Problem with NAs as separate class in transition matrix

[winanddj]

Hi,

I try to estimate a transition matrix for a specific matrix.
The matrix has some rows that have missing values , they are correctly specified as NA.
Now in the transition matrix I want four classes: (a,b,c,d).
The problem is that the commands:
dataframe <- read.table("C:Downloads/test.txt", header =F)
testdata<-as.matrix(dataframe)
transitionmatrix <-markovchainFit(data=testdata, method = "mle")
produces a 5-dimensional transition matrix, with the NAs as a seperate class.
I only want to consider the four classes a,b,c,d

How can I exclude the NAs from the estimated transition matrix.
The command na.Remove that is mentioned here: #122
does not work.

Thanks in advance for any suggestions and help.

[spedygiorgio]

Hi @winanddj , in order to investigate further Is it possible for you to upload the data?
Best

[winanddj]

Hi @spedygiorgio.
Yes this is the dataset:
test.txt