[Traminer-users] Traminer-users Digest, Vol 9, Issue 3

Wed Apr 20 18:01:21 CEST 2011

Thank you for your answers Matthias and Alexis,

Sorry but I still have a problem with the missings: I can not understand 
why my missings are not coded as void element. They are indeed located 
after the last valid state and I even tried to specify the default value 
right="DEL". I'm especially surprised because I made this observation 
on old scripts that did not react like this before (I think... maybe I'm 
going mad?)

Alexis, what do you mean by "the way your sequences are prepared"? I 
usually use csv file

An exemple to be clearer:

id,c1,c2,c3
21,8,1,

--> and import in TraMineR:

#########################

library(TraMineR)
library(foreign)

contact<-read.csv("base.csv")

names(contact)
[1] "id" "c1" "c2" "c3"

contact.seq <- seqdef(contact, 2:4, right="DEL")
[>] found missing values ('NA') in sequence data
[>] preparing 1 sequences
[>] coding void elements with '%' and missing values with '*'
[>] 2 distinct states appear in the data:
1 = 1
2 = 8
[>] alphabet (state labels):
1 = 1 (1)
2 = 8 (8)
[>] 1 sequences in the data set
[>] min/max sequence length: 2/2

count.miss <- rowSums(is.na(contact[,2:4]))

contact[count.miss>0, 2:4]
c1 c2 c3
1 8 1 NA

#########################

Should I not have a % at the end ?

Best (and beautifull easter)

Alexandre

Le 19.04.2011 12:00, traminer-users-request at r-forge.wu-wien.ac.at a écrit :
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> Today's Topics:
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>     1. Re: The substitution cost matrix is not symmetric
>        (Alexis Gabadinho)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 18 Apr 2011 13:54:12 +0200
> From: Alexis Gabadinho<Alexis.Gabadinho at unige.ch>
> Subject: Re: [Traminer-users] The substitution cost matrix is not
> 	symmetric
> To: Users questions<traminer-users at r-forge.wu-wien.ac.at>
> Message-ID:<4DAC2664.3090502 at unige.ch>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Alexandre,
>
> Regarding your second question, you have indeed missing values in your
> data, since we can see in the output of seqdist that the length of your
> sequences vary from 1 to 12.
>
> The way missing values (supposed to be NA's by default) are handled is
> set in seqdef with the arguments "gaps", "left" and "right". By
> default,  missing values found after the last valid state in a sequence
> are coded as void elements, meaning that your sequence is supposed to
> end with the last valid state. Thus if you have sequences of unequal
> length, ending with NA'S , this is the way your sequences are prepared.
> See user's guide for more information.
>
> To locate missing values in your data you can do for example:
>
> count.miss<- rowSums(is.na(contact[,2:15]))
>
> This counts the number of missing values in each row of your original data.
>
> To display the rows containing at least one missing value:
>
> contact[count.miss>0, 2:15]
>
> Best regards,
> Alexis.
>
> Alexandre Pollien a ?crit :
>> Hello,
>>
>> When I use seqsubm, now I get this message:
>>
>>>   contact.om<-
>> seqdist(contact.seq,method="OM",indel=2,sm=cout,with.missing=FALSE,
>> full.matrix=TRUE)
>> [>] 5764 sequences with 9 distinct events/states
>> [>] 496 distinct sequences
>> [>] min/max sequence length: 1/12
>> [>] computing distances using OM metric
>> [>] total time: 1.25 secs
>> Message d'avis :
>> The substitution cost matrix is not symmetric.
>>
>> cout is computed with seqsubm (method="TRATE")
>>
>>
>> A surprising aspect is that it is not systematic (3 / 4)
>>
>> I thought of a problem of missing value
>>
>>
>> Another amazing prompt is that seqdef shows this message:
>>>   contact.seq<- seqdef(contact, 2:15, states = contact.shortlab,labels
>> = contact.lab)
>> [>] found missing values ('NA') in sequence data
>>
>> ...even when there is no missing in my data! (How can I seethe
>> sequence containing the missing data?)
>>
>>
>> Does anyone have a idea?
>>
>> Thank you very much
>>
>> Best regards and good weekend
>>
>> Alexandre
>>
>>
>>
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> End of Traminer-users Digest, Vol 9, Issue 3
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-- 
_______________________

Alexandre Pollien
FORS - Swiss foundation for research in social sciences
c/o University of Lausanne – Vidy
Route de Chavannes 33
CH - 1015 Lausanne

Switzerland

Tel.: +41 21 692 37 39

alexandre.pollien at fors.unil.ch
http://www.fors.unil.ch
_______________________

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