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We use the Theil-Sen estimator [59, 60] to find the slope a of f as the median of the slopes ((y_j - y_i)(x_j - x_i)) determined by all pairs of sample points with distinct x-coordinates.
<img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0012060.e003.PNG" class= inline-graphic"/> <img src="http://journals.plos.org/plosone/article/asset?id=info:doi/10.1371/journal.pone.0012060.e004.PNG" class="inline-graphic"/> We repeat this procedure for all pairs of sample locations.
Similar(58)
Evaluating similarity for all pairs of samples in N (i.e., evaluating their weighted links) allows to generate a fully connected complex network.
(ARI) Adjusted Rand Index score: computes a similarity measure between two clusterings by considering all pairs of samples and counting pairs that are assigned in the same or different clusters in the predicted and true clusterings.
Computationally, the first step is to calculate a triangular matrix of dissimilarity among all pairs of samples.
10.7554/eLife.05166.005 Figure 2. Pairwise SNP distances between all pairs of samples with known RFLP.
We analyze the relationships among multiple samples using the dissimilarity matrix composed of the dissimilarities between all pairs of samples.
In all analyses, these were used as an index of genetic dissimilarity among all pairs of sampled individuals.
We calculated the genetic relationship matrix (GRM) between all pairs of samples using all the autosomal SNPs by "make-grm" option.
The pattern of genetic isolation by angular distance was investigated by analyzing the correlation between FST and differences in angle measured for all pairs of samples.
θ ST [45] (above diagonal) and R ST [46] (below diagonal) between all pairs of samples, along with tests of their significance.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com