[Rsiena-help] structural zeros
Sebastián Daza
sebastian.daza at gmail.com
Wed Jun 15 02:10:15 CEST 2011
Thank you Ruth. 3 NAs are isolates. I have additional information about
structural zeros (people who leave the network). For instance, this is
the edgelist for time 2 where nodes 9 and 13 are structural zeros (they
have valid ties in the time 1 edgelist).
mymat2
[,1] [,2] [,3]
[1,] 2 14 1
[2,] 2 6 1
[3,] 3 8 1
[4,] 3 7 1
[5,] 4 3 1
[6,] 5 11 1
[7,] 6 2 1
[8,] 6 28 1
[9,] 7 3 1
[10,] 8 3 1
[11,] 9 NA 10
[12,] 10 24 1
[13,] 10 6 1
[14,] 11 5 1
[15,] 13 NA 10
I excluded all NAs except for structural zeros. When I use this matrix
syntax, however, I got the following error:
library(Matrix)
> mymat2s <- spMatrix(nrow(friend2), nrow(friend2),
+ mymat2[, 1], mymat2[, 2], mymat2[, 3])
Error in validObject(.Object) :
invalid class "dgTMatrix" object: all column indices must be between
0 and ncol-1
I do not know what I am doing wrong. I would really appreciate if you
could give any example of this that I could follow.
Thank you again!
Sebastian
On 6/14/2011 5:24 PM, Ruth M. Ripley wrote:
> Dear Sebastian,
>
> I assumed rows with 3 NA's were isolates and there were no structural
> zeros. But maybe isolates were the missing sequence numbers and the 3
> NA's were structural zeros?
>
> Structural zeros need 10 in column 3 of the edgelist.
>
> Isolates need to be allowed for in the sequence numbering but will not
> appear in the edgelist.
>
> Regards,
>
> Ruth
>
> On Tue, 14 Jun 2011, Sebastián Daza wrote:
>
>> Dear Ruth,
>> Using your syntax to build matrices, I have a question about how to
>> define structural zeros and how isolated nodes (vertexes) are stored
>> in the edgelist format.
>>
>> My original dataset (friends) has this format:
>>
>> id tie1 tie2 tie3
>> 1 3984 NA NA NA
>> 2 3985 3997 NA 3989
>> 3 3986 3991 3990 NA
>> 4 3987 3986 NA NA
>> 5 3988 3994 NA NA
>> 6 3989 3985 4011 NA
>> ....
>>
>> your syntax to build the edgelist is:
>>
>> mymat1 <- matrix(0, nrow=3*nrow(friend1), ncol=3)
>> mymat1[, 1] <- rep(1:nrow(friend1), each=3)
>> mymat1[, 2] <- match(t(as.matrix(friend1[, -1])), friend1[, 1])
>> mymat1[, 3] <- rep(1, nrow(mymat1))
>> mymat1 <- na.omit(mymat1)
>> mymat1 <- unique(mymat1)
>>
>> I am not sure how I should define the structural zeros (using the code
>> 10), taking into account the structure of this edgelist:
>>
>> [,1] [,2] [,3]
>> [1,] 2 14 1
>> [2,] 2 6 1
>> [3,] 3 8 1
>> [4,] 3 7 1
>> [5,] 4 3 1
>> [6,] 5 11 1
>>
>>
>> I guess I should define the structural zero in the third column, but
>> because I omitted the NAs, I can not do it. In addition, I don not
>> know where the isolated nodes are stores in this format (for example,
>> node 1).
>>
>> Thank you in advance, and sorry for these very basic questions.
>> Sebastian.
>>
>> On 6/13/2011 1:40 PM, Ruth M. Ripley wrote:
>>> Dear Sebastian,
>>>
>>> Glad you got things to work.
>>>
>>> I don't think these messages are important, and I thought they always
>>> appeared, unrelated to covariates. You are not using sparse matrices to
>>> improve performance at this stage: you only read in your data once and
>>> will spend much more time fitting models. It is more a matter of
>>> convenience.
>>>
>>> Regards,
>>>
>>> Ruth
>>>
>>>
>>> On Mon, 13 Jun 2011, Sebastián Daza wrote:
>>>
>>>> Thank you very much, Ruth. It works great!
>>>>
>>>> However, when I include a covariate (e.g. sex) I get these messages:
>>>>
>>>> <sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
>>>> <sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient
>>>>
>>>> Sebastian
>>>>
>>>> On 6/11/2011 5:41 PM, Ruth M. Ripley wrote:
>>>>> Dear Sebastian,
>>>>>
>>>>> After looking at your data, I thought I would reply to the list as
>>>>> others may want to know the outcome:
>>>>>
>>>>> I discovered there is a single 2 in the second matrix. I am not quite
>>>>> sure of your data format but I think you have a duplicate in row
>>>>> 188 of
>>>>> friend2 which results in 2 links from 1706 to 1704.
>>>>>
>>>>> For the benefit of others, your data is, I think, a row for each actor
>>>>> with 3 nominations, NA if less than three, in an SPSS file. The actor
>>>>> numbers are not sequential.
>>>>>
>>>>> I have not tried reading the files in SPSS, but if all you want in
>>>>> your
>>>>> data is an integer 4 column matrix, I would think it easier to export
>>>>> from SPSS as a text file, if that is possible.
>>>>>
>>>>> I advise reading SPSS files using read.spss directly: I am not sure
>>>>> you
>>>>> gain anything by using Hmisc's wrapper version, but it seemed to
>>>>> work OK
>>>>> here. read.spss is in library(foreign).
>>>>>
>>>>> But once you have read the files in to create two data frames friend1
>>>>> and friend2, you could use siena edgelist format via sparse
>>>>> matrices or
>>>>> create normal matrices via the sparse ones, using the following code:
>>>>>
>>>>> mymat1 <- matrix(0, nrow=3*nrow(friend1), ncol=3)
>>>>> mymat1[, 1] <- rep(1:nrow(friend1), each=3)
>>>>> mymat1[, 2] <- match(t(as.matrix(friend1[, -1])), friend1[, 1])
>>>>> mymat1[, 3] <- rep(1, nrow(mymat1))
>>>>> mymat1 <- na.omit(mymat1)
>>>>> mymat1 <- unique(mymat1)
>>>>>
>>>>> mymat2 <- matrix(0, nrow=3*nrow(friend2), ncol=3)
>>>>> mymat2[, 1] <- rep(1:nrow(friend2), each=3)
>>>>> mymat2[, 2] <- match(t(as.matrix(friend2[, -1])), friend2[, 1])
>>>>> mymat2[, 3] <- rep(1, nrow(mymat2))
>>>>> mymat2 <- na.omit(mymat2)
>>>>> mymat2 <- unique(mymat2)
>>>>>
>>>>> #To get RSiena networks using sparse matrices:
>>>>>
>>>>> library(Matrix)
>>>>> mymat1s <- spMatrix(nrow(friend1), nrow(friend1),
>>>>> mymat1[, 1], mymat1[, 2], mymat1[, 3])
>>>>>
>>>>> mymat2s <- spMatrix(nrow(friend2), nrow(friend2),
>>>>> mymat2[, 1], mymat2[, 2], mymat2[, 3])
>>>>>
>>>>> mynet <- sienaNet(list(mymat1s, mymat2s))
>>>>>
>>>>> # to get real matrices
>>>>>
>>>>> mymat1d <- as.matrix(mymat1s)
>>>>> mymat2d <- as.matrix(mymat
>>>>>
>>>>> ## if you wish add IDs as row numbers to the matrices
>>>>>
>>>>> rownames(mymat1d) <- friend1[, 1]
>>>>> rownames(mymat2d) <- friend2[, 1]
>>>>> rownames(mymat1s) <- friend1[, 1]
>>>>> rownames(mymat2s) <- friend2[, 1]
>>>>>
>>>>> ## and add IDs as column numbers
>>>>> colnames(mymat1d) <- friend1[, 1]
>>>>> colnames(mymat2d) <- friend2[, 1]
>>>>> colnames(mymat1s) <- friend1[, 1]
>>>>> colnames(mymat2s) <- friend2[, 1]
>>>>>
>>>>> Please let me know if you do not understand the code or cannot get
>>>>> it to
>>>>> work. I think it is simpler than your method, and should give the same
>>>>> result apart from the duplicates.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Ruth
>>>>> --
>>>>> On Sat, 11 Jun 2011, Ruth M. Ripley wrote:
>>>>>
>>>>>> Dear Sebastian,
>>>>>>
>>>>>> If you would like to email me the data in some format (either save
>>>>>> the
>>>>>> workspace and send that, or send me the data files and the commands
>>>>>> you used to make the matrices) I will have a look for you.
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Ruth
>>>>>>
>>>>>>
>>>>>> On Sat, 11 Jun 2011, Sebastián Daza wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>> I am trying to load two 276x276 matrices using sienaNet, but I got
>>>>>>> this error. Both files are matrices (matrix class), and they have
>>>>>>> only 0s and 1s.
>>>>>>>
>>>>>>>> friendship <- sienaNet( array( c( mnet1, mnet2),
>>>>>>> + dim = c( 276, 276, 2 ) ) )
>>>>>>> Error in sienaNet(array(c(mnet1, mnet2), dim = c(276, 276, 2))) :
>>>>>>> entries in networks must be 0, 1, 10 or 11
>>>>>>>
>>>>>>> Does anyone know what could be the problem?
>>>>>>> Thank you in advance.
>>>>>>> Sebastian.
>>>>>>>
>>>>>>> --
>>>>>>> Sebastián Daza
>>>>>>> sebastian.daza at gmail.com
>>>>>>> _______________________________________________
>>>>>>> Rsiena-help mailing list
>>>>>>> Rsiena-help at lists.r-forge.r-project.org
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rsiena-help
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>> --
>>>> Sebastián Daza
>>>> sebastian.daza at gmail.com
>>>>
>>>>
>>
>> --
>> Sebastián Daza
>> sebastian.daza at gmail.com
>>
>>
--
Sebastián Daza
sebastian.daza at gmail.com
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