scipy.cluster.hierarchy.linkage — SciPy v0.14. Reference ..

This is also known as the WPGMC algorithm. method='ward' uses the Ward variance minimization algorithm. The new entry is computed as follows, where is the newly joined cluster consisting of clusters and , is an unused cluster in the forest, , and is the cardinality of its argument. This is also known as the incremental algorithm. Warning: When the minimum distance pair in the forest is. Performs median/WPGMC linkage on the observation matrix X using Euclidean distance as the distance metric. See linkage for more information on the return structure and algorithm. Parameters y ndarray. A condensed distance matrix. A condensed distance matrix is a flat array containing the upper triangular of the distance matrix. This is the form that pdist returns. Alternatively, a collection. WPGMC UPGMC SPHC; NMI: 0.9023: 0.0171: 0.6511: 0.0034: 0.3817: 0.0171: 0.0411: 0.7740: 4.4. MNIST dataset. The MNIST dataset (LeCun et al., 1998) consists of 70,000 hand- written digits of 28-by-28 pixel size. Thus each image is a 784-dimensional feature vector. For simplicity, we only consider the classes 1 and 7 and sample 100 points from each of the two classes, uniformly at random. The. What is the most effective hierarchical clustering algorithm (single / complete / average (UPGMA) / mcquitty (WPGMA) / median (WPGMC) / centroid (UPGMC))

scipy.cluster.hierarchy.median — SciPy v1.6.1 Reference Guid

GMC) and median (WPGMC) linkage (Everitt, Landau, Leese, and Stahl2011, Table 4.1) A variety of algorithms has been developed in the past decades to improve performance com-pared to the primitive algorithmic setup, in particularAnderberg(1973, page 135),Rohlf (1973),Sibson(1973),Day and Edelsbrunner(1984, Table 5),Murtagh(1984),Eppstein . 2 fastcluster: Fast Hierarchical, Agglomerative. Details. The SNPs are clustered using hclust, which performs a hierarchical cluster analysis using a set of dissimilarities for the nvar objects being clustered. There are 3 possible scenarios. If d = NULL, x is used to compute the dissimilarity matrix. The dissimilarity measure between two SNPs is 1 - LD (Linkage Disequilibrium), where LD is defined as the square of the Pearson correlation. average clustering (WPGMA) clustering (WPGMC) Unweighted arithmetic average clustering (UPGMA) Also called group average sorting and U nweighted P air- G roup M ethod using A rithmetic averages) , this technique must be applied. Dr. Daniel Borcard Université de Montréal 1 1 3. Dr. Daniel Borcard Université de Montréal 1. hclust - calculates hierarchical cluster analysis. Requires at least two arguments: d for distance matrix, and method for agglomerative algorithm, one of ward.D, ward.D2, single, complete, average (= UPGMA), mcquitty (= WPGMA), median (= WPGMC) or centroid (= UPGMC). Has it's own plot function West Point Buick-gmc is on Facebook. Join Facebook to connect with West Point Buick-gmc and others you may know. Facebook gives people the power to share and makes the world more open and connected

Hi Tal, yes I suspected it had something to do with the weird tree heights my data generated but since I was able to reproduce it in a random matrix I was curious if it's related to the cluster methods -- if these methods have tendency to generate these types of trees UPGMA and WPGMA clustering. Just a wrapper function around hclust kritisch, meinungsstark, informativ! Telepolis hinterfragt die digitale Gesellschaft und ihre Entwicklung in Politik, Wirtschaft & Medien The tool allows determining genetic distance between pairs-populations based on alleles frequencies. At first, users must determine the number of populations, number of loci, type of distance and type of dendrogram to render and then define a number of alleles in each locus

Hierarchical clustering with optimal transport - ScienceDirec

  1. istry director at WPGMC Greater Minneapolis-St. Paul Area Religious Institutions. WPGMC. 0 connections. View amy fuller's full profile. It's free! Your colleagues, classmates, and 500.
  2. The method used in this example is called WPGMA (Weighted Pair Group Method with Averaging) because the distance between clusters is calculated as a simple average. For example, in the last step the WPGMA distance between (AB) and C+(DE) = (55 + 90) / 2 = 72.5 .Though computationally easier, when there are unequal numbers of taxa in the clusters, the distances in the original matrix do not.
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  4. merge: an n-1 by 2 matrix. Row i of merge describes the merging of clusters at step i of the clustering. If an element j in the row is negative, then observation -j was merged at this stage. If j is positive then the merge was with the cluster formed at the (earlier) stage j of the algorithm. Thus negative entries in merge indicate agglomerations of singletons, and positive entries indicate.

NJ, Neighbour-joining; ML, maximum likelihood; UPGMA, unweighted pair-group method using arithmetic average; UPGMC, unweighted pair-group method using centroid average; WPGMA, weighted pair-group method using arithmetic average; WPGMC, weighted pair-group method using centroid average T = clusterdata(X,cutoff) returns cluster indices for each observation (row) of an input data matrix X, given a threshold cutoff for cutting an agglomerative hierarchical tree that the linkage function generates from X.. clusterdata supports agglomerative clustering and incorporates the pdist, linkage, and cluster functions, which you can use separately for more detailed analysis

Median clustering (WPGMC). Squared Euclidean distances are commonly used with this method. WARD. Ward's method. Squared Euclidean distances are commonly used with this method. Example. CLUSTER V1 V2 V3 /METHOD=SINGLE COMPLETE WARDS. This example clusters cases based on their values for the variables V1, V2, and V3 and uses three clustering methods: single linkage, complete linkage, and Ward. There are several different ways of defining the average distance. In literature some of these are referred to as WPGMA (weighted pair group method with arithmetic mean), UPGMA (unweighted pair group method with arithmetic mean), UPGMC (unweighted pair group method centroid) and WPGMC (weighted pair group method centroid) median WPGMC (Weighted Centroid) Methode average UPGMA (Group Average) Methode centroid UPGMC (Unweighted Centroid) Methode ward Wards Minimum Variance Methode Aufgaben: 1. Laden Sie den Datensatz bs1.datund replizieren Sie Tabelle 2.3-3. 2. Verwenden Sie den Befehl hclust, um eine hierarchische Klassifikation mittels der Single Link Methode. Median, or equilibrious centroid method (WPGMC) is the modified previous. Proximity between two clusters is the proximity between their geometric centroids ([squared] euclidean distance between those); while the centroids are defined so that the subclusters of which each of these two clusters were merged recently have equalized influence on its centroid - even if the subclusters differed in. median WPGMC (Weighted Centroid) Methode average UPGMA (Group Average) Methode centroid UPGMC (Unweighted Centroid) Methode ward Wards Minimum Variance Methode Aufgaben: 1. Laden Sie den Datensatz bs1.datund replizieren Sie Tabelle 2.3-3. 2. Verwenden Sie den Befehl diana,um mit der Abstandsmatrix aus Aufgab

produced if WPGMC is employed) are: {x 1, x 2, x 3, x 4} is formed at lower dissimilarity level than {x 1, x 2} (crossover) 16 Monotonicity condition: If clusters C i and C j are selected to be merged in cluster C q, at the tth level of the hierarchy, the condition d(C q,C k) d(C i,C j) must hold for all C k, k ≠i, j , q. In other words, the monotonicity condition implies that a cluster is. Use this program to create a dendrogram from (a) sets of variables, (b) a similarity matrix or (c) a distance matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) or Weighted Pair Group Method with Arithmetic Mean (WPGMA) algorithm

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The application offers the possibility to select several types of methods to construct dendrograms such as unweighted pair group method with arithmetic mean (UPGMA), weighted pair group method with averaging (WMPGA), centroid linkage clustering (UPGMC), weighted pair-group centroid clustering (WPGMC), single-linkage clustering and complete-linkage clustering Hierarchical Clustering in R Steps Data Generation R - Cluster Generation Apply Model Method Complete hc.complete=hclust(dist(xclustered),method=complete) plot(hc.complete) Single hc.single=hclust(dist(xclustered),method=single) plot(hc.single

What is the most effective algorithm for agglomerative

  1. imum method, connectedness method, elementary linkage analysis, or dendritic method). To reduce chaining, you can use the TRIM= option.
  2. ation of the cluster distance, the user can choose between the following linkage methods: Single linkage (Minimum), Complete linkage (Maximum), Average linkage (UPGMA), Weighted (WPGMA), Centroid (UPGMC), Median (WPGMC), and Ward's method (Incremental algorithm). (Credit: Hupfauf et al., 2020 (doi: 10.1016/j.biortech.2019.122671)
  3. Hierarchical clustering was applied to both axes using the weighted pair-group method with centroid average (WPGMC) (Sneath and Sokal 1973) as implemented in the program Cluster. The distance matrixes used were Pearson correlation for clustering the arrays and the inner product of vectors normalized to magnitude 1 for the genes (this is a slight variant of Pearson correlation; see Cluster.
  4. I am exploring the flexibility of partitional clustering algorithms. In particular, I would like to introduce more general distances than the ones which are used by default. Let us consider, fo

§ AAI-Distance clustering. Clustering method About. implement the clustering algorithms from 《pattern recognition 4th》 Resource Quitty),Ward,centroid(UPGMC)andmedian(WPGMC)linkage(seeEverittetal.,2011, Table 4.1). They are implemented in standard numerical and statistical software such as R (R Development Core Team,2011), MATLAB (The MathWorks, Inc.,2011), Mathematica (WolframResearch,Inc.,2010),SciPy(Jonesetal.,2001). The stepwise, procedural definition of these clustering methods directly gives a valid but. The latter two methods are termed the UPGMC and WPGMC criteria (respectively, unweighted and weighted pair-group method using centroids) by Sneath and Sokal (1973). Now, a problem with the cluster criteria used by these latter two methods is that the reducibility property is not satisfied by them. This means that the hierarchy constructed may not be unique as a result of inversions or.

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New Mexicans for Science and Reason. EXAMPLE CALCULATION OF PHYLOGENIES: THE UPGMA METHOD . Updated October 31st, 2002. by Dave Thomas : nmsrdaveATswcp.com (Help fight SPAM! Please replace the AT with an @ Performs median/WPGMC linkage on the observation matrix X using Euclidean distance as the distance metric. See linkage for more information on the return structure and algorithm. Parameters: Q : ndarray. A condensed or redundant distance matrix. A condensed distance matrix is a flat array containing the upper triangular of the distance matrix. This is the form that pdist returns. Alternatively.

Weighted Pair Group Method Centroid (WPGMC) PhyloTree = seqlinkage( Distances , Method , Names ) passes a list of unique names to label the leaf nodes (for example, species or products) in a phylogenetic tree object Some methods (UPGMA, UPGMC, WPGMA, WPGMC and single linkage) also produced ineffective clustering solutions. Our recluster.region procedures had higher consistency compared to classic clustering and performed best in recognizing the a priori determined regions in virtual data sets (mostly when in association with Ward clustering). Moreover, for the real butterfly data set, recluster.region.

We only examined eight (UPGMA, UPGMC, COM, FLE, WPGMA, WPGMC, SIN, and WAR) of many algorithms that cluster individuals into groups. For example, we did not test any non-hierarchical clustering algorithms (for example, K-means); all clustering algorithms used in this study are hierarchical clustering algorithms. We found a huge variation in model fit among the various combinations of the three. median, Gower's or WPGMC method; centroid or UPGMC method; hybrid hierarchical clustering the upper part of the tree is reconstructed above a cut; the lower part of the tree uses user-selected method; the upper part of the tree uses regional linkage method; multivariate clustering (MVC) filtering all variables before preprocessing ; detrending and standardization of each variable; applying. UPGMC, WPGMC, WPGMA and single clustering revealed solutions similar to UPGMA and solutions can be inspected in Appendix S2. The blue arrow indicates the single cell recognised as belonging to a different cluster. Due to the existence of a large number of equivalent trees, the 50% consensus tree among 100 random trees showed no structure and the root node revealed a strong polytomy. Actually. Function File: y = linkage (d) Function File: y = linkage (d, method) Function File: y = linkage (x, method, metric) Function File: y = linkage (x, method, arglist) Produce a hierarchical clustering dendrogram d is the dissimilarity matrix relative to n observations, formatted as a (n-1)*n/2x1 vector as produced by pdist.Alternatively, x contains data formatted for input to pdist, metric is a. Some new taxa have invalid IDs (either in newTaxa.txt or in the main profile input or both). IDs of non-NCBI taxa have to be greater than 999999005. Please replace those IDs before continuing

WPGMA - Wikipedi

  1. WPGMC 27. K-means Figure 3: Two-fold division Figure 4: Six-fold division 28. Jackknife and bootstrapping Two general-purpose techniques for empirically estimating the variability of an estimate Jackknife: involves dropping one observation at a time from one's sample and calculating the estimate each time Bootstrapping: involves resampling from one's sample with replacement and making the.
  2. /nearest linkage. 2. complete Perform complete/max/farthest point linkage. 3. average Perform average/UPGMA linkage. 4. weighted Perform weighted/WPGMA linkage. 5. centroid Perform centroid/UPGMC linkage. 6. median Perform median/WPGMC linkage. 7.
  3. Median-linkage clustering method: Weighted pair group method using centroids (WPGMC). Reference: J.C. Gower A comparison of some methods of cluster analysis Biometrics (1967): 623-637

This should be one of 'ward.D', 'ward.D2', 'single', 'complete', 'average' (= UPGMA), 'mcquitty' (= WPGMA), 'median' (= WPGMC) or 'centroid' (= UPGMC). nclust: The number of clusters to be formed. Set to NULL. Value. data The data that was used to compute the distances. cutpoint The cutpoint of the dendrogram according to Mojena (1977). distance The matrix with the distances. de The distances. This work links experimental data of unprecedented complexity with evolution theory and delineates the transcriptional landscape of the opportunistic pathogen Pseudomonas aeruginosa.We found that gene expression profiles are most strongly influenced by environmental cues, while at the same time the transcriptional profiles were also shaped considerably by genetic variation within global. WPGMC Weighted pair-group method, centroid average (assumes dissimilarity). WPGMS Weighted pair-group method, Spearman's average (assumes correlation). Neighbor-joining - The neighbor-joining (NJ) method is used to estimate phylogenetic trees. While the method is based on the idea of parsimony, the NJ method does not attempt to obtain the shortest possible tree for a set of data. Rather, it. Convergence of chemical mimicry in a guild of aphid predators DAVID J. LOHMAN,1 QING LIAO2 and NAOMI E. PIERCE1 1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, U.S.A. and 2Mass Spectrometry Facility, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, U.S.A

Hierarchische Clusteranalyse - Wikipedi

  1. Information theory is a branch of mathematics that overlaps with communications, biology, and medical engineering. Entropy is a measure of uncertainty in the set of information. In this study, for each gene and its exons sets, the entropy was calculated in orders one to four. Based on the relative entropy of genes and exons, Kullback-Leibler divergence was calculated
  2. Classification by type of data. Phylogenetic trees can be mainly built using either distance-based methods or character-state methods. Distance-based methods infer the relationship between individuals as the number of genetic differences between pairs of sequences, whereas an array of character states is used in character-state methods
  3. o-acid substitutions between molecular sequences

Diefds 5d Diamant malerei bohrmaschine Drachen Mosaik Kreuzstich Stickerei Hause Dekorative Kunst 50X70CM günstig auf Amazon.de: Kostenlose Lieferung an den Aufstellort sowie kostenlose Rückgabe für qualifizierte Artike The dendrogram for WPGMC only differs from that of Figure 3b by the position of the last fusion level, which is at S = 0.3 instead of S = 0.317. The two forms of centroid clustering can lead to reversals. A reversal occurs when a later fusion occurs at a similarity value larger than that of the previous fusion. This phenomenon, whic Different functional dendrograms could be obtained from the same dissimilarity matrix depending on the clustering method used (UPGMA, WPGMA, UPGMC, WPGMC or Ward's method). We recommend using the framework developed by Mouchet et al clustering (WPGMC)10 In this paper, we primarily concern the performance of average (UPGMA), centroid (UPGMC) and median (WPGMC) method. Furthermore, we compare the performance thereof to other, mostly used agglomerative hierarchical clustering methods. The selected methods differ in the way of computing dissimilarity measure d between a new cluster and other remaining clusters in the.

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(e.g. UPGMA, UPGMC, WPGMC, single linkage, complete linkage, etc) and to then maximise the correlation between pairwise distances in trait space and pairwise distances across the dendrogram (the cophenetic correlation) (Blackburn et al. 2005). This could, for example, result in Eulicdean distance being chosen over Gower distance (in the case where all traits are continuous). In a related vein. Different distance measures are available for clustering analysis. This article describes how to perform clustering in R using correlation as distance metrics NTSYSpc 2.02e Implementation in Molecular Biodata Analysis (Clustering, Screening, and Individual Selection) Soleiman Jamshidi 1 + and Samira Jamshidi2 1 Department of Plant Protection, Miyaneh Branch, Islamic Azad University, Miyaneh, Iran 2 Islamic Azad University, Miyaneh, Iran Abstract. NTSYSpc is one of the most popular softwares being used in molecular genetic qualitative dat credit default swaps [Marti et al., 2015]) that price time se-ries of traded assets have a hierarchical correlation structure. Another well-known stylized fact is the non-Gaussianity o

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UPGMA - an overview ScienceDirect Topic

My suggestions are: Bluefor: Scandinavian General- Get to know how they play: mobile, exceptional infantry, but Swede's have the best tanks. Code:WPgMc. median: This is also known as the WPGMC algorithm. ward: uses the Ward variance minimization algorithm. see scipy.cluster.hierarchy.linkage for more information. ax - Axes in which to draw the plot, otherwise use the currently-active Axes. kwargs - other keyword arguments. All other keyword arguments are passed to matplotlib.axes.Axes. Various agglomeration methods (single linkage, WPGMC, WPGMA, complete linkage, UPGMA and UPGMC) were used to construct images based-dendrograms. The relevance was tested in relation to either the treatment of the plants (i.e. inoculated vs. non-inoculated), or according to their apparent health status. This table indicates the percentages of mis-clustered plants for each agglomeration method.

Agglomerative hierarchical cluster tree - MATLAB linkag

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Module: core.acquisition_scheme ¶ dmipy.core.acquisition_scheme.get_sh_order_from_bval (bval) ¶ Estimates minimum sh_order to represent data of given b-value. class dmipy.core.acquisition_scheme.DmipyAcquisitionScheme (bvalues, gradient_directions, qvalues, gradient_strengths, delta, Delta, TE, min_b_shell_distance, b0_threshold) ¶. Class that calculates and contains all information needed. Evolving from years of teaching experience by one of the top experts in vegetation ecology, Data Analysis in Vegetation Ecology aims to explain the background and basics of mathematical (mainly multivariate) analysis of vegetation data. The book lays out the basic operations involved in the analysis, the underlying hypotheses, aims and points of views In contrast, the UPGMC (unweighted pair group method using centroids) and WPGMC (weighted pair group method using centroids) methods have direct geometric interpretations when the objects are represented as patterns in a d-dimensional space. The centroid method assess the dissimilarity between two clusters by the distance between centroids. The UPGMC method measures distance in terms of the. requests Gower's median method, which is weighted pair-group method using centroids (WPGMC). Distance data are squared unless you specify the NOSQUARE option. SINGLE | SIN requests single linkage (nearest neighbor, minimum method, connectedness method, elementary linkage analysis, or dendritic method). To reduce chaining, you can use the TRIM.

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WPGMC and single-link clustering were equally unsuccessful in detecting dialectological structure. Figure 6: Top left map: 2-way division produced by UPGMA, WPGMA and Ward's method. Top right map: 6-way division produced by UPGMA. Bottom maps: 6-way divisions produced by WPGMA and Ward's method respectively. Table 2: Cophenetic correlation coefficient Algorithm CCC p single link 0.7804 0. O. Nakoinz, Zentralortforschung und zentralörtliche Theorie. Arch. Korrbl. 39, 2009, 361-38

(= WPGMA), median (= WPGMC) or centroid (= UPGMC). dist.matrix A matrix with calculated distances to be used as a metric by hclust function. topGO A number of the most characteristic functions of groups of genes to be returned. sig.levelTUK A numeric value, a significance level used in Tukey's all pairwise comparison (groupByTukey). onto An ontology or ontologies to be searched for. WPGMC 1=21=2 1=40 Fig. 2. Algorithm comparison. JEON AND YOON: MULTI-THREADED HIERARCHICAL CLUSTERING BY PARALLEL NEAREST-NEIGHBOR CHAINING 2535. The NN-chain algorithm starts a chain from an arbitrary (singleton) cluster and grows the chain until discovering an RNN pair at the growing end of the chain (Fig. 3). The algo- rithm then merges the two clusters forming the discovered RNN pair into. WPGMC Hun 2017 - Ene 2019 1 taon 8 buwan. Edukasyon Asia-Pacific International University Asia-Pacific International University Bachelor's degree Computer Software Engineering Well deserve and Earned Excellence . 2002 - 2006. Just a regular person amongst others, who constantly made mistakes, but thrives to improve myself to its very best and eventually will rise beyond expectations. Alot had. ## ## @item median ## Weighted pair-group method using centroids (WPGMC). ## Assumes Euclidean metric. Distance between cluster centroids. When ## two clusters are joined together, the new centroid is the midpoint ## between the joined centroids. ## ## @item ward ## Ward's sum of squared deviations about the group mean (ESS)

cluster.snp: Hierarchical Clustering of SNP Data in ..

  1. troid (WPGMC) and unweighted centroid (UPGMC). Importantly, it contains a new parameter-ized method named versatile linkage, which includes single linkage, complete linkage and average linkage as particular cases, and which naturally defines two new methods, geometric linkage and harmonic linkage (hence the convenience to rename average linkage as arithmetic linkage, to em- phasize the.
  2. plete, average (= UPGMA), mcquitty (= WPGMA), median (= WPGMC) or centroid (= UPGMC). Usage TCGAanalyze_Clustering(tabDF, method, methodHC = ward.D2) Arguments tabDF is a dataframe or numeric matrix, each row represents a gene, each column rep-resents a sample come from TCGAPrepare. method is method to be used for generic cluster such as 'hclust' or 'consensus' methodHC is.
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  5. An object of class heatmapr includes all the needed information for producing a heatmap. The goal is to separate the pre-processing of the heatmap elements from the graphical rendering of the object, which could be done (Please submit an issue on github if you have a feature that you wish to have added) heatmaply_na is a wrapper for `heatmaply` which comes with defaults that are better for.
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en:hier-agglom_r [Analysis of community ecology data in R

median: the median/WPGMC algorithm. (alias) ward: the Ward/incremental algorithm. (alias) Distance matrix computation from a collection of raw observation vectors. pdist: computes distances between each observation pair D wardD2 single complete average UPGMA mcquitty WPGMA median WPGMC or centroid. D wardd2 single complete average upgma mcquitty wpgma. School The University of Queensland; Course Title INFS 4203; Uploaded By MagistrateMole7217. Pages 18 Ratings 100% (1) 1 out of 1 people found this document helpful; This preview shows page 14 - 17 out of 18 pages. of) one of ward.D, ward.D2, single. the weighted pair-group method using centroids (WPGMC), and two variants of ward's minimum variance method (ward.D and ward.D2). The degrees of data distortion from the eight methods were then assessed based on cophenetic correlation coe cients (Sokal and Rohlf 1962). Pairwise distances between sampling sites were calculated in the \vegan package ((Oksanen, et al. 2013), and clustering was.

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Vážený centroid skupin dvojic (WPGMC) - vážená vzdálenost dvou centroidů (váhy se určují podle velikosti shluků). Wardova metoda - odlišný přístup oproti předešlým, založený na principu analýzy rozptylu. Počítá součet druhých mocnin odchylek případů v potenciálním sloučeném shluku od centroidu. Sloučí ty dv

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