예: "maximal" Description. X=rand(10,2); dists=pdist(X,'euclidean'); It’s a nice function but the problem with it is that it is part of the Statistics Toolbox and that costs extra. These are basically 70,000 vectors of 300 elements each. The pdist_inputs argument consists of the 'seuclidean', 'minkowski', or 'mahalanobis' metric and an additional distance metric option. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. You’ll start by getting your system ready with t he MATLAB environment for machine learning and you’ll see how to easily interact with the Matlab. D = seqpdist (Seqs) returns D , a vector containing biological distances between each pair of sequences stored in the M sequences of Seqs , a cell array of sequences, a vector of structures, or a matrix or sequences. Share. 2954 1. weightFcn to 'dist'. The tutorial purpose is to teach you how to use the Matlab built-in functions to calculate the statistics for different data sets in different applications; the tutorial is intended for users running a professional version of MATLAB 6. For example, you can find the distance between observations 2 and 3. Share. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. Sign in to answer this question. This course indicates that having 10000 features makes sense. This MATLAB function returns the Euclidean distance between pairs of observations in X. . Well, I guess there are two different ways to calculate mahalanobis distance between two clusters of data like you explain above: 1) you compare each data point from your sample set to mu and sigma matrices calculated from your reference distribution (although labeling one cluster sample set and the other reference distribution may be arbitrary. Z = linkage (meas, 'average', 'chebychev' ); Find a maximum of three clusters in the data. pdist(X, metric='euclidean', *args, **kwargs) [source] ¶. The Chebyshev distance between two n-vectors u and v is the maximum norm-1 distance between their respective elements. In human motion analysis, a commond need is the computation of the distance between defferent point sets. MATLAB Language Fundamentals Matrices and Arrays Resizing and Reshaping Matrices. Add a comment. 6 Why does complex Matlab gpuArray take twice as much memory than it should? 1 Different behaviour for pdist and pdist2. % Call a mex file to compute distances for the standard distance measures % and full real double or single data. 6 (7) 7. Generate C code that assigns new data to the existing clusters. I'd like to compute the average distance between each observation in my matrix, but pdist() fails here, because app. clear A = rand (132,6); % input matrix diss_mat = pdist (A,'@kullback_leibler_divergence'); % calculate the. 创建包含三个观测值和两个变量的矩阵。 rng ( 'default') % For reproducibility X = rand (3,2); 计算欧几里德距离。 D = pdist (X) D = 1×3 0. 9448. Add a comment. The code is fully optimized by vectorization. My problem is pdist2 doesn't like that the column length is different. I'm not sure whether that's pairwise for every one of your 262322*4 (=1049288) elements, but if so then a matrix of doubles 1049228^2 in size is hundreds of GB, clearly not going to fit in RAM. I need to build a for loop to calculate the pdist2 between the first row of A and all the rows of B, the second row of A and all. 2954 1. A Nearest neighbor search locates the k -nearest neighbors or all neighbors within a specified distance to query data points, based on the specified distance metric. 2. Las funciones de peso aplican pesos a una entrada para obtener entradas ponderadas. First, create the distance matrix and pass it to cmdscale. Hey guys, I'm trying to do hierarchical clustering in MATLAB using linkage and pdist funcitons. 0. The goal of implementing a parallel function similar in functionality to the Matlab sequential pdist function [3] was to speedup computation of ˜ D employing Parallel Computing Toolbox. This norm is also. Theme. 9448. 9448. I have a 70,000 x 300 matrix. Find more on Shifting and Sorting Matrices in Help Center and File Exchange. 13. – Nicky Mattsson. 0000 To make it easier to see the relationship between the distance information generated by pdistand the objects in the original data set, you can reformat the distance vector into a matrix using thesquareformfunction. e. '; If the diagonal of is zerod then one could reproduce mX from vX using MySquareForm(). Find more on Random Number Generation in Help Center and File Exchange. Thanks. For example if matrix A was 102x3 and Matrix B was 3x15, is there a MATLAB function that can do this calculation for me or do I need to use nested for loops? 0 Comments Show -1 older comments Hide -1 older commentsDescription. ParameterSpace object as an input to the sdo. Hi, So if I have one 102x2 matrix of x,y coordinates, and another 102x2 matrix of x,y coordinates, can pdist be used to compare all the rows in matrix 1 with the rows in matrix 2? As in for matrix. Matlab provides a knnsearch function that uses K-D-trees for this exact purpose. For example I have a data set S which is a 10*2 matrix , by using pdist(S(:,1)) and pdist(S(:,2)) to get the. txt format. Y = pdist(X) computes the Euclidean distance between pairs of objects in m-by-n matrix X, which is treated as m vectors of size n. Distance is calculated using two distance funstions: Haversine and Pythagoran. Also, you are using anonymous function handles and conversions to and from cell arrays, all of which slow the process down. Rows of X and Y correspond to observations, That is, it works on the ROWS of the matrices. As you can read in the docs, you have some options, but haverside distance is not within the list of supported metrics. pdist2 Pairwise distance between two sets of observations. m. inputWeights{i,j}. Basically it compares two vectors, say A and B (which can also have different. rng ( 'default') % For reproducibility X = rand (3,2); Compute the Euclidean distance. For MATLAB's knnsearch, X is a 2D array that consists of your dataset where each row is an observation and each column is a variable. pdist2 Pairwise distance between two sets of observations. r is the position of points in 2D. P is the input vector Z is the weighted input. layerWeights{i,j}. This syntax returns the standard distance as a linear distance in the same units as the semimajor axis of the reference ellipsoid. 1. I need to add a toolbox to the existing installation. dist = stdist (lat,lon,ellipsoid,units,method) specifies the calculation method. MATLAB - passing parameters to pdist custom distance function. CanberraSimilarity. – am304. Puede especificar DistParameter solo cuando Distance sea 'seuclidean', 'minkowski' o 'mahalanobis'. The distance function must be of the form d2 = distfun(XI,XJ), where XI is a 1-by-n vector corresponding to a single row of the input matrix X, and XJ is an m 2-by-n matrix corresponding to multiple rows of X. 0. The software generates these samples using the distributions specified for each. 计算 X 中各对行向量的相互距离 (X是一个m-by-n的矩阵). 7 249] these are (x, y, z) coordinates in mm, What is the easiest way to compute the distance (mm) between these two points in matlab, Thanks. Finally, there is a function called pdist that would do everything for you :. How can I install an additional "Statistic and ML" toolbox into an existing installation of MATLAB on the _offline_ machine? 1 Comment. tree = linkage (X, 'average' ); dendrogram (tree,0) Now, plot the dendrogram with only 25 leaf nodes. . Generate Code. ¶. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. 否则，pdist 使用标准算法来计算欧几里德距离。 如果距离参数为 'fasteuclidean'、'fastsquaredeuclidean' 或 'fastseuclidean'，并且 cache 值太大或为 "maximal"，则 pdist 可能会尝试分配超出可用内存容量的格拉姆矩阵。在这种情况下，MATLAB ® 会引发错误。 示例： "maximal" Sort Classes by Precision or Recall. 5,First, Pdist Pairwise distance between pairs of objects Syntax D = Pdist (X) D = Pdist (x,distance) Description D = Pdist (X) Calculates the distance between each pair of row vectors in X (x is a m-by-n matrix). TagsObjectives: 1. BUT: The code shown here is 10-100 times faster, utilizing the. The sizes of A and B must be the same or be compatible. Different behaviour for pdist and pdist2. I want to calculate the Jaccard similarity in Matlab, between the vectors A, B, C and D. MATLAB contains a function called pdist that calculates the ‘Pairwise distance between pairs of objects’. For example, you can find the distance between observations 2 and 3. @alirazi In pdist, each row is an observation. . The builtin pdist gets about 15:1, but still runs much slower overall (on a dual-cpu 16-core machine). If the sizes of A and B are compatible, then the two arrays implicitly expand to match each other. Z = linkage(Y) creates a hierarchical cluster tree, using the Single Linkage algorithm. Fowzi barznji on 16 Mar 2020. Hi everyone. For example, you can find the distance between observations 2 and 3. I have a set of points from a complex function that I am trying to produce a 3D shape of, and have had no luck so far. As for the PDist itself, it does appear to have some construct support for. Basically it compares two vectors, say A and B (which can also have different lengths) and checks if their elements "co-occur with tolerance": A(i) and B(j) co-occur with tolerance tol if. load patients X = [Age Weight]; Y = [20 162; 30 169; 40 168]; % New patients. For example, you can find the distance between observations 2 and 3. To match the centroids, you can use the "matchpairs" function, which finds the indices of the closest pairs of points. I'm trying to use the pdist2 function and keep getting this error: "??? Undefined function or method 'pdist2' for input arguments of type 'double'" The 'double' part changes depending on what data. Now, it is confirmed that I do not have a license. All the points in the two clusters have large silhouette values (0. I'm familiar with the functions, but I'm attempting to cluster by the absolute value of the correlation values. Learn more about clustergram, pearson correlation, pdist, columnpdist, rowpdist MATLAB, Bioinformatics Toolbox I am doing the Hierarchical cluster analysis. This function will compute the pairwise distance between every two points in your array. Nov 8, 2013 at 9:26. Add a comment. |x intersect y| indicates the number of common items which. I'm producing m amount of nx1 vectors, and storing them all in an nxm matrix A (each column is a vector). Given the matrix mx2 and the matrix nx2, each row of matrices represents a 2d point. When the values of X are all real numbers (as is the case here), this is the same as the basic transpose function. y = squareform(Z) y = 1×3 0. % Autor: Ana C. function Distance = euclidean (x,y) % This function replaces the function pdist2 available only at the Machine. Z = dist (W,P) takes an S -by- R weight matrix, W, and an R -by- Q matrix of Q input (column) vectors, P, and returns the S -by- Q matrix of vector distances, Z. T = cluster (Z, 'maxclust' ,3); Create a dendrogram plot of Z. Y = pdist (X, 'canberra') Computes the Canberra distance between the points. of matlab I do not have the pdist2 function. D is a 1 -by- (M* (M-1)/2) row vector corresponding to the M* (M-1)/2 pairs of sequences in Seqs. ParameterSpace to specify the probability distributions for model parameters that define a parameter space for sensitivity analysis. Note that generating C/C++ code requires MATLAB® Coder™. distance. . MATLAB compatibility module. You can use the ' pdist' function to calculate the pairwise distance between time series using the DTW distance metric. the clusters match with the labels) if compared to using the original. Basically it compares two vectors, say A and B (which can also have different. See Also. This example shows how to use cmdscale to perform classical (metric) multidimensional scaling, also known as principal coordinates analysis. A. I would like to sort these using the DTW algorithm. ) The -r switch is also supported for Windows Enhanced Metafiles but is not supported for Ghostscript. If we want to calculate the Minkowski distance in MATLAB, I think we can do the following (correct me if I'm wrong): Theme. 1 MATLAB - passing parameters to pdist custom distance function. pdist is working fine and the stats toolbox is set in the path. between each pair of observations in the MX-by-N data matrix X and. The most efficient pairwise distance computation. Calculate the pixel distance to three defined pixel in matlab. For example, you can find the distance between observations 2 and 3. Ridwan Alam on 20 Nov 2019. Generate Code. cmdscale takes as an input a matrix of inter-point distances and creates a configuration of points. with loops, something like this will work:Description. The built in linear algebra methods in Matlab 2016a are pretty efficient and well parallelized. a = a*1-48; b = b*1-48; dist = sum (bitxor (a,b),2); end. Z is a matrix of size (m– 1)-by-3, with distance information in the third column. What I want is to now create an mxm matrix B where B(i,j) = norm(vi -vj). Specify a cell array if the distance metric requires extra arguments. Distance metric to pass to the pdist function to calculate the pairwise distances between columns, specified as a character vector or cell array. MATLAB Vectorised Pairwise Distance. To see the three clusters, use 'ColorThreshold' with a cutoff halfway between the third-from-last and. 欧氏距离(Euclidean Distance) 欧氏距离是最易于理解的一种距离计算方法，源自欧氏空间中两点间的距离公式。(1)二维平面上两点a(x1,y1)与b(x2,y2)间的欧. For example running my code I get a ratio of 11:1 for cputime to walltime. pdist(x) computes the Euclidean distances between each pair of points in x. To save your figure as a graphics-format file, specify a format switch and filename. y = squareform (Z) squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. c = cophenet(Z,Y) Description. You can use one of the following methods for your utility: norm (): distance between two points as the norm of the difference between the vector elements. Statistics and Machine Learning Toolbox™ offers two ways to find nearest neighbors. Idx = knnsearch (X,Y) finds the nearest neighbor in X for each query point in Y and returns the indices of the nearest neighbors in Idx, a column vector. Description. If it is then you could also use them depending what level of accuracy you requie. 否则，pdist 使用标准算法来计算欧几里德距离。 如果距离参数为 'fasteuclidean'、'fastsquaredeuclidean' 或 'fastseuclidean'，并且 cache 值太大或为 "maximal"，则 pdist 可能会尝试分配超出可用内存容量的格拉姆矩阵。在这种情况下，MATLAB ® 会引发错误。 示例： "maximal"silhouette (X,clust) The silhouette plot shows that the data is split into two clusters of equal size. It computes the distances between rows of X. Este argumento se aplica solo cuando Distance es 'fasteuclidean', 'fastsquaredeuclidean' o 'fastseuclidean'. The input Z is the output of the linkage function for an input data matrix X . find (T==7) ans = 7×1 7 33 60 70 74 76 86. EDIT: Context. T = cluster (Z, 'maxclust' ,3); Create a dendrogram plot of Z. See Elements of Statistical Learning by Rob Tibshirani. The Euclidean distance between two vectors b. You need to understand what those numbers mean before anything else is useful. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. Learn more about distance bigdata MATLAB So I have a matrix that is 330,000 observations = rows x 160 variables = columns. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. Currently I am using bsxfun and calculating the distance as below ( i am attaching a. I used Python to find the points in a . Description. Weight functions apply weights to an input to get weighted inputs. This example shows how to construct a map of 10 US cities based on the distances between those cities, using cmdscale. numberPositionsDifferent = size (A,2)*pdist (A,'hamming'); If that's not what you meant, you might want to give more information (including the answer to Walter's. If you realize that. 0. Otherwise consider this equivalent vectorized code (using only built-in functions):matlab use my own distance function for pdist. use. MY-by-N data matrix Y. I want to cluster the above four sentences to see which are more similar. Note that generating C/C++ code requires MATLAB® Coder™. Pass Z to the squareform function to reproduce the output of the pdist function. Para la generación de código, defina una función de punto de entrada que acepte las posiciones de los centroides de los grupos y el nuevo conjunto de datos, y devuelva el índice del grupo más cercano. If I have two points in 3d, A = [1579. Contact Sales. squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. In a MATLAB code I am using the kullback_leibler_divergence dissimilarity function that can be found here. Currently avaliable codes in FEX are also insufficient as they can only compute (squared. Note that generating C/C++ code requires MATLAB® Coder™. To see the three clusters, use 'ColorThreshold' with a cutoff halfway between the third-from-last and. I suspect that the solution is to calculate distribution matrices on subsets of the data and then fuse them together, however, I am not sure how to do this in a way that. [D,idx] = bwdist (BW) also computes the closest-pixel map in the form of an index array, idx. 0. For this you don't need to use pdist function when calling kmedoid, You can simply pass the function handle of your custom function (dtwdist) and get your output. I want to deal with 500x500m scale global data in Matlab. Your a matrix is a 1D vector and is incompatible with the nested loop, which computes distance in 2D space from each point to each other point. Search Help. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. spatial. pdist2 (X,Y,Distance): distance between each pair of observations in X and Y using the metric specified by Distance. Generate C code that assigns new data to the existing clusters. See Also. I need standard euclidean distance between two vectors. By default, mdscale uses Kruskal's. Pass Z to the squareform function to reproduce the output of the pdist function. hi, I am having two Images I wanted compare these two Images by histograms I have read about pdist that provides 'chisq' but i think the way i am doing is not correct, and what to do to show the result afterwards because this is giving a black image. Sign in to comment. Python: Dendogram with Scipy doesn´t work. I'm doing this because i want to know which point has the smallest average distance to all the other points (the medoid). You can loop through the coordinate locations (i. The generated code of pdist uses parfor (MATLAB Coder) to create loops that run in parallel on supported shared-memory multicore platforms in the generated code. pdist. There is no in-built MATLAB function to find the angle between two vectors. ^2); issymmetric (S) ans = logical 1. Pairwise distances between observations, specified as a numeric row vector that is the output of pdist, numeric square matrix that is the output of pdist2, logical row vector, or logical square matrix. 거리 인수가 'fasteuclidean', 'fastsquaredeuclidean' 또는 'fastseuclidean'이고 cache 값이 너무 크거나 "maximal"인 경우, pdist 함수는 사용 가능한 메모리를 초과하는 그람 행렬을 할당하려고 시도할 수 있습니다. Construct a Map Using Multidimensional Scaling. For a dataset made up of m objects, there are pairs. hi, I am having two Images I wanted compare these two Images by histograms I have read about pdist that provides 'chisq' but i think the way i am doing is not correct, and what to do to show the result afterwards because this is giving a black image. % Autor: Ana C. 21. Z (2,3) ans = 0. Utilice kmeans para crear grupos en MATLAB® y utilice pdist2 en el código generado para asignar nuevos datos a grupos existentes. d(u, v) = max i | ui − vi |. Description. Supervised and semi-supervised learning algorithms for binary and multiclass problems. To obtain the combinations of all point pairs (without repetitions), use nchoosek: pairs = nchoosek (1:size (A, 2), 2) Then calculate the Euclidean distance like so:Hierarchical Clustering Correlations - Pdist Fnc. {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"+local","path":"+local","contentType":"directory"},{"name":"+lp","path":"+lp","contentType. Right-click Group 18, then select Export Group to Workspace. pdist and pdist2 can calculate the city block distance. pdist_oneLine. 2. Sign in to answer this question. Try something like E = pdist2 (X,Y-mean (X),'mahalanobis',S); to see if that gives you the same results as mahal. The output, Y, is a. com account, please see github. , 'PropertyName', PropertyValue,. Show -1 older comments Hide -1 older comments. How can I calculate the 399x399 matrix with all distances between this 399 cities?. See Also. @Masi step 1 is to understand what the results of pdist are. T = cluster (Z, 'maxclust' ,3); Create a dendrogram plot of Z. This function fully supports thread-based environments. The sizes of A and B must be the same or be compatible. Note that generating C/C++ code requires MATLAB® Coder™. I would like to make a loop that computes a distance between all matrix arrays, and save them in a distance matrix. Learn more about custom distance function, pdist, pdist2, @distfun, divergence, kl divergenceGenerate Code. Syntax. . HC1992 on 6 Feb 2018. 2 Answers. Z (2,3) ans = 0. Note that generating C/C++ code requires MATLAB® Coder™. There are 100 data points in the original data set, X. Add the %#codegen compiler directive (or pragma) to the entry. which -all pdist will list all the pdist MATLAB files in your MATLAB path. I'm trying to use the pdist2 function and keep getting this error: "??? Undefined function or method 'pdist2' for input arguments of type 'double'" The 'double' part changes depending on what data. 5 4. Not exactly. . awpathum. (Matlab) Dimensional indexing using indices returned by min function. basically it is used a*1-48 is converting a binary string to row vector so that we can use. Classification is a type of supervised machine learning in which an algorithm “learns” to classify new. distance. loop on matrix array. Generate Code. Una métrica de distancia es una función que define la distancia entre dos observaciones. Learn more about knn, pdist, fitcknn, k-nearest neighbor, inverse distance weighting, euclidean distance Statistics and Machine Learning Toolbox I have this distance matrix for kNN points (given from the function pdist()) and I'm trying to predict if point 6 is either ‘unacceptable’ or ‘acceptable’ using the kNN technique with the 3. El código generado de pdist usa parfor (MATLAB Coder). Y contains the distances or dissimilarities used to construct Z, as output by the pdist function. You can achieve that if you. More precisely, the distance is given by. 1. e. I find that dist function is the best on in less time. Cophenetic correlation coefficient. Learn more about pdist, euclidean distance, too large MATLAB. PDIST and SQUAREFORM are functions from the Statistics Toolbox. 9448. Note that generating C/C++ code requires MATLAB® Coder™. Create a hierarchical cluster tree using the 'average' method and the 'chebychev' metric. I am using the Matlab function pdist to calculate the distance between two points. See Also. There are 100 data points in the original data set, X. Here d is to pay special attention to the fact that D is a line vector long m (m–1)/2. This function can do both - it will function like pdist if only one set of observations is provided and will function like pdist2 if two. To change a network so an input weight uses dist, set net. Helllo. The first output is based on Haversine function, which is more accurate especially for longer distances. Learn more about astronomy, pattern matching, stars Hi, I am relatively new to Matlab, and I have a question regarding the function pdist(), I have a following code: % RA Dec. Copy. spatial. Now I want to create a mxn matrix such that (i,j) element represents the distance from ith point of mx2 matrix to jth point of nx2 matrix. Find the distance between each pair of observations in X by using the pdist and squareform functions with the default Euclidean distance metric. 1. Sign in to answer this question. The behavior of this function is very similar to the MATLAB linkage function. My one-line implementation of both MATLAB's pdist and pdist2 functions which compute the univariate (pdist) or bivariate (pdist2) Euclidean distances between all pairs of input observations. For 8192 partcies the pdist version of this averaging is 2 seconds, while the suggested averaging takes 2 minutes. 2. Pass Z to the squareform function to reproduce the output of the pdist function. 3. Function "pdist" in Matlab. [arclen,az] = distance (pt1,pt2) calculates the arc length and azimuth from the starting point with coordinates pt1 and ending point with coordinates pt2. calculate_distance. Z (2,3) ans = 0. Goncalves. Product of a multi-dimensional array (or tensor) and vectors. Z = linkage(X,method,pdist_inputs) passes pdist_inputs to the pdist function, which computes the distance between the rows of X. Calculating cosine distance between the rows of matrix. given subscripts of an array with size SZ. Option 1 - pdist. Sorted by: 3. The Canberra distance between two points u and v is. how can I add a dot product as a distance function in pdist of matlab. dim = dist ('size',S,R,FP) takes the layer dimension S, input dimension R, and function. For example, list A has 50 xyz coordinates and list B has 50 xyz coordinates and I want to know the distance for each coordinate in list A to all of the 50 coordinates in list B. matlab use my own distance function for pdist. Accepted Answer. Z = linkage(Y,'single') If 0 < c < 2, use cluster to define clusters from. In Matlab there exists the pdist2 command. d(u, v) = max i | ui − vi |. Pairwise Distance Matrix. 0670 0. The resulting vector has to be put into matrix form using squareform in order to find the minimal value for each pair: N = 100; Z = rand (2,N); % each column is a 2-dimensional. It will do what you want, but is kind of overkill. In human motion analysis, a commond need is the computation of the distance between defferent point sets. Minkowski's distance equation can be found here. Z is the output of the linkage function. % n = norm (v) returns the Euclidean norm of vector v. Then execute 'memory' command in the Command Window and send the output. MATLAB use custom function with pdist. Generate C code that assigns new data to the existing clusters. 这里 D 要特别注意，D 是一个长为m (m–1)/2的行向量. ^2 ). 7. Follow. Generate Code. For example, you can find the distance between observations 2 and 3. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. Find the largest index of the minimum in Matlab. 1 Different behaviour for pdist and pdist2. 8 or greater), indicating that the clusters are well separated. Add the %#codegen compiler directive (or pragma) to the entry. I am looking for an alternative to this in. Rows of X and Y correspond to observations, That is, it works on the ROWS of the matrices. Generate C code that assigns new data to the existing clusters. This approximate integration yields a final value of 42. Different behaviour for pdist and pdist2. Hi folks, I have very large matrices in the order of 100k+ rows and even more columns containing only 3 possible integer values 0, 1, 2, most frequent of which is 0. c = cophenet(Z,Y) computes the cophenetic correlation coefficient which compares the distance information in Z, generated by linkage, and the distance information in Y, generated by pdist. ) Y = pdist(X,'minkowski',p) Description . sorry for the delayed reply. LatLon distance. Explanation: pdist (S1,'cosine') calculates the cosine distance between all combinations of rows in S1.