r - Find specific patterns in sequences

Question

I'm using R package TraMineR to make some academic research on sequence analysis.

I want to find a pattern defined as someone being in the target company, then going out, then coming back to the target company.

(simplified) I've define state A as target company; B as outside industry company and C as inside industry company.

So what I want to do is find sequences with the specific patterns A-B-A or A-C-A.

After looking at this question (Strange number of subsequences? ) and reading the user guide, specially the following passages:

4.3.3 Subsequences A sequence u is a subsequence of x if all successive elements ui of u appear >in x in the same order, which we simply denote by u x. According to this denition, unshared >states can appear between those common to both sequences u and x. For example, u = S; M is a >subsequence of x = S; U; M; MC.

and

7.3.2 Finding sequences with a given subsequence The seqpm() function counts the number of sequences that contain a given subsequence and collects their row index numbers. The function returns a list with two elements. The rst element, MTab, is just a table with the number of occurrences of the given subsequence in the data. Note that only one occurrence is counted per sequence, even when the sub-sequence appears more than one time in the sequence. The second element of the list, MIndex, gives the row index numbers of the sequences containing the subsequence. These index numbers may be useful for accessing the concerned sequences (example below). Since it is easier to search a pattern in a character string, the function rst translates the sequence data in this format when using the seqconc function with the TRUE option.

I concluded that seqpm() was the function I needed to get the job done.

So I have sequences like: A-A-A-A-A-B-B-B-B-B-A-A-A-A-A

And out of the definition of subsequences that i found on the mentiod sources, i figure I could find that kind of sequence by using:

seqpm(sequence,"ABA")

But that does not happen. In order to find that example sequence i need to input

seqpm(sequence,"ABBBBBA")

which is not very useful for what I need.

1. So do you guys see where I might've missed something ?
2. How can I retrieve all the sequences that do go from A to B and Back to A?
3. Is there a way for me to find go from A to anything else and then back to A ?

Thanks a lot !

Answer 1

The title of the seqpm help page is "Find substring patterns in sequences", and this is what the function actually does. It searches for sequences that contain a given substring (not a subsequence). Seems there is a formulation error in the user's guide.

A solution to find the sequences that contain given subsequences, is to convert the state sequences into event sequences with seqecreate , and then use the seqefsub and seqeapplysub function. I illustrate using the actcal data that ships with TraMineR.

library(TraMineR)
data(actcal)
actcal.seq <- seqdef(actcal[,13:24])

## displaying the first state sequences
head(actcal.seq)

## transforming into event sequences
actcal.seqe <- seqecreate(actcal.seq, tevent = "state", use.labels=FALSE)

## displaying the first event sequences
head(actcal.seqe)

## now searching for the subsequences
subs <- seqefsub(actcal.seqe, strsubseq=c("(A)-(D)","(D)-(B)"))
## and identifying the sequences that contain the subsequences
subs.pres <- seqeapplysub(subs, method="presence")
head(subs.pres)

## we can now, for example, count the sequences that contain (A)-(D)
sum(subs.pres[,1])
## or list the sequences that contain (A)-(D)
rownames(subs.pres)[subs.pres[,1]==1]

Hope this helps.