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Questions tagged [mds]

Questions regarding MDS - Multidimensional Scaling R functions

101 questions
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Stress attribute -- sklearn.manifold.MDS / Python

I'm using the scikit-learn method MDS to perform a dimensionality reduction in some data. I would like to check the stress value to access the quality of the reduction. I was expecting something between 0 - 1. However, I got values outside this…
pceccon
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Why does metaMDS() produce a horizontal distribution of our data?

We have a species presence table (so binary: 1=present, 0=absent). When using metaMDS of the vegan package, it produces a horizontal distribution of our data when plotted, instead of clusters. We tried using different distance methods (Euclidean,…
Kaiser
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MDS plots of binary data: counterintuitive clustering

Say I have the following binary data frame, df. structure(list(a = c(0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0), b = c(0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1), c = c(0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0), d = c(1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0), e = c(0, 0, 1, 0, 0,…
Dan
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Convert co-occurrence matrix to dissimilarity matrix for MDS in scikit-learn

I have a matrix of word co-occurrence, like below. I'd like to use MDS to reduce the dimension and plot it. In sklearn there's a function model = MDS(n_components=2, dissimilarity='precomputed', random_state=1) and to apply the model output =…
user3735871
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What is the difference between metric and non-metric MDS for a beginner?

I am fairly new to data science and would like to know in simple words (like teaching your grandmother) what the difference between metric and non-metric Multidimensional scaling is. I have been googling for 2 days and watching different videos and…
Najati Al-imam
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What does the parameter "mds" mean in the pyLDAvis.sklearn.prepare () - function?

I want to visualize the topic modeling made with the LDA-algorithm. I use the python module called "pyldavis" and as environment the jupyter notebook. import pyLDAvis.sklearn ... pyLDAvis.sklearn.prepare(lda_tf, dtm_tf,…
rakael
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resolve metaMDS error : "veg_distance" not available for .C() for package "vegan"

I keep getting the following error when trying to run metaMDS() from the vegan package: my_mds <- vegan::metaMDS(df_species, distance="bray", k=2, trymax=1000, autotransform=TRUE) Error in .C("veg_distance", x = as.double(x), nr = N, nc =…
Rachael Blake
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sklearn.manifold import MDS No module named 'numpy.random.bit_generator'

I'm trying to set up an analysis pipeline to generate MDS figures. I imported what I think is necessary, but its resulting in an error: import numpy as np import pandas as pd from sklearn.manifold import MDS File "biasedurn.pyx", line 1, in init…
Jyoon
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Coding Isomap (& MDS) function using only numpy and scipy in python

I have coded Isomap function starting with computing the eulidean distance matrix (using scipy.spatial.distance.cdist), next basing on K-nearest neighbors method and Dijkstra algorithm (to determinate the shortest path) I have Computed the full…
Abdelfattah Boutanes
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Determining autotransformation applied with metaMDS

How do I determine the type of transformation that metaMDS is applying to my community data when autotransform=TRUE?
Michael Spear
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Nonmetric Multi-Dimensional Scaling using sklearn.manifold.MDS with Large data is not possible?

I am trying to visualize my high dimensional data set in two axis or components using nonmetric multi-dimensional scaling. This function is available in scikit-learn library. Here is my code: from sklearn.manifold import MDS embedding = MDS…
ilearn
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pyspark multidimensional scaling

I would like to perform a multidimensional scaling on pyspark DataFrame. I know how to solve my problem using pandas + sklearn, but I am struggling with spark dataframe. Here is the pandas based solution: from sklearn.metrics.pairwise import…
user1877600
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plot vectors on MDS using ggplot

I need to plot a MDS with vectors showing changes in abundance for my species. I need the plot with just vectors This is my data with abundance for each species and code library(vegan) A <- c(54.67, 37.67, 19.33, 0, 6, 8, 84.67, 0,0,0,0,0,0,0) B…
Claire
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what is the tsne initial pca step doing

Looking at the parameters to the Rtsne function: https://cran.r-project.org/web/packages/Rtsne/Rtsne.pdf There is a parameter called "pca" defined as "logical; Whether an initial PCA step should be performed (default: TRUE)" Let's say you have a 10…
user3022875
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Multidimensional Scaling to plot points from distance matrix

I am trying to plot a distance matrix of 7000*7000 using MDS.When i tried to plot just 500 points i got the plot but when i tried for all 7000 points the program is running endlessly Plot for 500 points I just want to visualize the distance…
skag
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