[R] nMDS with R: missing values

[David L Carlson]

I think you will have to provide some more information. What function/package are you using for nMDS (eg. isoMDS in MASS, monoMDS in vegan)? What function/package are you using to compute your distance/dissimilarities (eg. dist in stats, vegdist in vegan)? 

Zero represents absence. It is not a missing value, so that part of your question is not clear.

The dist() function computes distance ignoring missing values if they are properly represented as NAs in the data. The vegdist() function does this if na.rm=TRUE. 

The results will be affected by how much data is missing. It would be useful to know if the missing values are concentrated in particular rows or columns so that eliminating a few rows and columns could substantially reduce the percentage of missing values.

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David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352


0-----Original Message-----
From: R-help <r-help-bounces using r-project.org> On Behalf Of Jessie Woodbridge
Sent: Tuesday, April 17, 2018 2:05 PM
To: r-help using r-project.org
Subject: [R] nMDS with R: missing values

Dear All,

I was wondering whether anyone might be able to provide some advice with an nMDS / R problem. I’m trying to run nMDS on a dataset that contains many missing values and was wondering how I can account for the missing values when running nMDS? It seems as though the data are being grouped depending on where the zero values appear. Any suggestions greatly appreciated. Thank you very much in advance.

Apologies if this message isn’t relevant to you.

Kind regards,

Jessie

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