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Questions tagged [multi-dimensional-scaling]

84 questions
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Assign columns to grouping variable for use with ordihull plotting

I have a dataframe consisting of dissimilarity ratings for pairs of 12 nations, and what I wish to do is essentially divide the columns (the nations) into three different groups (not combining their scores). I am performing a non-metric…
Hello
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Multidimensional Histogram with R

Suppose we have a data frame like this: dat <- data.frame( a = rnorm(1000), b = 1/(rnorm(1000))^2, c = 1/rnorm(1000), d = as.factor(sample(c(0, 1, 2), 1000, replace=TRUE)), e = as.factor(sample(c('X', 'Y'), 1000,…
Dimon
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Multidimensional scaling plot in R

I have a dataset ("data") that looks like this: PatientID Visit Var1 Var2 Var3 Var4 Var5 1 ID1 0 44.28 4.57 23.56 4.36 8.87 2 ID1 1 58.60 5.34 4.74 3.76 6.96 3 ID1 2 72.44 11.18 21.22 2.15 8.34 4 …
VasoGene
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Is sklearn.manifold.MDS comparable with MATLAB's mdscale called with the metricsstress parameter?

I am recreating a project that uses multidimensional scaling (MDS) to visualise the data in the final stage. Specifically, the original work uses MATLAB's mdscale with the metricsstress parameter which according to the documentation uses 'Squared…
lovelyzoo
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sklearn MDS crashes my kernel?

I have a 50,000 x 15 numpy matrix with continuous data. I want to use MDS (Multi-Dimensional Scaling) to scale down to 2 components in order to visualise the data in a 2-D vector space. For some reason, whenever I go to run the MDS on my data, my…
daniel3412
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Issue using mdpref function in R

I have a set of data with a set of preference rankings for different items for each participant. A subset of the data sample is included below: Participant <- c("P1", "P2", "P3", "P4", "P5", "P6", "P7") I1 <-…
Chelsea
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How to use dissimilarity matrix with function metaMDS?

I have a matrix derived from a table with three original columns: column 1 = site codes, column 2 = species codes and column 3 = biomass weight for each species. The biomass weight of each species in each plot is displayed in the matrix. The matrix…
tabtimm
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Windows Store App not Scaling

I am developing a Windows Store app, and I hit a problem with scaling to different screen sizes - namely, 140 and 180%. Everything works perfectly on my computer, which is scaled to 100%, but when I test it on the Surface Pro and on the different…
user2509848
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Java: Multidimensional Scaling?

I'm doing a Natural Language Processing project where I compute a bunch of attributes of a text, giving me a vector of values for each text. I want to compare these vectors with multidimensional scaling. What Java libraries/toolkits do you recommend…
Nick Heiner
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Best approach for redrawing weighted 2-D graph when weights change (MDS maybe)?

I'll try to describe my problem as simplest as possible. Assume I have a map where I plot as points the cities within the map. Cities are then connected by line segments representing roads, so now there's a graph with line segments that represent…
user2570551
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How does sklearn.manifold.MDS find point locations when given a precomputed dissimilarity matrix?

I am using sklearn.manifold.MDS to find a MDS solution using pre-computed (non-Euclidean) distances (i.e., I use the attribute "dissimilarity='precomputed'" and call the package with my own dissimilarity matrix). According to the API, the…
user1234
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Can Kruskal stress be used with metric mds?

On this site(Stress attribute -- sklearn.manifold.MDS / Python), Kruskal stress is used to metric mds. However, looking at the wiki(https://en.wikipedia.org/wiki/Multidimensional_scaling), metric mds uses raw stress and non-metric mds uses Kruskal…
user45546
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Ordination analysis of different sampling points based on physicochemical analyzes with NA values

For a research I'm conducting I need to analyze chemical data to "group" or "see how the sampling points lay out based on the chemical data". This is the reproducible dataset: Chem<- data.frame( stringsAsFactors = FALSE, Sample =…
Raffaele Bruschi
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PHP initialize multimensional arrays before increment

I have to perform a big code fix in an old php project. The issue is the following: I have a number statements where the code tries to add integers to non-initialized multimensional arrays, like this: $array_test['first']['two']['three'] += 10; But…
Alberto Lancellotti
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Is there a way to extract and/or translate summary.ordisurf output to view the relationship with each ordination axis in R?

I have a question regarding plotting and interpreting the relationship between continuous environmental variables to an NMDS ordination of species abundances using R. This is a programming follow-up question to a question on Cross-Validated…
theforestecologist
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