Re: [R] norm package prelim.norm

From: Leo Gürtler <leog_at_anicca-vijja.de>
Date: Fri 03 Feb 2006 - 00:31:35 EST

(Ted Harding) schrieb:

Dear Elizabeth,

the R-package "mice" has

?md.pattern

and "Hmisc" also contains some software to describe missing data. I think both do not have limitations like prelim.norm.

best wishes,

leo

>On 01-Feb-06 Ted Harding wrote:
>
>
>>On 01-Feb-06 Elizabeth Lawson wrote:
>>
>>
>>>Hey eveyone! I hope someone can help wiht this question. I have a
>>>matirux of all zeros and ones and I would like to indentify all unique
>>>patterns in the rows andthe number of times the pattern occurs. I
>>>changed all zeros to NA tried to use prelim.norm to identify all
>>>patterns of missing data in the rows. I got the message
>>>
>>> Warning message:
>>>NAs introduced by coercion
>>>
>>> Any ideas of how to get this to work? Or are there any way to
>>>indentify all the unique patterns in a huge matrix? ( 10000 x 71)
>>>
>>> Thanks for any suggestions!!
>>>
>>> Elizabeth Lawson
>>>
>>>
>>I think Chuck Celand has pretty well answered it: Don't worry
>>about the warning, since I'm pretty sure it is generated when
>>prelim.norm is calculating something else (e.g. the covariance
>>matrix) and it is not related to generating prelim.norm(X)$r
>>which is the list of patterns and the numbers of times they occur.
>>
>>Best wsihes,
>>Ted.
>>
>>
>
>Sorry -- I should have read the detail of your original message
>more carefully. In short, you have too many columns for prelim.norm
>to work.
>
>The long answer: prelim.norm analyses the missing data patterns
>by representing the locations of NAs as integers, where the jth
>bit in the binary representation of the integer is 1 for an NA,
>0 for a non-NA. Hence the representation of the pattern runs out
>of steam when there are more than a certain number of columns,
>corresponding to the highest power of 2 that can be represented
>as an integer in R.
>
> .Machine$integer.max
> [1] 2147483647
>
> 2^31 -1
> [1] 2147483647
>
>so that prelim.norm can only encode NA-patterns in an R integer
>for up to 31 columns. More than that, and it will not work properly
>or at all.
>
>Check:
>
> X<-matrix(sample(c(0,1),87,replace=TRUE),ncol=29)
> Y<-X; Y[Y==0]<-NA
> prelim.norm(Y)$r
> [...] (no warning, 3 rows)
>
> X<-matrix(sample(c(0,1),90,replace=TRUE),ncol=30)
> Y<-X; Y[Y==0]<-NA
> prelim.norm(Y)$r
> [...] (no warning, 3 rows)
>
> X<-matrix(sample(c(0,1),93,replace=TRUE),ncol=31)
> Y<-X; Y[Y==0]<-NA
> prelim.norm(Y)$r
> [...] (no warning, 3 rows)
>
> X<-matrix(sample(c(0,1),93,replace=TRUE),ncol=32)
> Y<-X; Y[Y==0]<-NA
> prelim.norm(Y)$r
> [...] (3 rows, "Warning message: NAs introduced by coercion")
>
> X<-matrix(sample(c(0,1),93,replace=TRUE),ncol=33)
> Y<-X; Y[Y==0]<-NA
> prelim.norm(Y)$r
> [...] (2 rows, "Warning message: NAs introduced by coercion")
>
> X<-matrix(sample(c(0,1),93,replace=TRUE),ncol=34)
> Y<-X; Y[Y==0]<-NA
> prelim.norm(Y)$r
> [...] (1 row, "Warning message: NAs introduced by coercion")
>
>(Try a few of these for yourself; it is very unlikely that you get
>one 1 or 2 distinct rows when you have 3 rows of 30+ 0s and 1s
>sampled at random).
>
>A similar issue came up some time ago (I can't locate the thread
>in the archive at the moment) in vennection with the 'mix'
>package.
>
>However, you can have as many columns as you like if you use
>'unique' to identify the distinct patterns of 0s and 1s, rather
>than using 'prelim.norm'.
>
>Hoping this helps,
>Ted.
>
>
>
>--------------------------------------------------------------------
>E-Mail: (Ted Harding) <Ted.Harding@nessie.mcc.ac.uk>
>Fax-to-email: +44 (0)870 094 0861
>Date: 02-Feb-06 Time: 01:42:13
>------------------------------ XFMail ------------------------------
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>

-- 

email: leog@anicca-vijja.de
www: http://www.anicca-vijja.de/

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Received on Fri Feb 03 00:38:37 2006

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