Find the treasures in MATLAB Central and discover how the community can help you!Dendrograms using clustergram vs traditional ways in Matlab. Get an overview of what functions in MATLAB® are, and learn how to use them. Define and Use Enumerations. 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. Find the patients in the patients data set that are within a certain age and weight range of the patients in Y. [arclen,az] = distance (pt1,pt2) calculates the arc length and azimuth from the starting point with coordinates pt1 and ending point with coordinates pt2. Python: Dendogram with Scipy doesn´t work. 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. This is consistent with, for example, the R dist function, as well as MATLAB, I believe. Euclidean distance between two points. Note that generating C/C++ code requires MATLAB® Coder™. This example shows how to construct a map of 10 US cities based on the distances between those cities, using cmdscale. I was told that by removing unnecessary for loops I can reduce the execution time. See Also. Rows of X and Y correspond to observations, That is, it works on the ROWS of the matrices. Solution 1: In fact it is possible to have dynamic structures in Matlab environment too. 1 How to use KNN in Matlab. @Masi step 1 is to understand what the results of pdist are. 9 I need to calculate the euclidean distance between 2 matrices in matlab. There are 100 data points in the original data set, X. The Mahalanobis distance from a vector y to a distribution with mean μ and covariance Σ is. sz = size (A); A1 = reshape (A, [1 sz]); A2 = permute (A1, [2 1 3]); D = sqrt (sum (bsxfun (@minus, A1, A2). y = squareform (Z) squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. Supervised and semi-supervised learning algorithms for binary and multiclass problems. Or you can do k mediods which works with a distance matrix - as. At higher values of N, the speed is much slower. I would like to use the linkage function in matlab with a custom distance. 0. subscripts. 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. I studied about pdist2 function , I used it : Theme. Currently avaliable codes in FEX are also insufficient as they can only compute (squared. 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. Contact Sales. Find the largest index of the minimum in Matlab. The pdist(D) gives the sum of the distance of the multiple dimension, however, I want to get the distance separately. Z is a matrix of size (m-1)-by-3, with distance information in the third column. More precisely, the distance is given by. 예: "maximal" Description. function D2 = distfun(ZI,ZJ) where. 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. 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. 231 4 13. Copy. (2 histograms) into a row vector and then I used pdist formulas. 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. We can turn that into a square matrix where element (i,j) corresponds to the similarity between rows i and j with squareform (1-pdist (S1,'cosine')). You can try the following workarounds: 1. D is a 1 -by- (M* (M-1)/2) row vector corresponding to the M* (M-1)/2 pairs of sequences in Seqs. Would be cool to see what you have in python, and how it compares. Which is "Has no license available". Description. If it is then you could also use them depending what level of accuracy you requie. Use cumtrapz to integrate the data with unit spacing. The pdist function in MatLab, running on an AWS cloud computer, returns the following error: Requested 1x252043965036 (1877. The patristic distances are computed by following paths through the branches of the tree and adding the patristic branch distances originally created with the seqlinkage function. There are various ways to do this. Pass Z to the squareform function to reproduce the output of the pdist function. Generate Code. which -all pdist will list all the pdist MATLAB files in your MATLAB path. Upgrade is not an option. 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. Which is "Has no license available". 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. between each pair of observations in the MX-by-N data matrix X and. 357 views (last 30 days) Show older comments. For example, if one of A or B is a scalar, then the scalar is combined with each element of the other array. Share. So, you showed the formula for the square of the distance. Return the mapping of the original data points to the leaf nodes shown in the plot. If we want to calculate the Minkowski distance in MATLAB, I think we can do the following (correct me if I'm wrong): dist=pdist ( [x (i);y (j)],'minkowski'); Up till here, the above command will do the equation shown in the link. % n = norm (v) returns the Euclidean norm of vector v. Generate C code that assigns new data to the existing clusters. From pdist documentation (emphasis mine):. For example |A| number of items that is not zero is 2, for |B| and |C| it is 1, and for |D| it is 2. Hi, I'm trying to perform hierarchical clustering on my data. (Matlab) Dimensional indexing using indices returned by min function. (Matlab pdist does support the option though, see here) you need to do the calculation "manually", i. Go to MATLAB > Preferences > Workspace and ensure the Maximum array size limit is set to 100%. Really appreciate if somebody can help me. What I want is to now create an mxm matrix B where B(i,j) = norm(vi -vj). As with MATLAB(TM), if force is equal to 'tovector' or 'tomatrix', the input will be treated as a distance matrix or distance vector respectively. if ~exist ('xtemp') xtemp = A1*rand (1,N); ytemp = A1*rand (1,N); end. 0. BUT: The code shown here is 10-100 times faster, utilizing the. Hooray!!! You have just reached the end of this article. Implement Matlab functions for comparing two vectors in terms of: a. y = squareform (Z) Create a matrix with three observations and two variables. Contrary to what your post says, you can use the Euclidean distance as part of pdist. pdist -> linkage -> dendrogram I found they are different, but cannot find an explanation for that difference. In thismatlab中自带的计算距离矩阵的函数有两个pdist和pdist2。 前者计算一个向量自身的距离矩阵，后者计算两个向量之间的距离矩阵。 基本调用形式如下： D=pdist(X) D=pdist2(X,Y) 这两个函数都提供多种距离度量形式，非常方便，还可以调用自己编写的距离. >>> x = np. Typical usage is. Learn more about pdist, matrix, matrix manipulation, distances MATLAB, Statistics and Machine Learning Toolbox. This is my forst class using the app and I am at beginner level, so please bear with me ;) (Also, english. cityblockSimilarity. {"payload":{"allShortcutsEnabled":false,"fileTree":{"classify":{"items":[{"name":"private","path":"classify/private","contentType":"directory"},{"name":"Contents. 3541 2. If you believe that you should have this licence, contact mathworks support. Using pdist with two matrix's. The matrix with the coordinates is formatted as: points [ p x n x d ]. Then pdist returns a [3 x 3] D matrix in which the (i, j) entry represents the distance between the i-th observation in X and the j-th. Goncalves. squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. Answered: Muhammd on 14 Mar 2023. Distance metric to pass to the pdist function to calculate the pairwise distances between columns, specified as a character vector or cell array. is there an alternative to pdist2 that calculates the distance between a matrices with different column numbers. If you want to not recalculate xtemp and ytemp when the script is re-run, use exist. . From there, I copy the data to Excel to transpose the columns into rows for Matlab use. 1 Matlab pdist2 : Out of memory. distance import pdist dm = pdist(X, lambda u, v: np. 2. example. Given the matrix mx2 and the matrix nx2, each row of matrices represents a 2d point. 0670 0. Z = linkage(X,method,pdist_inputs) passes pdist_inputs to the pdist function, which computes the distance between the rows of X. 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. how can I add a dot product as a distance function in pdist of matlab. {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"+local","path":"+local","contentType":"directory"},{"name":"+lp","path":"+lp","contentType. Using pdist with two matrix's. Thanks for your help. Y = pdist(X) Y = pdist(X,'metric') Y = pdist(X,distfun,p1,p2,. Commented: Walter Roberson on 6 Feb 2014. Show 1 older comment Hide 1 older comment. Z = linkage(Y,'single') If 0 < c < 2, use cluster to define clusters from. Learn more about for loop, matrix array MATLAB. Description. tutorial, we assume that you know the basics of Matlab (covered in Tutorial 1) and the basics of statistics. pdist and pdist2 can calculate the city block distance. The results are not the best in the world as I used LBP (Local. This syntax is equivalent to [arclen,az] = distance (pt1 (:,1),pt1 (:,2),pt2. If you want this to be stable between MATLAB sessions, save your tag points to file and tell the script to load the file if those variables aren't in the workspace. % Learning toolbox. The angle between two vectors Deliverables: - Your code for 'eucdist' contained in 'eucdist. This norm is also. Create a hierarchical cluster tree using the 'average' method and the 'chebychev' metric. m. e. xA etc. Sorted by: 1. of matlab I do not have the pdist2 function. I need the distance matrix (distances between each pair of vectors). sqrt(((u-v)**2). Pairwise distance between observations. out = pdist(X, 'euclidian') 0. 0. 2954 1. What I want is to now create an mxm matrix B where B(i,j) = norm(vi -vj). Find more on Random Number Generation in Help Center and File Exchange. 2 Answers. Generate C code that assigns new data to the existing clusters. You will need to look for it in the code you are using, and then put the function somewhere in your MATLAB search path. I know matlab has a built in pdist function that will calculate pairwise distances. Hot Network QuestionsGraphics Format Files. I searched for the best-optimized way of calculating distance between point. Different behaviour for pdist and pdist2. The builtin pdist gets about 15:1, but still runs much slower overall (on a dual-cpu 16-core machine). MY-by-N data matrix Y. In this example, D is a full distance matrix: it is square and symmetric, has positive entries off the diagonal, and has. The statstics toolbox offers pdist and pdist2, which accept many different distance functions, but not weighting. This example shows how to construct a map of 10 US cities based on the distances between those cities, using cmdscale. 13. cophenet. Typical usage is X=rand (10,2); dists=pdist. I agree with Tal Darom, pdist2 is exactly the function you need. However i have some coordinates that i cannot remove from the matrix, but that i want pdist to ignore. Follow. between each pair of observations in the MX-by-N data matrix X and. dim = dist ('size',S,R,FP) takes the layer dimension S, input dimension R, and function. Syntax. Fowzi barznji on 16 Mar 2020. I believe that pdist does this automatically if you provide more than 2 points, as seen in the first example on the linked page: % Compute the Euclidean distance between pairs of observations, and convert the distance vector to a matrix using squareform. distance. Documentation. Impute missing values. If your compiler does not support the Open Multiprocessing (OpenMP) application interface or you disable OpenMP library, MATLAB Coder™ treats the parfor -loops as for -loops. 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. MATLAB pdist function. 2 Answers. 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. A question and answers forum for MATLAB users to discuss various topics, including the pdist function that calculates the distance between points in a matrix. Specify a cell array if the distance metric requires extra arguments. 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. EDIT: Context. The builtin function `pdist2` could be helpful, but it is inefficient for multiple timeframes data. Is there a way to make pdist ignore. d(u, v) = max i | ui − vi |. The most efficient pairwise distance computation. Now, to Minkowski's distance, I want to add this part |-m (i)|^p. example. Note that generating C/C++ code requires MATLAB® Coder™. ParameterSpace to specify the probability distributions for model parameters that define a parameter space for sensitivity analysis. % n = norm (v) returns the Euclidean norm of vector v. 2. 🄳. Copy. If you need to create a list with the indeces, see the method below to avoid loops, since that was the real time-consuming part of your code, rather than the distance method itself. First, create the distance matrix and pass it to cmdscale. This syntax returns the standard distance as a linear distance in the same units as the semimajor axis of the reference ellipsoid. 9448 两两距离按 (2,1)、. How to separately compute the Euclidean Distance in different dimension? 0. 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. Create a hierarchical cluster tree using the 'average' method and the 'chebychev' metric. Tagsxtrack = 1 x 1166 ytrack = 1 x 1166. Pass Z to the squareform function to reproduce the output of the pdist function. You can also specify a function for the distance metric using a function handle. a = a*1-48; b = b*1-48; dist = sum (bitxor (a,b),2); end. Additional Resources: Watch other videos on managing code in MATLAB: If a is m x r and b is n x r then. For more information, see Run MATLAB Functions in Thread-Based Environment. To see the three clusters, use 'ColorThreshold' with a cutoff halfway between the third-from-last and. Learn more about distance, euclidean, pdist, coordinates, optimisation MATLAB Hi all, Many of the codes I am currently using depend on a simple calculation: the distance between a single point and a set of other points. 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. D can also be a more general dissimilarity vector or matrix that conforms to the output format of pdist or pdist2, respectively. Regards, BhavyaMore Answers (1) Depending on how much over memory it is you could try converting your data to single before you pass it to pdist. Updated. I am looking for an alternative to this in. If you don't have that toolbox, you can also do it with basic operations. Sign in to comment. d = ( y − μ) ∑ − 1 ( y − μ). Description. I would use reshape, subtraction, and vecnorm. 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. I think what you are looking for is what's referred to as "implicit expansion", a. distance. 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. % Autor: Ana C. the program has this error: Struct contents reference from a non-struct array object. This function fully supports thread-based environments. 1. Pass Z to the squareform function to reproduce the output of the pdist function. Can anyone give me a little tint for this one? If pdist is not working for this one, is there any other function that I can use? Or I have to write some code to calculate the dissimilarity every time, merge the points with smallest dissimilarity, update the dissimilarity matrix and original data matrix, merge, and do the circle. Accepted Answer: Anand. The function must accept a matrix ZJ with an arbitrary number of observations. sum (any (isnan (imputedData1),2)) ans = 0. Currently I am using bsxfun and calculating the distance as below ( i am attaching a. Modified 5 years, 11 months ago. Create a hierarchical binary cluster tree using linkage. You can also use pdist, though it's a little more complicated, and I attach a demo for that. 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. Sorted by: 1. MATLAB - passing parameters to pdist custom distance function. 5000 2. This norm is also. 1. In later versions of MATLAB, this is not an “Undefined function or variable” error, and MATLAB lets you know the new, preferred function to use. Helllo. Learn more about custom distance function, pdist, pdist2, @distfun, divergence, kl divergenceGenerate Code. pdist2 Pairwise distance between two sets of observations. Y = pdist(X) Y = pdist(X,'metric') Y = pdist(X,distfun,p1,p2,. You can create a standard network that uses dist by calling newpnn or newgrnn. But it is not open because of lack of memory,, I wonder how other people deal with such global data such as MODIS data. It finds the distance for each pair of coordinates specified in two vectors and NOT the distance between two matrices. mX = mX + mX. Answers (1) In my understanding you want to use your custom distance function (dtwdist) with kmediod (). See Also. pdist2 Pairwise distance between two sets of observations. As stated in the error, knnimpute uses pdist, the pairwise distance. If you realize that. Sign in to answer this question. pdist2 (X,Y,Distance): distance between each pair of observations in X and Y using the metric specified by Distance. Hye, can anybody help me, what is the calculation to calculate euclidean distance for 3D data that has x,y and z value in Matlab? Thank you so much. Minkowski's distance equation can be found here. Nov 8, 2013 at 9:26. cmdscale takes as an input a matrix of inter-point distances and creates a configuration of points. I would like to sort these using the DTW algorithm. Then, plot the dendrogram for the complete tree (100 leaf nodes) by setting the input argument P equal to 0. As for the PDist itself, it does appear to have some construct support for. weightFcn to 'dist'. 1. Answers (1) This issue could be due to RAM limitations. Is there any workaround for this computational inefficiency. pdist. Add the %#codegen compiler directive (or pragma) to the entry. MATLAB pdist function. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. function Distance = euclidean (x,y) % This function replaces the function pdist2 available only at the Machine. function Distance = euclidean (x,y) % This function replaces the function pdist2 available only at the Machine. Is it possible to get only one value as a distance result using pdist2 function or another Matlab function? I also tried Jeffrey's distance code I found in file exchange, but I get the same (matrix of results). I've implemented a custom distance function for k-medoids algorithm in Matlab, following the directions found in pdist. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. Distance metric to pass to the pdist function to calculate the pairwise distances between columns, specified as a character vector or cell array. At the moment pdist returns a distance matrix with a nan-entry whenever a vector with any nan-element is part of the respective pair. I want to calculate Euclidean distance in a NxN array that measures the Euclidean distance between each pair of 3D points. However, my matrix is so large that its 60000 by 300 and matlab runs out of memory. Matlab: binary image open to minimum rectangle size. 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. If the sizes of A and B are compatible, then the two arrays implicitly expand to match each other. El código generado de pdist usa parfor (MATLAB Coder). 5 4. The most efficient pairwise distance computation. This function computes pairwise distance between two sample sets and produce a matrix of square of Euclidean or Mahalanobis distances. 0. basically it is used a*1-48 is converting a binary string to row vector so that we can use. 4 86. In a MATLAB code I am using the kullback_leibler_divergence dissimilarity function that can be found here. MATLAB - passing parameters to pdist custom distance function I've implemented a custom distance function for k-medoids algorithm in Matlab, following the directions found in pdist. The same piece of code seems to work just fine on later versions of the data, but going back in time (when observations should be less similar) the 'NaN's start appearing. Categories MATLAB Mathematics Random Number Generation. I have a naive so. Sign in to comment. First, create the distance matrix and pass it to cmdscale. Faster than pdist for cityblock on integers? . 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. dist () in R will convert a matrix to a. The pdist command requires the Statistics and Machine Learning toolbox. PDIST and SQUAREFORM are functions from the Statistics Toolbox. Unlike sub2ind, it computes a field of all combinations of. Therefore the similarity between all combinations is 1 - pdist (S1,'cosine') . Accepted Answer. ), and you can see that each histogram gives a different set of values. Add the %#codegen compiler directive (or pragma) to the entry. Note that generating C/C++ code requires MATLAB® Coder™. 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. The pdist_inputs argument consists of the 'seuclidean', 'minkowski', or 'mahalanobis' metric and an additional distance metric option. Add the %#codegen compiler directive (or pragma) to the entry. 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. At your example: W is the (random) weight matrix. Learn more about pdist, euclidean distance, too large MATLAB. You can even include your own anonymous distance function in the call to. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. Minkowski's distance equation can be found here. Copy. Any help. 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. When two matrices A and B are provided as input, this function computes the. The Name-Value pair 'Distance' only expect string or function handle. 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. Idx has the same number of rows as Y. Load 7 more. Improve this answer. Dear @zhang-chi-IGGCAS,. Z (2,3) ans = 0. Generate Code. Follow. Use pdist and squareform: D = squareform ( pdist (X, 'euclidean' ) ); For beginners, it can be a nice exercise to compute the distance matrix D using bsxfun (hover to see the solution). m' Matlab's built-in function for calculating the Euclidean distance between two vectors is strangely named (i. Use sdo. Available distance metrics include Euclidean, Hamming, and Mahalanobis, among others. Let X be an MxP matrix representing m points in P-dimensional space and Y be an NxP matrix representing another set of points in the same space. I am using pdist to calculate euclidian distances between three dimensional points (in Matlab). @all, thanks a lot. Use sdo. This MATLAB function returns the Euclidean distance between pairs of observations in X. For 8192 partcies the pdist version of this averaging is 2 seconds, while the suggested averaging takes 2 minutes. Hi @beaker, I got another question when using pdist, it would be so many thanks if you could give me some advice. 0. All the points in the two clusters have large silhouette values (0. If you type in the matlab prompt 'edit dist. Plot distances between points matlab. D = pdist(X,distance) computes the distance between objects in the data matrix, X, using the method specified by distance, which can be any of the following: MetricMATLAB pdist function. Then it computes the distances between observation 2 and observations 3 through n, and so on. This functions finds distance (in km) between two points on Earth using latitude-longitude coordinates of the two points. pdist. Generate Code. Sign in to answer this question. squareform时进行向量矩阵转换以及出现“The matrix argument must be square“报错的解决方案Use matlab's 'pdist' and 'squareform' functions 0 Comments. squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. . This function computes the M-by-N distance matrix D where D(i,j) is the distance between. If you don't have that toolbox, you can also do it with basic operations. The built in linear algebra methods in Matlab 2016a are pretty efficient and well parallelized. Calculate cosine similarity for between all cases in a dataframe fast. For example, you can find the distance between observations 2 and 3. 1 Different behaviour for pdist and pdist2. I have seen extensions of these functions that allow for weighting, but these extensions do not allow users to select different distance functions. Classification. 3. P is the input vector Z is the weighted input. pdist supports various distance metrics: Euclidean distance, standardized Euclidean distance, Mahalanobis distance, city block distance, Minkowski distance, Chebychev. Y = pdist(X). ^2,3)); This calculates the distance between any two points explicitly (thus, does twice as much work, and takes over twice as much space: 6400 instead of 3180 elements). It computes the distances between rows of X. Also remember that MATLAB now supports implicit expansion (also called broadcasting) so you can directly subtract a 1x3 to a 15x3x3. T = cluster (Z, 'maxclust' ,3); Create a dendrogram plot of Z. The Chebyshev distance between two n-vectors u and v is the maximum norm-1 distance between their respective elements. [D,idx] = bwdist (BW) also computes the closest-pixel map in the form of an index array, idx. I am looking for a code that will result in a list of distances between two lists of xyz coordinates. r is the position of points in 2D. Load the patients data set. It will do what you want, but is kind of overkill. MATLAB pdist function. Generate C code that assigns new data to the existing clusters. e loop through the "loc_i" variable) to find the distance between a particular coordinate and the rest of the coordinates. – Nicky Mattsson. D is a 1 -by- (M* (M-1)/2) row vector corresponding to the M* (M-1)/2 pairs of sequences in Seqs. distance. m. Different behaviour for pdist and pdist2. Can I somehow have the user specify which distance to use in my function? Something like the following: function out = my_function(input_1, input_2, 'euclidian'). Y contains the distances or dissimilarities used to construct Z, as output by the pdist function. @all, thanks a lot. Generate Code.