Simulations connecting metacommunity characteristics and biodiversity patterns

Summary

Abstract: 

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...

Date Range: 

Saturday, August 1, 2015

ESM_sim_data parameter settings used in metacommunity simulation (MCSim), definitions and labels.

Variables: 

Scenario ID
  • Label: Scenario ID
  • Definition: Scenario ID, an integer used as identifier to distinguish the simulation run or realization.
  • Type: Nominal
  • Missing values: None specified
nu
  • Label: Probability of invasion
  • Definition: nu - Metacommunity openness, probability of invasion by a novel taxon, a log uniform distribution
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: .00001
  • Minimum: .01
  • Precision: Not specified
  • Missing values: None specified
m
  • Label: Recruitment proportion from inmmigrants
  • Definition: m - Metacommunity connectivity, proportion of recruitment events drawing from immigrant pool
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: .999
  • Minimum: .001
  • Precision: Not specified
  • Missing values: None specified
w
  • Label: Dispersal Slope
  • Definition: w - Dispersal kernel slope, pooled from a log-uniform distribution
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: 200
  • Minimum: 0
  • Precision: Not specified
  • Missing values: None specified
sigma
  • Label:
  • Definition: sigma - Niche-breadth, constant among all taxa in a simulation. Pooled from a log-uniform distribution
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: 2
  • Minimum: 0.01
  • Precision: Not specified
  • Missing values: None specified
alpha_Fisher
  • Label:
  • Definition: alpha_Fisher - determines shape of the initial rank-abundance curve. Pooed from a uniform distribution
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: 50
  • Minimum: 1
  • Precision: Not specified
  • Missing values: None specified
n_sites
  • Label:
  • Definition: n_sites - Number of patches in a metacommunity. Pooled from a log-uniform distro.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: 200
  • Minimum: 20
  • Precision: Not specified
  • Missing values: None specified
s
  • Label:
  • Definition: s - Scale of environmental heterogeneity, standardized rank PCNM eigenvector used to model spatial variation in E. Pooled from a uniform distribution
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: .988
  • Minimum: 0
  • Precision: Not specified
  • Missing values: None specified
JM
  • Label:
  • Definition: JM Metacommunity size (no. of individuals in a metacommunity at a single point in time). Value pooled from Log-uniform distribution
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: 1000000
  • Minimum: 400
  • Precision: Not specified
  • Missing values: None specified

ESM_sim_data_2. Biodiversity outcomes for 100 different simulated metacommunity (MCSim) scenarios -- Definitions, ranges, labels.

Variables: 

Simulation ID
  • Label:
  • Definition: Simulation ID - an alphanumeric identifier used to distinguish the simulation realization.
  • Type: Nominal
  • Missing values: None specified
Time Step
  • Label:
  • Definition: Time Step used in simulation
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
Diversity Type
  • Label:
  • Definition: Diversity Type
  • Type: Code list
  • Codes:
    • dis.sat = dissimilarity saturation
    • varpart = variation partitions
    • divpart = diversity partitions
  • Missing values: None specified
Metric Type
  • Label:
  • Definition: Metric Type
  • Type: Nominal
  • Missing values: None specified
Metric ID
  • Label:
  • Definition: Metric ID
  • Type: Nominal
  • Missing values: None specified
Metric Value
  • Label:
  • Definition: Metric Value
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified

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.

Variables: 

Diversity Metric ID
  • Label:
  • Definition: Diversity Metric ID
  • Type: Nominal
  • Missing values: None specified
Predictor Variable
  • Label:
  • Definition: Predictor Variable
  • Type: Nominal
  • Missing values: None specified
Predictor contribution to variation in response variable
  • Label:
  • Definition: Predictor contribution to variation in response variable
  • Type: Nominal
  • Missing values: None specified
Contribution p value
  • Label:
  • Definition: Contribution p value
  • Type: Nominal
  • Missing values: None specified
Predictor relative importance (RI) to variatino in response variable
  • Label:
  • Definition: Predictor relative importance (RI) to variatino in response variable
  • Type: Nominal
  • Missing values: None specified
RI p value
  • Label:
  • Definition: RI p value
  • Type: Nominal
  • Missing values: None specified
Keep predictor in pruned model?
  • Label:
  • Definition: Keep predictor in pruned model?
  • Type: Nominal
  • Missing values: None specified
N permutations used to estimate p values
  • Label:
  • Definition: N permutations used to estimate p values
  • Type: Nominal
  • Missing values: None specified

DOI: 

10.6073/pasta/2e686e58243cd1e7a2fc4825e916bd2f

Short name: 

ESM

Data set ID: 

8016
People

Owner/Creator: 

Contact: 

Additional Project roles: 

Associated Researcher
Associated Researcher