All of this can be done without for loops.
Use head(..., -1), tail(..., -1) to get the pre and post states.
Use factor or pmin to recode them as necessary
Use table(pre, post) to get the transition counts.
Use prop.table(table_of_counts,1) to get the probabilities.
HTH,
Chuck
> On Aug 28, 2017, at 8:31 AM, Elie Canonici Merle
> <elie.canonicime...@gmail.com> wrote:
>
> Hi,
>
> I think you overthought this one a little bit, I don't know if this is the
> kind of code you are expecting but I came up with something like that:
>
> generate_transition_matrix <- function(data, n_states) {
>
> #To be sure I imagine you should check n_states is right at this point
>
> transitions <- matrix(0, n_states, n_states)
>
> #we could improve a little bit here because at step N+1 source is dest
> from step N
> #but it would not be as readable
> for (k in 1:(length(data) - 1)) {
> source_state <- data[k]
> dest_state <- data[k+1]
> transitions[source_state, dest_state] <- transitions[source_state,
> dest_state] + 1
> }
>
> for (k in 1:n_states)
> transitions[k,] <- transitions[k,] / sum(transitions[k,])
> transitions
> }
>
> checkdf=data.frame(clusterNum=c(3,2,3,1,1,3,4,3,2,1,1,3,2,1,3,2))
> no_of_state=4
>
> transition_matrix= generate_transition_matrix(checkdf$clusterNum,
> no_of_state)
> transition_matrix
>
>
>
> 2017-08-28 16:37 GMT+02:00 niharika singhal <niharikasinghal1...@gmail.com>:
>
>> Hello,
>>
>> I am trying to implement a formula
>>
>> aij= transition from state S_i to S_j/no of transition at state S_i
>>
>>
>>
>> Code I have written is working with three state {1,2,3 }, but if the number
>> of states become={1,2,3,4,......n} then the code will not work, so can some
>> help me with this.
>>
>> For and some rows of my data frame look like
>>
>> checkdf=data.frame(clusterNum=c(3,2,3,1,1,3,4,3,2,1,1,3,2,1,3,2)
>> no_of_state=3
>> transition_matrix=matrix(NA,nrow=no_of_state, ncol=no_of_state)
>> for(k in 1: no_of_state)
>> {
>> count1=0
>> count2=0
>> count3=0
>> #For last point no transition takes place
>> for(j in 1: (nrow(checkdf)-1))
>> {
>>
>> if(checkdf$clusterNum[j]==k)
>> {
>> if(checkdf$clusterNum[j+1]==1){
>> count1=count1+1
>> }
>> else if(checkdf$clusterNum[j+1]==2){
>> count2=count2+1
>> }
>> else {
>> count3=count3+1
>> }
>> }
>> }
>>
>> no_of_points=(count1+count2+count3)
>> s1=count1/no_of_points
>> s2=count2/no_of_points
>> s3=count3/no_of_points
>> transition_matrix[k,]=c(s1, s2, s3)
>>
>> }
>>
>> I know the code is not written nicely and I want to improve it.
>>
>> Thanks in advance
>> Niharika
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> [[alternative HTML version deleted]]
>
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