[Rsiena-help] structural zeros

Wed Jun 15 19:52:09 CEST 2011

Thank you very much! It worked perfect!

Sebastian

On 6/15/2011 11:07 AM, Ruth M. Ripley wrote:
> Dear Sebastian,
>
> You need to specify each individual link that is structural: eg 9 to all
> of 1 to 276 (except 9).
>
> If you wait till you have created the sparse matrix, you can do
>
> mymat2s[9, ] <- 10
>
> to fill the row and
>
> mymat2s[9, 11] <- 10
>
> would fill the column if you do not want to allow incoming links either.
>
> For safety, remove the diagonal:
>
> mymat2s[9, 9] <- 0
>
> or to do more than 1 at once
>
> struct <- c(9, 13)
>
> mymat2s[struct, ] <- 10
>
> mymat2s[, struct] <- 10
>
> diag(mymat2s) <- 0
>
> BTW, the code I gave you will only work if each of the SPSS files has
> the same actor ids in the first column. I think yours did.
>
> Regards,
>
> Ruth
>
> On Tue, 14 Jun 2011, Sebastián Daza wrote:
>
>> 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
>>
>>

-- 
Sebastián Daza
sebastian.daza at gmail.com