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In order to reduce fieldwork costs, the sample was clustered by neighbourhood code and a new selection was done proportional to the size of the target population in the cluster, which transformed the sample into a clustered random one still allowing the calculation of selection probabilities.
This is a major advantage in comparison with other methods based on exact calculation of selection probabilities of surveyed units.
Determining evolutionary rates would depend on the calculation of selection responses, which are the product of selection differentials and heritabilities (Hilborn and Minte-Vera 2008).
Comparison of vectors can be done in two related ways (details below); doing so first required calculation of selection gradients for the traits under study.
Since fast and stable calculation of selection intensities in multistage breeding programs is possible even for highly correlated EBV of successive stages and small proportions of selected individuals, the optimum selection index is the method of choice for the deterministic optimisation of breeding schemes using the selection index methodology.
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All traits but Urel were transformed to a mean zero before calculations of selection differentials [ 38].
It has been shown, however, that small variations in tree topologies have minor impact on the parameters of phylogenetic models (Yang et al. 1994), and we would not expect it to significantly affect our calculations of selection coefficients.
Here we used PAML 4.0 [45] for calculation of heterogeneous selection pressure at each codon and HyPhy [55] for directional selection in 335 non-egg-adapted and 32 egg-adapted human A(H1N1) HA sequences.
The calculation of this selection criterion will be described in the QTL mapping section.
Calculation of the selection rate constant by time series analysis led to highly similar estimates (data not shown).
The calculation of the selection intensity of an optimum index in a multistage breeding program used the FORTRAN routines of Genz [ 21] and Brent [ 22].
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