The maximum Gini Index over all the genes in every permutation was recorded and thereby an empirical distribution of the maximum importance was estimated, as in similar analyses [ 49, 50].
Any SNP whose importance score is greater than the maximum importance score of the shadow SNPs is considered as important.
When q = 1, then an equal importance or weight is given to each deviation and when q = 2, then each deviation is weighted proportionately with the maximum deviation with the maximum importance or weight (Lai et al. 1994).
The results in fact show that 43% of the cluster attributes the maximum importance to this association (score of 7 out of 7 on the Likert scale).
The experts gave the maximum importance to 5 variables: number of native potato varieties cultivated (D1), use of own seed (D1), form in which cultivation knowledge was acquired by the keeper (D2), exchange of own seed (D3), and number of other potato keepers known (D3).
Extract the maximum importance score of each replicate to form the comparison sample of R elements.
The maximum importance score IMP p (1)=0.09, corresponds to the score at node S3 where position 1 is completely conserved.
For each SNP, we computed Wilcoxon test to check whether its mean importance score is greater than the maximum importance score of noisy SNPs.
In the first stage we build R random forests to obtain raw importance scores and then use Wilcoxon rank-sum test [ 22] to compare the importance score of an SNP with the maximum importance scores of generated noisy SNPs called shadows.
Based on this, the LD value has maximum importance and its value is the primary factor to determine the total uW.
