I am trying to write a code to do sequence analysis. However, I get the error Seqdist Error: ‘sm’ invalid type or unknown value. I tried it all to find why it happens but I am stuck. I could find out that it works if I have a single variable and single substitution matrix.

Any help would be greatly appreciated

See some simplified example of the code below:

# Libraries
library(TraMineR)
library(cluster)
library(ggplot2)

# Simplified Sample Data
dimension_1_reduced <- data.frame(
  contract_inst = c(1, 2, 3, 4, 1, 4, 3, 2, 1, 4, 3, 2, 1, 4, 3, 2, 1, 4, 3, 2), # 20 items, 4 levels
  contract_temp = c(1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2) # 20 items, 2 levels
)

# Reduced Sequence Object
seq_obj_1_reduced <- seqdef(dimension_1_reduced, 
                            states = list(
                              contract_inst = c("1", "2", "3", "4"),
                              contract_temp = c("1", "2")
                            ))

# Print the sequence object
print(seq_obj_1_reduced)

# Check structure of the sequence object
str(seq_obj_1_reduced)

# Access attributes
# 1. Sequence data
seq_data <- attr(seq_obj_1_reduced, "data")
print(seq_data)

# 2. Column names
column_names <- colnames(seq_data)
print(column_names)

# 3. State levels
state_levels <- attr(seq_obj_1_reduced, "labels")
print(state_levels)

# Substitution Matrices with State Labels
matrix_inst <- matrix(c(0, 1, 2, 3,
                        1, 0, 1, 2, 
                        2, 1, 0, 1, 
                        3, 2, 1, 0), nrow = 4, 
                      dimnames = list(c("1", "2", "3", "4"), c("1", "2", "3", "4")))

matrix_temp <- matrix(c(0, 1, 
                        1, 0), nrow = 2, 
                      dimnames = list(c("1", "2"), c("1", "2")))

# List of substitution matrices for reduced dimensions
sm_list_reduced <- list(contract_inst = matrix_inst,
                        contract_temp = matrix_temp)

# Compute reduced dissimilarity matrix
dissimilarity_reduced <- tryCatch({
  seqdist(seq_obj_1_reduced, method = "OM", sm = sm_list_reduced, indel = 1)
}, error = function(e) {
  print(e)
  NULL
})

# Check for errors
if (!is.null(dissimilarity_reduced)) {
  print(dissimilarity_reduced)
} else {
  print("Error in calculating the dissimilarity matrix")
}

I tried to print all variables to check that the substitution matrixes matched the corresponding dimension. I tried running a dimension with a single variable, which works. I tried looking into forums or posts to see if someone encountered the same problem. I tried reading the R package TraMineR.