Markov transition probabilities

What is a Markov transition?

A first-order Markov chain models the brain state sequence as a memoryless process: the probability of entering state $j$ at time $t+1$ depends only on the current state $i$ at time $t$ , not on any earlier history.

clusters_markov() estimates these transition probabilities empirically from observed state sequences. For each subject (or group), it:

Lags the state sequence by one time point to create source–target pairs.
Counts every observed source → target transition.
Normalises by the total number of transitions out of each source state, giving a row-stochastic estimate of the transition matrix.

The result captures which states the brain tends to move to and from, and how probable each transition is — information that fractional occupancy alone cannot provide.

Simulated data

set.seed(99)

tbl <- tibble::tibble(
  subject = rep(paste0("sub-", 1:8), each = 60),
  group   = rep(c("term", "preterm"), each = 4 * 60),
  time    = rep(seq_len(60), 8),
  state   = sample(0:3, 8 * 60, replace = TRUE,
                   prob = c(0.35, 0.25, 0.25, 0.15))
)

Computing transitions

trans <- clusters_markov(
  tbl      = tbl,
  vars     = c("subject", "group"),
  cVar     = "state",
  sortBy   = "time",
  groupBy  = "subject",
  remIntra = FALSE
)

trans
#> # A tibble: 16 × 4
#> # Groups:   tag, source, target [16]
#>    source target tag   data            
#>     <int>  <int> <chr> <list>          
#>  1      0      0 0_0   <tibble [8 × 5]>
#>  2      0      1 0_1   <tibble [8 × 5]>
#>  3      0      2 0_2   <tibble [8 × 5]>
#>  4      0      3 0_3   <tibble [7 × 5]>
#>  5      1      0 1_0   <tibble [8 × 5]>
#>  6      1      1 1_1   <tibble [8 × 5]>
#>  7      1      2 1_2   <tibble [8 × 5]>
#>  8      1      3 1_3   <tibble [7 × 5]>
#>  9      2      0 2_0   <tibble [8 × 5]>
#> 10      2      1 2_1   <tibble [8 × 5]>
#> 11      2      2 2_2   <tibble [7 × 5]>
#> 12      2      3 2_3   <tibble [8 × 5]>
#> 13      3      0 3_0   <tibble [8 × 5]>
#> 14      3      1 3_1   <tibble [8 × 5]>
#> 15      3      2 3_2   <tibble [7 × 5]>
#> 16      3      3 3_3   <tibble [7 × 5]>

The output is nested by tag — one row per unique source–target pair. Unnest to see the per-subject probabilities:

trans_long <- trans %>%
  tidyr::unnest(data)

trans_long %>%
  dplyr::select(tag, source, target, subject, group, nCount) %>%
  head(16)
#> # A tibble: 16 × 6
#> # Groups:   tag, source, target [2]
#>    tag   source target subject group   nCount     
#>    <chr>  <int>  <int> <chr>   <chr>   <table[1d]>
#>  1 0_0        0      0 sub-1   term    0.3333333  
#>  2 0_0        0      0 sub-2   term    0.3600000  
#>  3 0_0        0      0 sub-3   term    0.2500000  
#>  4 0_0        0      0 sub-4   term    0.3809524  
#>  5 0_0        0      0 sub-5   preterm 0.1250000  
#>  6 0_0        0      0 sub-6   preterm 0.3333333  
#>  7 0_0        0      0 sub-7   preterm 0.4000000  
#>  8 0_0        0      0 sub-8   preterm 0.2631579  
#>  9 0_1        0      1 sub-1   term    0.2777778  
#> 10 0_1        0      1 sub-2   term    0.3200000  
#> 11 0_1        0      1 sub-3   term    0.1875000  
#> 12 0_1        0      1 sub-4   term    0.2857143  
#> 13 0_1        0      1 sub-5   preterm 0.3750000  
#> 14 0_1        0      1 sub-6   preterm 0.3333333  
#> 15 0_1        0      1 sub-7   preterm 0.3666667  
#> 16 0_1        0      1 sub-8   preterm 0.4210526

The transition matrix

To reconstruct the full $K \times K$ transition matrix averaged across subjects, summarise nCount by source and target:

trans_long %>%
  dplyr::group_by(source, target) %>%
  dplyr::summarise(mean_prob = mean(nCount), .groups = "drop") %>%
  tidyr::pivot_wider(
    names_from  = target,
    values_from = mean_prob,
    names_prefix = "to_"
  ) %>%
  dplyr::arrange(source)
#> # A tibble: 4 × 5
#>   source  to_0  to_1  to_2  to_3
#>    <int> <dbl> <dbl> <dbl> <dbl>
#> 1      0 0.306 0.321 0.262 0.127
#> 2      1 0.346 0.245 0.236 0.198
#> 3      2 0.419 0.270 0.172 0.160
#> 4      3 0.387 0.267 0.277 0.119

Each row sums to 1 (within rounding error): given the brain is in state source, the row entries are the probabilities of transitioning to each possible target on the next time step.

Removing self-transitions

By default remIntra = FALSE, so self-transitions (state $i$ → state $i$ ) are included. These reflect dwell time in the transition matrix. If you want to study only genuine state changes, you can filter self-transitions out of the unnested output using source != target:

trans_change <- clusters_markov(
  tbl      = tbl,
  vars     = c("subject", "group"),
  cVar     = "state",
  sortBy   = "time",
  groupBy  = "subject",
  remIntra = FALSE
)

# Filter out self-transitions manually (source == target)
trans_change %>%
  tidyr::unnest(data) %>%
  dplyr::filter(source != target) %>%
  dplyr::group_by(tag) %>%
  dplyr::summarise(mean_prob = mean(nCount, na.rm = TRUE), .groups = "drop") %>%
  dplyr::arrange(dplyr::desc(mean_prob))
#> # A tibble: 12 × 2
#>    tag   mean_prob
#>    <chr>     <dbl>
#>  1 2_0       0.419
#>  2 3_0       0.387
#>  3 1_0       0.346
#>  4 0_1       0.321
#>  5 3_2       0.277
#>  6 2_1       0.270
#>  7 3_1       0.267
#>  8 0_2       0.262
#>  9 1_2       0.236
#> 10 1_3       0.198
#> 11 2_3       0.160
#> 12 0_3       0.127

With remIntra = TRUE, rows no longer sum to 1 because the diagonal has been removed and the remaining probabilities are re-normalised over inter-state transitions only.

The `tag` convention

Transition tags follow the "<source>_<target>" pattern. For a four-state system (states 0–3), there are 16 possible tags including self-transitions, or 12 excluding them.

To work with a specific transition of interest:

trans %>%
  tidyr::unnest(data) %>%
  dplyr::filter(tag == "1_0") %>%
  dplyr::select(subject, group, nCount)
#> Adding missing grouping variables: `tag`, `source`, `target`
#> # A tibble: 8 × 6
#> # Groups:   tag, source, target [1]
#>   tag   source target subject group   nCount     
#>   <chr>  <int>  <int> <chr>   <chr>   <table[1d]>
#> 1 1_0        1      0 sub-1   term    0.1333333  
#> 2 1_0        1      0 sub-2   term    0.4666667  
#> 3 1_0        1      0 sub-3   term    0.3333333  
#> 4 1_0        1      0 sub-4   term    0.3125000  
#> 5 1_0        1      0 sub-5   preterm 0.3043478  
#> 6 1_0        1      0 sub-6   preterm 0.3333333  
#> 7 1_0        1      0 sub-7   preterm 0.5714286  
#> 8 1_0        1      0 sub-8   preterm 0.3125000

`vars` vs `groupBy`

Two arguments control grouping in clusters_markov(), and it is worth understanding the distinction:

groupBy — the variable used to compute transitions. Lag and pair operations are performed within each level of groupBy. This should always be the subject (or session) identifier, so that transitions are never computed across subjects.
vars — the variables carried through to the output. Include everything you want available for downstream analysis: subject ID, group, covariates. groupBy should be a subset of (or equal to) vars.

# groupBy = "subject" ensures no cross-subject transitions are counted.
# vars includes "group" so group membership is available for testing.
clusters_markov(
  tbl      = tbl,
  vars     = c("subject", "group"),
  cVar     = "state",
  sortBy   = "time",
  groupBy  = "subject"
) %>%
  tidyr::unnest(data) %>%
  dplyr::filter(tag == "0_1") %>%
  dplyr::select(subject, group, nCount)
#> Adding missing grouping variables: `tag`, `source`, `target`
#> # A tibble: 8 × 6
#> # Groups:   tag, source, target [1]
#>   tag   source target subject group   nCount     
#>   <chr>  <int>  <int> <chr>   <chr>   <table[1d]>
#> 1 0_1        0      1 sub-1   term    0.2777778  
#> 2 0_1        0      1 sub-2   term    0.3200000  
#> 3 0_1        0      1 sub-3   term    0.1875000  
#> 4 0_1        0      1 sub-4   term    0.2857143  
#> 5 0_1        0      1 sub-5   preterm 0.3750000  
#> 6 0_1        0      1 sub-6   preterm 0.3333333  
#> 7 0_1        0      1 sub-7   preterm 0.3666667  
#> 8 0_1        0      1 sub-8   preterm 0.4210526