R help - Mar 2006 - PCA, Source analysis and Unmixing, environmental forensics

I am using R for environmental forensics (determination of the sources
and/or groupings in mixtures of organic chemicals in the field). The
goal is to determine in there are groups of samples with
similar/dissimilar compositions, and to assign samples to a potential
source or a mixture of sources based on the composition (unmixing and
source allocation). Typically there are 10 to 50 chemicals that have
been analyzed in all of the samples. In most cases concentrations are
converted to proportion of total as we are interested in composition
rather that simple dilution.

I have had great success with ratio analysis; simple exploratory
analysis such a property property plots etc; and cluster analysis such
as principal components analysis (PCA) and hierarchal cluster analysis.
I have also been experimenting with glyph representation, k-means
clusters, and similar procedures as documented in MASS. More recently I
have been experimenting with Independent Components Analysis (ICA).
Another commonly used procedure is polytopic vector analysis (PVA), a
procedure for which I have no implementation in R sand so I have not
tried it out. My question is can anyone suggest :
A) Other procures in R that I may have missed and should investigate
B) Your experience and/or hints for using ICA and presenting the results
C) An implementation for PVA in R I have not found

Thanks in advance,

Mike




	[[alternative HTML version deleted]]

Review all the task views at:

http://cran.r-project.org/src/contrib/Views/



On 3/23/06, Mike Bock <mbock at environcorp.com>
wrote:
>
> I am using R for environmental forensics (determination of the sources
> and/or groupings in mixtures of organic chemicals in the field). The
> goal is to determine in there are groups of samples with
> similar/dissimilar compositions, and to assign samples to a potential
> source or a mixture of sources based on the composition (unmixing and
> source allocation). Typically there are 10 to 50 chemicals that have
> been analyzed in all of the samples. In most cases concentrations are
> converted to proportion of total as we are interested in composition
> rather that simple dilution.
>
> I have had great success with ratio analysis; simple exploratory
> analysis such a property property plots etc; and cluster analysis such
> as principal components analysis (PCA) and hierarchal cluster analysis.
> I have also been experimenting with glyph representation, k-means
> clusters, and similar procedures as documented in MASS. More recently I
> have been experimenting with Independent Components Analysis (ICA).
> Another commonly used procedure is polytopic vector analysis (PVA), a
> procedure for which I have no implementation in R sand so I have not
> tried it out. My question is can anyone suggest :
> A) Other procures in R that I may have missed and should investigate
> B) Your experience and/or hints for using ICA and presenting the results
> C) An implementation for PVA in R I have not found
>
> Thanks in advance,
>
> Mike
>
>
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>