checks the normalized population variation, <i>Y</i>, as function of population size. The graph is linear.
DOI: 10.6084/m9.figshare.3559545.v1
title: Supplement 2. Matlab code simulating the alpha-beta-gamma model to check Eq. 3.

description: File List abc.m (MD5: 00196d8d3afef5257cb3d380ef8e0f1d) Description abc.m is a matlab script that simulates the alpha-beta-gamma model we introduced in thearticle. It checks the normalized population variation, <i>Y</i>, as function of population size. The graph is linear.
DOI: 10.6084/m9.figshare.3559542
title: Supplement 3. Matlab code calculating the variance of Y for different time lags, used to analyze the BBS data.

description: File List varY_lag.m (MD5: ac6cef05a4f087a2f14fc91ab62d0cd4) Description varY_lag.m is a matlab script that calculates the variance of <i>Y</i> over increasing timelags. The main output is the y_lag matrix of calculated variances, with columns denoting time lag and rows - size group. The code receives as output a very specific data structure: a STRUCT vector of sites, each site containing a STRUCT vector of species (+some metadata, i.e., all the lags and species at that site), each species having it's time series at this site. the time series is represented by a matrix with the first row denoting years and the second row denoting population size at that year. For example, sites(3).species(10).ts=[1970 1971; 10 15] means that at site3 for species 10, in 1970 there were 10 individuals and in 1971 there were 15. Some metadata are sites.all_lags (all available lags for this site) and sites.tot_abundance (which species are available at the site?). The grouping requires entering the minimum edges of each group. For example, if group_min = [1 31], the variance would be calculated separately for two groups, one with initial size 1-30, the other 30 and beyond.
DOI: 10.6084/m9.figshare.3559542.v1
title: Supplement 3. Matlab code calculating the variance of Y for different time lags, used to analyze the BBS data.

description: File List varY_lag.m (MD5: ac6cef05a4f087a2f14fc91ab62d0cd4) Description varY_lag.m is a matlab script that calculates the variance of <i>Y</i> over increasing timelags. The main output is the y_lag matrix of calculated variances, with columns denoting time lag and rows - size group. The code receives as output a very specific data structure: a STRUCT vector of sites, each site containing a STRUCT vector of species (+some metadata, i.e., all the lags and species at that site), each species having it's time series at this site. the time series is represented by a matrix with the first row denoting years and the second row denoting population size at that year. For example, sites(3).species(10).ts=[1970 1971; 10 15] means that at site3 for species 10, in 1970 there were 10 individuals and in 1971 there were 15. Some metadata are sites.all_lags (all available lags for this site) and sites.tot_abundance (which species are available at the site?). The grouping requires entering the minimum edges of each group. For example, if group_min = [1 31], the variance would be calculated separately for two groups, one with initial size 1-30, the other 30 and beyond.
DOI: 10.6084/m9.figshare.3559539
title: Appendix A. Descriptive summaries of the data sets included in our analyses, including source information and representative times series of species abundances over time.

description: Descriptive summaries of the data sets included in our analyses, including source information and representative times series of species abundances over time.
DOI: 10.6084/m9.figshare.3559536
title: Appendix A. Detailed description of antibody preparation and detection, and additional figures describing the relationships between parasite characteristics in single and co-infected rabbits.

description: Detailed description of antibody preparation and detection, and additional figures describing the relationships between parasite characteristics in single and co-infected rabbits.
DOI: 10.6084/m9.figshare.3559536.v1
title: Appendix A. Detailed description of antibody preparation and detection, and additional figures describing the relationships between parasite characteristics in single and co-infected rabbits.

description: Detailed description of antibody preparation and detection, and additional figures describing the relationships between parasite characteristics in single and co-infected rabbits.
DOI: 10.6084/m9.figshare.3559533
title: Appendix A. A table of amino acid compound-specific results for migrant and resident Pacific bluefin tuna Thunnus orientalis and eastern Pacific Ocean residents yellowfin tuna (T. albacares), jack mackerel (Trachurus symmetricus), and Pacific saury (Cololabis saira).

description: A table of amino acid compound-specific results for migrant and resident Pacific bluefin tuna Thunnus orientalis and eastern Pacific Ocean residents yellowfin tuna (T. albacares), jack mackerel (Trachurus symmetricus), and Pacific saury (Cololabis saira).
DOI: 10.6084/m9.figshare.3559533.v1
title: Appendix A. A table of amino acid compound-specific results for migrant and resident Pacific bluefin tuna Thunnus orientalis and eastern Pacific Ocean residents yellowfin tuna (T. albacares), jack mackerel (Trachurus symmetricus), and Pacific saury (Cololabis saira).

description: A table of amino acid compound-specific results for migrant and resident Pacific bluefin tuna Thunnus orientalis and eastern Pacific Ocean residents yellowfin tuna (T. albacares), jack mackerel (Trachurus symmetricus), and Pacific saury (Cololabis saira).
DOI: 10.6084/m9.figshare.3559530
title: Appendix B. A table of all specific prey δ15N values used to generate regional estimates of mean prey δ15N values for the western and eastern Pacific Ocean.

description: A table of all specific prey δ15N values used to generate regional estimates of mean prey δ15N values for the western and eastern Pacific Ocean.
DOI: 10.6084/m9.figshare.3559530.v1
title: Appendix B. A table of all specific prey δ15N values used to generate regional estimates of mean prey δ15N values for the western and eastern Pacific Ocean.

description: A table of all specific prey δ15N values used to generate regional estimates of mean prey δ15N values for the western and eastern Pacific Ocean.
DOI: 10.6084/m9.figshare.3559527
title: Appendix C. A table showing Pacific bluefin tuna white muscle bulk δ15N values, age, size, and classification as migrant or resident by discriminant analysis.

description: A table showing Pacific bluefin tuna white muscle bulk δ15N values, age, size, and classification as migrant or resident by discriminant analysis.
DOI: 10.6084/m9.figshare.3559527.v1
title: Appendix C. A table showing Pacific bluefin tuna white muscle bulk δ15N values, age, size, and classification as migrant or resident by discriminant analysis.

description: A table showing Pacific bluefin tuna white muscle bulk δ15N values, age, size, and classification as migrant or resident by discriminant analysis.
DOI: 10.6084/m9.figshare.3559524
title: Supplement 1. Summary of Millepora spp. observations across the Gulf of Chiriquí from 1973–2010 compiled from field notes and data.

description: File List Supp1.csv (MD5: 73db5e598bf4eb9ad2d5b004f3f7c96f) Description Summary of <i>Millepora</i> spp. observations across the Gulf of Chiriquí from 1973–2010 compiled from field notes, data, and published sources. Year = Year of observation Month = Month of observation. May not be given if the observation is compiled over multiple time points within a year. Source = source of information for the observation. Initial codes: PWG = Peter W. Glynn, JLM = Juan L. Maté, TBS = Tyler B. Smith. Year is listed to refer to the year of the archived notebook. Date = Specific date of the observation. May not be given if the observation is compiled over multiple time points within a year. Site = Study site referenced in the observation Location = Area of the study site referenced in the observation Observation = A verbal description of the observation or data Presence 0 – 11 m = Indicates presence or absence of <i>Millepora intricata</i> in the range between 0 and 11 m depth during the specific observation. Observation marked as "---" or a blank cell indicate that the observation did not include information on the presence or absence of <i>Millepora intricata</i> between the 0 and 11 m depth range. Presence &gt; 11 m = Indicates presence or absence of <i>Millepora intricata</i> in depths greater than 11 m during the specific observation. Observation marked as "---" or a blank cell indicates that the observation did not include information on the presence or absence of <i>Millepora intricata</i> in depths greater than 11 m.