[Rsiena-help] structural zeros
Ruth M. Ripley
ruth at stats.ox.ac.uk
Wed Jun 15 00:24:19 CEST 2011
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
>
>
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