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Once K was identified, we ran 100 replicates of the model with the same parameters as above and K held constant.
When resampling strategies are adopted to obtain a valid estimate of the classification error, the relevance of individual predictors can be indirectly inferred from how often they are present in the different replicates of the model.
We also ran 40 additional replicates of the model for the highest harvesting intensity (bH = 0.2), to determine the size of the brook charr population during the course of harvesting.
For the 100 replicates of the model that were run without harvesting for 15 000 years, we fit an exponential decay model (e.g., Ritz and Streibig 2005) to the difference between the PMRN traits in a given year and the PMRN traits after 15 000 years.
To assess the plausibility of the model's evolutionary equilibrium, we also ran 100 replicates of the model without harvesting for 15 000 years, i.e., for the approximate number of years since the brook charr colonized the study area (e.g., Angers and Bernatchez 1998).
In the pathogen parameterization tests, we compared the above three metrics across high (85 out of 100), moderate (50 out of 100), and low (15 out of 100) levels of virulence, infectivity, and infectiousness, with 200 replicates of the model run for each scenario.
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Therefore it is not meaningful to compare community descriptors derived from this single replicate with mean values of descriptors derived from many replicates of the models.
Further increases in the computational needs are brought on by the need for running multiple replicates of the models and generating reliable output summaries.
We compared the final model parameter estimates to the mean of the parameter estimates obtained from 1000 bootstrap replicates of the final model.
Bootstrap values were generated using with 1000 replicates of the same model with NNI swapping.
The abundances of all species show reduced year-to-year variability within replicates of the neutral model due to the temporal correlation in community composition described above.
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