R Special Interest Group for the use of R in ecological and environmental data analysis

Jason S | 3 Apr 14:37

Re: missing data in PCA

Dear Jari,

Thanks for the hints. A package such as mvnmle would be ideal, but it provides only the estimate of the
covariance matrix, not the raw data. However, comments like princomp and pca require the raw data.

Do you (or anyone else) know a command to do PCA straight from a covariance matrix?

best,

Jason

________________________________
From: Jari Oksanen <jari.oksanen@...>

Cc: Jari Oksanen <jari.oksanen@...>; r-sig-ecology@...
Sent: Friday, April 3, 2009 2:55:20 AM
Subject: Re: [R-sig-eco] missing data in PCA

On 03/04/2009, at 00:32 AM, Jason S wrote:

> 
> Dear all,
> 
> I was wondering if you have good options to deal with missing data on a PCA in R. I guess I could simply delete
those cases, but I think there should be better options in terms of predicting them. Any hints?
> 
Howdy,

There may be better ways, but they are not easy... Check paragraph on missing data in multivariate task

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Stéphane Dray | 3 Apr 16:34

Re: missing data in PCA

ade4 has nipals() which deals with row data.

Cheers.

Jason S wrote:
> Dear Jari,
>
> Thanks for the hints. A package such as mvnmle would be ideal, but it provides only the estimate of the
covariance matrix, not the raw data. However, comments like princomp and pca require the raw data.
>
> Do you (or anyone else) know a command to do PCA straight from a covariance matrix?
>
> best,
>
> Jason
>
>
>
>
> ________________________________
> From: Jari Oksanen <jari.oksanen@...>
>
> Cc: Jari Oksanen <jari.oksanen@...>; r-sig-ecology@...
> Sent: Friday, April 3, 2009 2:55:20 AM
> Subject: Re: [R-sig-eco] missing data in PCA
>
>
> On 03/04/2009, at 00:32 AM, Jason S wrote:
>
>

(Continue reading)

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Farrar.David | 6 Apr 18:21

Re: missing data in PCA

For combining imputation with PCA, transcan{Design} could be interest. 

For imputation, I have been hearing about the mice program. 

The documentation for princomp() suggests that a covariance matrix can be 
entered via the covmat argument. 

David F

r-sig-ecology-bounces@... wrote on 04/03/2009 10:34:51 AM:

> [image removed] 
> 
> Re: [R-sig-eco] missing data in PCA
> 
> Stéphane Dray 
> 
> to:
> 
> Jason S
> 
> 04/03/2009 10:48 AM
> 
> Sent by:
> 
> r-sig-ecology-bounces@...
> 
> Cc:
> 
> r-sig-ecology

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Jari Oksanen | 3 Apr 16:00

Re: missing data in PCA


On 3 Apr 2009, at 15:37, Jason S wrote:

>
> Dear Jari,
>
> Thanks for the hints. A package such as mvnmle would be ideal, but  
> it provides only the estimate of the covariance matrix, not the raw  
> data. However, comments like princomp and pca require the raw data.
>
> Do you (or anyone else) know a command to do PCA straight from a  
> covariance matrix?
>
princomp() does. See its documentation and argument 'covmat'.

cheers, jari oksanen