uid=MCM,o=EDI,dc=edirepository,dc=org all public read ESM Simulations connecting metacommunity characteristics and biodiversity patterns Eric Sokol sokole@gmail.com http://sokole.blogspot.com/ https://orcid.org/0000-0001-5952-0917 McMurdo Dry Valleys LTER http://mcmlter.org/ John "Jeb" Barrett jebarre@vt.edu https://www.biol.vt.edu/faculty/barrett/index.html https://orcid.org/0000-0002-7610-0505 associated researcher Bryan Brown associated researcher 2016-10-21 English
The data and model described here with the purpose of understanding controls over biodiversity. A multi-scale approach to understand how local and regional factors affect the community assembly processes that drive emergent patterns. These data allows us to examin a wide range of parameter settings representing ecologically relevant scenarios. We used artificial neural networks (ANNs) to assess the sensitivity of diversity and variation partitioning metrics (calculated from simulation outcomes) to metacommunity parameter settings. Here you will find metadata details,  dor detailed information about the simulations results and conclusions, please visit the associated publication at http://onlinelibrary.wiley.com/doi/10.1111/oik.03690/abstract;jsessionid...
dispersal dispersion diversity simulation LTER Controlled Vocabulary distribution Station Keywords population dynamics LTER Core Areas This simulation is atemporal and non-localized.  There is no physical geo-location or calendar time frame or specific season.  However, simulations were performed in Aug 2016. 
Data Policies This data package is released under the Creative Commons Attribution 4.0 International License (CC BY 4.0; http://creativecommons.org/licenses/by/4.0/), which allows consumers (hereinafter referred to as “Data Users”) to freely reuse, redistribute, transform, or build on this work (even commercially) so long as appropriate credit is provided. Accordingly, Data Users are required to properly cite this data package in any publications or in the metadata of any derived products that result from its use (in whole or in part). A recommended citation is provided on the summary metadata page associated with this data package in the McMurdo Dry Valleys LTER Data Catalog (https://mcmlter.org/data), and a generic citation may be found on the summary metadata page in the repository where this data package was obtained. When these data contribute significantly to the contents of a publication, Data Users must also acknowledge that data were provided by the NSF-supported McMurdo Dry Valleys Long Term Ecological Research program (OPP-1637708). This data package has been released in the spirit of open scientific collaboration. Hence, Data Users are strongly encouraged to consider consultation, collaboration, and/or co-authorship (as appropriate) with the data package creator(s). Data Users should be aware these data may be actively used by others for ongoing research; thus, coordination may be necessary to prevent duplicate publication. Data Users should also recognize that misinterpretation of data may occur if they are used outside the context of the original study. Hence, Data Users are urged to contact the data package creator(s) if they have any questions regarding methodology or results. While substantial efforts are made to ensure the accuracy of this data package (with all its components), complete accuracy cannot be guaranteed. Periodic updates to this data package may occur, and it is the responsibility of Data Users to check for new versions. This data package is made available “as is” and comes with no warranty of accuracy or fitness for use. The creator(s) of this data package and the repository where these data were obtained shall not be liable for any damages resulting from misinterpretation, use, or misuse of these data. Finally, as a professional courtesy, we kindly request Data Users notify the primary contact referenced in the metadata when these data are used in the production of any derivative work or publication. Notification should include an explanation of how the data were used, along with a digital copy of the derived product(s). Thank you.
https://mcm.lternet.edu/content/simulations-connecting-metacommunity-characteristics-and-biodiversity-patterns 2015-08-01 McMurdo Dry Valleys LTER http://mcmlter.org/ McMurdo Dry Valleys LTER http://mcmlter.org/ McMurdo Dry Valleys LTER
Methods, code description and heuristics are posted in the appendix of the associated publication at http://onlinelibrary.wiley.com/doi/10.1111/oik.03690/abstract;jsessionid... The Metacommunities simulation code used is posted at http://doi.org/10.5281/zenodo.153999
ESM_SIM_DATA_INPUT ESM_sim_data parameter settings used in metacommunity simulation (MCSim), definitions and labels. ESM_SIM_DATA_INPUT.csv 84676 1 column , https://mcm.lternet.edu/sites/default/files/data/ESM_SIM_DATA_INPUT.csv Scenario ID Scenario ID Scenario ID, an integer used as identifier to distinguish the simulation run or realization. string Scenario ID, an integer used as identifier to distinguish the simulation run or realization. nu Probability of invasion nu - Metacommunity openness, probability of invasion by a novel taxon, a log uniform distribution dimensionless real .01 .00001 m Recruitment proportion from inmmigrants m - Metacommunity connectivity, proportion of recruitment events drawing from immigrant pool dimensionless real .001 .999 w Dispersal Slope w - Dispersal kernel slope, pooled from a log-uniform distribution dimensionless real 0 200 sigma sigma sigma - Niche-breadth, constant among all taxa in a simulation. Pooled from a log-uniform distribution dimensionless real 0.01 2 alpha_Fisher alpha_Fisher alpha_Fisher - determines shape of the initial rank-abundance curve. Pooed from a uniform distribution dimensionless real 1 50 n_sites n_sites n_sites - Number of patches in a metacommunity. Pooled from a log-uniform distro. dimensionless real 20 200 s s s - Scale of environmental heterogeneity, standardized rank PCNM eigenvector used to model spatial variation in E. Pooled from a uniform distribution dimensionless real 0 .988 JM JM JM Metacommunity size (no. of individuals in a metacommunity at a single point in time). Value pooled from Log-uniform distribution dimensionless real 400 1000000 ESM_SIM_DATA_OUTPUT ESM_sim_data_2. Biodiversity outcomes for 100 different simulated metacommunity (MCSim) scenarios -- Definitions, ranges, labels. ESM_SIM_DATA_OUTPUT.csv 4964745 1 column , https://mcm.lternet.edu/sites/default/files/data/ESM_SIM_DATA_OUTPUT.csv Simulation ID Simulation ID Simulation ID - an alphanumeric identifier used to distinguish the simulation realization. string Simulation ID - an alphanumeric identifier used to distinguish the simulation realization. Time Step Time Step Time Step used in simulation dimensionless real Diversity Type Diversity Type Diversity Type string dis.sat dissimilarity saturation varpart variation partitions divpart diversity partitions Metric Type Metric Type Metric Type string Metric Type Metric ID Metric ID Metric ID string Metric ID Metric Value Metric Value Metric Value dimensionless real ESM_SIM_DATA_ANN_UNPRUNNED ESM_sim_data_3. Estimates of contribution of MCSim parameters to variation in biodiversity metrics based on contribution statistics from artificial neural networks (ANNs) trained and validated on simulated metacommunity outcomes. ESM_SIM_DATA_ANN_UNPRUNNED.csv 29130 1 column , https://mcm.lternet.edu/sites/default/files/data/ESM_SIM_DATA_ANN_UNPRUNNED.csv Diversity Metric ID Diversity Metric ID Diversity Metric ID string Diversity Metric ID Predictor Variable Predictor Variable Predictor Variable string Predictor Variable Predictor contribution to variation in response variable Predictor contribution to variation in response variable Predictor contribution to variation in response variable string Predictor contribution to variation in response variable Contribution p value Contribution p value Contribution p value string Contribution p value Predictor relative importance (RI) to variatino in response variable Predictor relative importance (RI) to variatino in response variable Predictor relative importance (RI) to variatino in response variable string Predictor relative importance (RI) to variatino in response variable RI p value RI p value RI p value string RI p value Keep predictor in pruned model? Keep predictor in pruned model? Keep predictor in pruned model? string Keep predictor in pruned model? N permutations used to estimate p values N permutations used to estimate p values N permutations used to estimate p values string N permutations used to estimate p values