issue with biofam3c data in SeqHMM

Question

I have the data which is biofam3c in package SeqHMM in list format. I wanted to see it in matrix form. I used this command

matrix_biofam3c= matrix(unlist(biofam3c), ncol=16, byrow= TRUE)

But its results was confusing . Then I also tried to change matrix_biofam3c into list using a command

U= as.list(as.data.frame(matrix_biofam3c))

it gives not similar results like given form in package (List of length 4). I request please, suggest the right way to make biofam3c in matrix data (like biofam in package TraMineR). And also how to convert it again so it becomes like list as it is given there.

user_1586731 · Answer

The data biofam3c is a list of three matrices that contain sequence data of three channels, namely children, married, and left (for left home). Tables children and left have binary data (children vs childless, left home vs with parents), while there are three states for married: single, married, and divorced.

The help page of biofam3c gives the code used to generate these three channels from the biofam data that ships with TraMineR. Note that this code assumes that we do not have divorced people living with their parents. The biofam data does not distinguish between divorced with and without children, nor between divorced who have left home and those who did not. See also the example in the help page of the seqdistmc function of TraMineR.

You can reconstruct biofam from the three channels using interaction

library(seqHMM)
data(biofam3c)
## the 3 channels
children <- biofam3c[[1]]
married <- biofam3c[[2]]
left <- biofam3c[[3]]

## Reconstructing biofam
bf.rec <- matrix(NA,nrow(children),ncol(children))
for (i in 1:ncol(children)) {
  bf.rec[,i] <- as.matrix(interaction(children[,i],married[,i],left[,i]))
}

alph <- seqstatl(bf.rec)
## reordering states as in biofam
alphabet <- alph[c(6,5,4,3,10,9,8,7,2,1)]
## creating a single state divorced as in biofam
bf.rec[bf.rec %in% alphabet[8:10]] <- "divorced"
alphabet[8] <- "divorced"
alphabet <- alphabet[1:8]
    
seq.bf.rec <- seqdef(bf.rec, alphabet=alphabet)
seqdplot(seq.bf.rec)

You get the same figure using the original biofam

## in biofam sequence data are in columns 10 to 25
library(TraMineR)
bf <- biofam[,10:25]
seq.bf <- seqdef(bf)
seqdplot(seq.bf)

issue with biofam3c data in SeqHMM

1 Answers